Copper in PDB 1v6p: Crystal Structure of Cobrotoxin
Protein crystallography data
The structure of Crystal Structure of Cobrotoxin, PDB code: 1v6p
was solved by
X.Lou,
X.Tu,
J.Wang,
M.Teng,
L.Niu,
Q.Liu,
Q.Huang,
Q.Hao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
10.00 /
0.87
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.808,
47.287,
90.018,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
11.9 /
15.3
|
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Cobrotoxin
(pdb code 1v6p). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 18 binding sites of Copper where determined in the
Crystal Structure of Cobrotoxin, PDB code: 1v6p:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
11;
12;
13;
14;
15;
16;
17;
18;
Copper binding site 1 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 1 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu302
b:6.4
occ:0.57
|
CU
|
A:CU302
|
0.0
|
6.4
|
0.6
|
|
CU
|
A:CU302
|
0.7
|
7.7
|
0.2
|
|
CU
|
A:CU302
|
0.8
|
9.7
|
0.1
|
|
CU
|
A:CU302
|
1.5
|
26.6
|
0.2
|
|
NE2
|
A:HIS4
|
2.0
|
8.2
|
1.0
|
|
OD1
|
A:ASN62
|
2.0
|
8.8
|
0.7
|
|
OD1
|
A:ASN62
|
2.2
|
17.5
|
0.3
|
|
O
|
A:HOH1219
|
2.3
|
7.8
|
0.8
|
|
CD2
|
A:HIS4
|
3.0
|
7.8
|
1.0
|
|
CE1
|
A:HIS4
|
3.0
|
8.6
|
1.0
|
|
CG
|
A:ASN62
|
3.0
|
8.0
|
0.7
|
|
ND2
|
A:ASN62
|
3.4
|
9.1
|
0.7
|
|
CG
|
A:ASN62
|
3.4
|
11.5
|
0.3
|
|
NA
|
A:NA501
|
3.4
|
40.5
|
0.5
|
|
CB
|
A:PRO12
|
4.0
|
9.6
|
1.0
|
|
O
|
A:ARG59
|
4.0
|
7.6
|
1.0
|
|
ND1
|
A:HIS4
|
4.1
|
7.8
|
1.0
|
|
ND2
|
A:ASN62
|
4.1
|
13.9
|
0.3
|
|
CG
|
A:HIS4
|
4.1
|
6.8
|
1.0
|
|
CG
|
A:PRO12
|
4.2
|
10.4
|
1.0
|
|
NA
|
A:NA501
|
4.3
|
8.2
|
0.5
|
|
CB
|
A:ASN62
|
4.4
|
8.3
|
0.7
|
|
CB
|
A:ASN62
|
4.5
|
12.5
|
0.3
|
|
CA
|
A:ASN62
|
4.7
|
10.5
|
0.3
|
|
CB
|
A:ARG59
|
4.8
|
7.3
|
1.0
|
|
O
|
A:HOH1214
|
4.8
|
13.4
|
1.0
|
|
CA
|
A:ASN62
|
4.8
|
7.7
|
0.7
|
|
Copper binding site 2 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 2 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu302
b:7.7
occ:0.16
|
CU
|
A:CU302
|
0.0
|
7.7
|
0.2
|
|
CU
|
A:CU302
|
0.7
|
6.4
|
0.6
|
|
CU
|
A:CU302
|
1.2
|
9.7
|
0.1
|
|
NE2
|
A:HIS4
|
2.0
|
8.2
|
1.0
|
|
CU
|
A:CU302
|
2.1
|
26.6
|
0.2
|
|
OD1
|
A:ASN62
|
2.6
|
8.8
|
0.7
|
|
CE1
|
A:HIS4
|
2.8
|
8.6
|
1.0
|
|
OD1
|
A:ASN62
|
2.8
|
17.5
|
0.3
|
|
O
|
A:HOH1219
|
2.8
|
7.8
|
0.8
|
|
CD2
|
A:HIS4
|
3.2
|
7.8
|
1.0
|
|
NA
|
A:NA501
|
3.4
|
40.5
|
0.5
|
|
CB
|
A:PRO12
|
3.4
|
9.6
|
1.0
|
|
CG
|
A:ASN62
|
3.6
|
8.0
|
0.7
|
|
CG
|
A:PRO12
|
3.6
|
10.4
|
1.0
|
|
ND1
|
A:HIS4
|
3.9
|
7.8
|
1.0
|
|
CG
|
A:ASN62
|
4.0
|
11.5
|
0.3
|
|
ND2
|
A:ASN62
|
4.0
|
9.1
|
0.7
|
|
CG
|
A:HIS4
|
4.1
|
6.8
|
1.0
|
|
NA
|
A:NA501
|
4.4
|
8.2
|
0.5
|
|
O
|
A:ARG59
|
4.7
|
7.6
|
1.0
|
|
ND2
|
A:ASN62
|
4.7
|
13.9
|
0.3
|
|
O
|
A:HOH1214
|
4.8
|
13.4
|
1.0
|
|
CB
|
A:ASN62
|
4.9
|
8.3
|
0.7
|
|
CA
|
A:PRO12
|
5.0
|
8.0
|
1.0
|
|
CD
|
A:PRO12
|
5.0
|
10.5
|
1.0
|
|
Copper binding site 3 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 3 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu302
b:9.7
occ:0.09
|
CU
|
A:CU302
|
0.0
|
9.7
|
0.1
|
|
CU
|
A:CU302
|
0.8
|
6.4
|
0.6
|
|
CU
|
A:CU302
|
1.2
|
7.7
|
0.2
|
|
CU
|
A:CU302
|
1.2
|
26.6
|
0.2
|
|
O
|
A:HOH1219
|
1.7
|
7.8
|
0.8
|
|
NE2
|
A:HIS4
|
2.2
|
8.2
|
1.0
|
|
OD1
|
A:ASN62
|
2.6
|
17.5
|
0.3
|
|
OD1
|
A:ASN62
|
2.7
|
8.8
|
0.7
|
|
CE1
|
A:HIS4
|
3.0
|
8.6
|
1.0
|
|
CD2
|
A:HIS4
|
3.4
|
7.8
|
1.0
|
|
CG
|
A:ASN62
|
3.5
|
8.0
|
0.7
|
|
ND2
|
A:ASN62
|
3.6
|
9.1
|
0.7
|
|
CG
|
A:ASN62
|
3.8
|
11.5
|
0.3
|
|
O
|
A:ARG59
|
3.8
|
7.6
|
1.0
|
|
NA
|
A:NA501
|
4.1
|
40.5
|
0.5
|
|
ND2
|
A:ASN62
|
4.2
|
13.9
|
0.3
|
|
ND1
|
A:HIS4
|
4.3
|
7.8
|
1.0
|
|
CB
|
A:ARG59
|
4.3
|
7.3
|
1.0
|
|
CG
|
A:HIS4
|
4.4
|
6.8
|
1.0
|
|
CB
|
A:PRO12
|
4.5
|
9.6
|
1.0
|
|
CG
|
A:PRO12
|
4.8
|
10.4
|
1.0
|
|
C
|
A:ARG59
|
4.8
|
6.6
|
1.0
|
|
CB
|
A:ASN62
|
5.0
|
8.3
|
0.7
|
|
NA
|
A:NA501
|
5.0
|
8.2
|
0.5
|
|
Copper binding site 4 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 4 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu302
b:26.6
occ:0.18
|
CU
|
A:CU302
|
0.0
|
26.6
|
0.2
|
|
O
|
A:HOH1219
|
1.2
|
7.8
|
0.8
|
|
CU
|
A:CU302
|
1.2
|
9.7
|
0.1
|
|
CU
|
A:CU302
|
1.5
|
6.4
|
0.6
|
|
CU
|
A:CU302
|
2.1
|
7.7
|
0.2
|
|
NE2
|
A:HIS4
|
2.1
|
8.2
|
1.0
|
|
OD1
|
A:ASN62
|
2.4
|
17.5
|
0.3
|
|
OD1
|
A:ASN62
|
2.4
|
8.8
|
0.7
|
|
O
|
A:ARG59
|
2.7
|
7.6
|
1.0
|
|
CD2
|
A:HIS4
|
2.9
|
7.8
|
1.0
|
|
CG
|
A:ASN62
|
3.1
|
8.0
|
0.7
|
|
CE1
|
A:HIS4
|
3.1
|
8.6
|
1.0
|
|
ND2
|
A:ASN62
|
3.3
|
9.1
|
0.7
|
|
CG
|
A:ASN62
|
3.3
|
11.5
|
0.3
|
|
CB
|
A:ARG59
|
3.6
|
7.3
|
1.0
|
|
C
|
A:ARG59
|
3.7
|
6.6
|
1.0
|
|
ND2
|
A:ASN62
|
3.9
|
13.9
|
0.3
|
|
CG
|
A:HIS4
|
4.0
|
6.8
|
1.0
|
|
ND1
|
A:HIS4
|
4.1
|
7.8
|
1.0
|
|
CA
|
A:ARG59
|
4.2
|
6.5
|
1.0
|
|
CB
|
A:ASN62
|
4.5
|
12.5
|
0.3
|
|
CB
|
A:ASN62
|
4.5
|
8.3
|
0.7
|
|
CG
|
A:ARG59
|
4.6
|
7.9
|
1.0
|
|
NA
|
A:NA501
|
4.6
|
40.5
|
0.5
|
|
CA
|
A:ASN62
|
4.7
|
10.5
|
0.3
|
|
N
|
A:ASN62
|
4.8
|
9.3
|
0.7
|
|
CA
|
A:ASN62
|
4.9
|
7.7
|
0.7
|
|
N
|
A:ASN62
|
4.9
|
6.4
|
0.3
|
|
N
|
A:CYS60
|
4.9
|
6.5
|
1.0
|
|
Copper binding site 5 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 5 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu303
b:8.0
occ:0.77
|
OE1
|
A:GLU2
|
1.9
|
8.6
|
0.5
|
|
O
|
A:HOH1205
|
2.0
|
7.5
|
0.4
|
|
OE1
|
A:GLU2
|
2.0
|
9.0
|
0.4
|
|
OD2
|
A:ASP58
|
2.1
|
10.7
|
1.0
|
|
O
|
A:HOH1206
|
2.4
|
13.1
|
1.0
|
|
OD1
|
A:ASP58
|
2.7
|
8.6
|
1.0
|
|
CG
|
A:ASP58
|
2.7
|
8.0
|
1.0
|
|
CD
|
A:GLU2
|
2.9
|
8.5
|
0.5
|
|
CD
|
A:GLU2
|
3.0
|
8.1
|
0.4
|
|
CU
|
A:CU307
|
3.1
|
6.2
|
0.1
|
|
OE2
|
A:GLU2
|
3.2
|
10.9
|
0.5
|
|
O
|
A:HOH1281
|
3.3
|
10.1
|
0.2
|
|
OE2
|
A:GLU2
|
3.3
|
10.8
|
0.4
|
|
CG
|
A:GLU2
|
4.0
|
9.1
|
0.1
|
|
OE2
|
A:GLU2
|
4.0
|
9.6
|
0.1
|
|
O
|
A:HOH1208
|
4.1
|
10.3
|
0.2
|
|
O
|
A:HOH1207
|
4.1
|
10.5
|
0.9
|
|
N
|
A:GLU2
|
4.1
|
7.1
|
0.5
|
|
N
|
A:GLU2
|
4.1
|
7.1
|
0.1
|
|
CA
|
A:LEU1
|
4.2
|
8.3
|
1.0
|
|
CB
|
A:ASP58
|
4.2
|
7.7
|
1.0
|
|
N
|
A:GLU2
|
4.2
|
6.7
|
0.4
|
|
CG
|
A:GLU2
|
4.2
|
8.0
|
0.5
|
|
N
|
A:LEU1
|
4.3
|
10.7
|
1.0
|
|
CG
|
A:GLU2
|
4.4
|
9.1
|
0.4
|
|
C
|
A:LEU1
|
4.4
|
7.6
|
1.0
|
|
CD
|
A:GLU2
|
4.5
|
9.1
|
0.1
|
|
O
|
A:HOH1218
|
4.6
|
16.2
|
0.4
|
|
CB
|
A:GLU2
|
4.7
|
7.6
|
0.5
|
|
CB
|
A:GLU2
|
4.7
|
8.2
|
0.1
|
|
CB
|
A:GLU2
|
4.7
|
8.3
|
0.4
|
|
O
|
A:HOH1276
|
5.0
|
10.8
|
0.4
|
|
Copper binding site 6 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 6 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu304
b:9.7
occ:0.11
|
OE2
|
A:GLU51
|
2.0
|
15.2
|
0.5
|
|
O
|
A:HOH1271
|
2.0
|
19.1
|
0.7
|
|
O
|
A:HOH1270
|
2.6
|
17.9
|
0.3
|
|
CD
|
A:GLU51
|
2.9
|
13.0
|
0.5
|
|
O
|
A:HOH1271
|
3.2
|
17.0
|
0.3
|
|
OE1
|
A:GLU51
|
3.2
|
21.2
|
0.5
|
|
O
|
A:HOH1249
|
3.2
|
45.7
|
0.6
|
|
O
|
A:HOH1287
|
3.5
|
26.0
|
0.6
|
|
O
|
A:HOH1267
|
4.2
|
19.6
|
0.4
|
|
OE2
|
A:GLU51
|
4.2
|
29.7
|
0.5
|
|
CG
|
A:GLU51
|
4.3
|
11.3
|
0.5
|
|
OE1
|
A:GLU51
|
4.5
|
27.1
|
0.5
|
|
CD
|
A:GLU51
|
4.5
|
19.2
|
0.5
|
|
O
|
A:HOH1248
|
4.6
|
19.8
|
0.4
|
|
Copper binding site 7 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 7 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 7 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu305
b:9.1
occ:0.45
|
NH2
|
A:ARG59
|
3.1
|
9.3
|
1.0
|
|
O
|
A:HOH1288
|
3.2
|
24.2
|
1.0
|
|
CZ
|
A:ARG59
|
4.1
|
7.5
|
1.0
|
|
NH1
|
A:ARG59
|
4.2
|
8.1
|
1.0
|
|
Copper binding site 8 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 8 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 8 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu306
b:18.9
occ:0.38
|
CU
|
A:CU306
|
0.0
|
18.9
|
0.4
|
|
CU
|
A:CU306
|
1.2
|
15.7
|
0.2
|
|
O
|
B:HOH375
|
1.6
|
7.8
|
0.4
|
|
O
|
B:HOH376
|
1.6
|
26.2
|
0.4
|
|
O
|
B:HOH375
|
1.6
|
13.9
|
0.3
|
|
OD2
|
B:ASP58
|
1.9
|
22.5
|
1.0
|
|
OD2
|
A:ASP31
|
2.1
|
25.4
|
0.4
|
|
CG
|
B:ASP58
|
2.8
|
16.7
|
1.0
|
|
OD1
|
A:ASP31
|
2.8
|
23.6
|
0.6
|
|
OD1
|
B:ASP58
|
2.9
|
17.8
|
1.0
|
|
OE1
|
B:GLU2
|
3.1
|
26.1
|
0.3
|
|
OD2
|
A:ASP31
|
3.1
|
28.9
|
0.6
|
|
CG
|
A:ASP31
|
3.2
|
24.6
|
0.4
|
|
CG
|
A:ASP31
|
3.3
|
23.4
|
0.6
|
|
O
|
B:HOH321
|
3.5
|
30.8
|
0.5
|
|
OD1
|
A:ASP31
|
3.5
|
26.0
|
0.4
|
|
O
|
A:HOH1244
|
4.0
|
34.1
|
1.0
|
|
O
|
A:HOH1255
|
4.1
|
73.7
|
1.0
|
|
CD
|
B:GLU2
|
4.2
|
20.7
|
0.3
|
|
CB
|
B:ASP58
|
4.2
|
13.8
|
1.0
|
|
OE2
|
B:GLU2
|
4.4
|
26.2
|
0.3
|
|
O
|
A:HOH1257
|
4.5
|
20.6
|
1.0
|
|
CB
|
A:ASP31
|
4.6
|
22.0
|
0.4
|
|
CB
|
A:ASP31
|
4.7
|
21.1
|
0.6
|
|
CA
|
B:LEU1
|
4.8
|
14.8
|
1.0
|
|
N
|
B:LEU1
|
5.0
|
17.9
|
1.0
|
|
CD
|
A:ARG36
|
5.0
|
20.7
|
0.3
|
|
Copper binding site 9 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 9 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 9 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu306
b:15.7
occ:0.22
|
CU
|
A:CU306
|
0.0
|
15.7
|
0.2
|
|
CU
|
A:CU306
|
1.2
|
18.9
|
0.4
|
|
OD2
|
A:ASP31
|
1.8
|
25.4
|
0.4
|
|
OD2
|
B:ASP58
|
2.0
|
22.5
|
1.0
|
|
OD1
|
A:ASP31
|
2.0
|
23.6
|
0.6
|
|
O
|
B:HOH376
|
2.2
|
26.2
|
0.4
|
|
O
|
B:HOH375
|
2.7
|
7.8
|
0.4
|
|
O
|
B:HOH375
|
2.8
|
13.9
|
0.3
|
|
CG
|
A:ASP31
|
2.8
|
23.4
|
0.6
|
|
OD2
|
A:ASP31
|
2.9
|
28.9
|
0.6
|
|
CG
|
A:ASP31
|
2.9
|
24.6
|
0.4
|
|
CG
|
B:ASP58
|
3.1
|
16.7
|
1.0
|
|
OD1
|
B:ASP58
|
3.5
|
17.8
|
1.0
|
|
OD1
|
A:ASP31
|
3.6
|
26.0
|
0.4
|
|
O
|
A:HOH1257
|
3.9
|
20.6
|
1.0
|
|
CB
|
A:ASP31
|
4.1
|
22.0
|
0.4
|
|
OE1
|
B:GLU2
|
4.1
|
26.1
|
0.3
|
|
CD
|
A:ARG36
|
4.2
|
20.7
|
0.3
|
|
O
|
A:HOH1244
|
4.2
|
34.1
|
1.0
|
|
CB
|
A:ASP31
|
4.2
|
21.1
|
0.6
|
|
CB
|
B:ASP58
|
4.2
|
13.8
|
1.0
|
|
O
|
B:HOH321
|
4.7
|
30.8
|
0.5
|
|
NH1
|
A:ARG36
|
4.8
|
23.3
|
0.3
|
|
O
|
A:HOH1255
|
4.9
|
73.7
|
1.0
|
|
NE
|
A:ARG36
|
5.0
|
23.7
|
0.3
|
|
Copper binding site 10 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 10 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 10 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu307
b:6.2
occ:0.13
|
OE2
|
A:GLU2
|
1.6
|
10.8
|
0.4
|
|
OE2
|
A:GLU2
|
1.9
|
10.9
|
0.5
|
|
O
|
A:HOH1208
|
2.0
|
10.3
|
0.2
|
|
O
|
A:HOH1205
|
2.0
|
7.5
|
0.4
|
|
O
|
A:HOH1218
|
2.1
|
16.2
|
0.4
|
|
O
|
A:HOH1281
|
2.1
|
10.1
|
0.2
|
|
CD
|
A:GLU2
|
2.7
|
8.1
|
0.4
|
|
CD
|
A:GLU2
|
2.7
|
8.5
|
0.5
|
|
OE1
|
A:GLU2
|
3.0
|
8.6
|
0.5
|
|
OE1
|
A:GLU2
|
3.0
|
9.0
|
0.4
|
|
O
|
A:HOH1206
|
3.1
|
13.1
|
1.0
|
|
CU
|
A:CU303
|
3.1
|
8.0
|
0.8
|
|
O
|
A:HOH1209
|
3.7
|
47.4
|
0.5
|
|
CG
|
A:GLU2
|
4.0
|
9.1
|
0.4
|
|
CG
|
A:GLU2
|
4.0
|
8.0
|
0.5
|
|
N
|
A:LEU1
|
4.3
|
10.7
|
1.0
|
|
O
|
A:HOH1204
|
4.8
|
15.2
|
1.0
|
|
C
|
A:LEU1
|
4.8
|
7.6
|
1.0
|
|
CA
|
A:LEU1
|
4.9
|
8.3
|
1.0
|
|
OD2
|
A:ASP58
|
5.0
|
10.7
|
1.0
|
|
Copper binding site 11 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 11 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 11 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu308
b:10.5
occ:0.15
|
CU
|
A:CU308
|
0.0
|
10.5
|
0.1
|
|
CU
|
A:CU308
|
1.6
|
28.9
|
0.3
|
|
OG1
|
B:THR14
|
3.1
|
15.9
|
0.9
|
|
NZ
|
A:LYS47
|
3.1
|
33.8
|
1.0
|
|
NZ
|
A:LYS27
|
3.2
|
13.2
|
0.6
|
|
CE1
|
B:HIS4
|
3.5
|
9.4
|
1.0
|
|
O
|
B:PRO12
|
3.9
|
12.1
|
1.0
|
|
CB
|
B:PRO12
|
3.9
|
13.2
|
1.0
|
|
ND1
|
B:HIS4
|
3.9
|
8.8
|
1.0
|
|
C
|
B:PRO12
|
3.9
|
9.7
|
1.0
|
|
C
|
B:THR13
|
3.9
|
9.5
|
1.0
|
|
CE
|
A:LYS47
|
4.0
|
20.3
|
1.0
|
|
CA
|
B:THR13
|
4.0
|
10.3
|
1.0
|
|
N
|
B:THR13
|
4.0
|
9.3
|
1.0
|
|
CB
|
B:THR14
|
4.0
|
13.5
|
0.9
|
|
CE
|
A:LYS27
|
4.1
|
13.9
|
0.6
|
|
NZ
|
A:LYS27
|
4.1
|
13.8
|
0.4
|
|
N
|
B:THR14
|
4.2
|
10.5
|
1.0
|
|
CB
|
B:THR14
|
4.2
|
13.2
|
0.1
|
|
NH1
|
B:ARG59
|
4.2
|
32.9
|
1.0
|
|
O
|
B:THR13
|
4.3
|
9.0
|
1.0
|
|
O
|
B:HOH407
|
4.3
|
28.6
|
0.6
|
|
O
|
A:HOH1312
|
4.4
|
49.8
|
1.0
|
|
CG2
|
B:THR14
|
4.4
|
12.0
|
0.1
|
|
CA
|
B:PRO12
|
4.6
|
9.5
|
1.0
|
|
CL
|
A:CL401
|
4.6
|
9.4
|
0.3
|
|
CD
|
B:ARG59
|
4.7
|
15.3
|
1.0
|
|
NE2
|
B:HIS4
|
4.7
|
9.5
|
1.0
|
|
CA
|
B:THR14
|
4.7
|
11.1
|
1.0
|
|
O
|
A:HOH1310
|
4.8
|
16.9
|
0.7
|
|
CD1
|
A:ILE50
|
4.8
|
24.9
|
0.6
|
|
O
|
B:HOH331
|
4.9
|
22.4
|
1.0
|
|
CZ
|
B:ARG59
|
5.0
|
24.6
|
1.0
|
|
Copper binding site 12 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 12 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 12 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu308
b:28.9
occ:0.30
|
CU
|
A:CU308
|
0.0
|
28.9
|
0.3
|
|
CU
|
A:CU308
|
1.6
|
10.5
|
0.1
|
|
NZ
|
A:LYS27
|
2.5
|
13.2
|
0.6
|
|
CE
|
A:LYS27
|
2.9
|
13.9
|
0.6
|
|
NH1
|
B:ARG59
|
3.1
|
32.9
|
1.0
|
|
NZ
|
A:LYS27
|
3.4
|
13.8
|
0.4
|
|
CL
|
A:CL401
|
3.5
|
9.4
|
0.3
|
|
OG1
|
B:THR14
|
3.6
|
15.9
|
0.9
|
|
CE1
|
B:HIS4
|
3.8
|
9.4
|
1.0
|
|
CD
|
B:ARG59
|
3.8
|
15.3
|
1.0
|
|
NZ
|
A:LYS47
|
3.9
|
33.8
|
1.0
|
|
CD1
|
A:ILE50
|
3.9
|
24.9
|
0.6
|
|
CD
|
A:LYS27
|
4.0
|
13.4
|
0.4
|
|
CZ
|
B:ARG59
|
4.1
|
24.6
|
1.0
|
|
CE
|
A:LYS47
|
4.2
|
20.3
|
1.0
|
|
O
|
A:HOH1312
|
4.3
|
49.8
|
1.0
|
|
NE
|
B:ARG59
|
4.3
|
20.1
|
1.0
|
|
CD
|
A:LYS27
|
4.3
|
12.1
|
0.6
|
|
CE
|
A:LYS27
|
4.4
|
14.3
|
0.4
|
|
ND1
|
B:HIS4
|
4.6
|
8.8
|
1.0
|
|
CD1
|
A:ILE50
|
4.6
|
23.2
|
0.4
|
|
CU
|
B:CU301
|
4.6
|
19.2
|
0.2
|
|
NE2
|
B:HIS4
|
4.7
|
9.5
|
1.0
|
|
CB
|
B:THR14
|
4.7
|
13.5
|
0.9
|
|
CB
|
B:PRO12
|
4.7
|
13.2
|
1.0
|
|
O
|
B:HOH377
|
4.8
|
44.8
|
0.8
|
|
CB
|
B:THR14
|
4.8
|
13.2
|
0.1
|
|
O
|
A:HOH1241
|
4.8
|
16.6
|
1.0
|
|
CG2
|
B:THR14
|
5.0
|
12.0
|
0.1
|
|
Copper binding site 13 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 13 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 13 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu310
b:12.7
occ:0.18
|
OG
|
A:SER8
|
1.7
|
14.6
|
0.4
|
|
NE
|
A:ARG36
|
2.5
|
32.3
|
0.7
|
|
O
|
A:HOH1252
|
2.7
|
20.5
|
0.4
|
|
NH2
|
A:ARG36
|
2.9
|
33.6
|
0.7
|
|
CB
|
A:SER8
|
3.0
|
12.8
|
0.4
|
|
CZ
|
A:ARG36
|
3.0
|
34.3
|
0.7
|
|
N
|
A:THR37
|
3.2
|
8.8
|
1.0
|
|
CD
|
A:ARG36
|
3.3
|
24.2
|
0.7
|
|
CB
|
A:SER8
|
3.4
|
14.5
|
0.6
|
|
CA
|
A:ARG36
|
3.4
|
12.9
|
1.0
|
|
O
|
A:HOH1217
|
3.5
|
23.6
|
1.0
|
|
CB
|
A:ARG36
|
3.5
|
18.6
|
0.7
|
|
N
|
A:SER8
|
3.6
|
11.2
|
0.6
|
|
CA
|
A:SER8
|
3.6
|
11.7
|
0.6
|
|
O
|
A:THR37
|
3.6
|
8.9
|
1.0
|
|
N
|
A:SER8
|
3.8
|
10.9
|
0.4
|
|
O
|
A:HOH1221
|
3.8
|
11.2
|
0.5
|
|
CB
|
A:ARG36
|
3.8
|
16.8
|
0.3
|
|
C
|
A:ARG36
|
3.9
|
9.0
|
1.0
|
|
CA
|
A:SER8
|
3.9
|
10.6
|
0.4
|
|
CG
|
A:ARG36
|
3.9
|
21.6
|
0.7
|
|
CZ
|
A:ARG36
|
4.0
|
23.4
|
0.3
|
|
NH2
|
A:ARG36
|
4.1
|
17.5
|
0.3
|
|
NH1
|
A:ARG36
|
4.2
|
35.9
|
0.7
|
|
OG
|
A:SER8
|
4.2
|
19.9
|
0.6
|
|
NE
|
A:ARG36
|
4.2
|
23.7
|
0.3
|
|
CB
|
A:GLN7
|
4.2
|
10.5
|
1.0
|
|
O
|
A:TYR35
|
4.3
|
19.3
|
1.0
|
|
CA
|
A:THR37
|
4.3
|
7.9
|
1.0
|
|
C
|
A:THR37
|
4.4
|
7.5
|
1.0
|
|
NH1
|
A:ARG36
|
4.4
|
23.3
|
0.3
|
|
C
|
A:GLN7
|
4.5
|
8.9
|
1.0
|
|
N
|
A:ARG36
|
4.6
|
12.1
|
1.0
|
|
O
|
A:HOH1221
|
4.7
|
14.8
|
0.5
|
|
CD
|
A:ARG36
|
4.8
|
20.7
|
0.3
|
|
CA
|
A:GLN7
|
4.8
|
8.3
|
1.0
|
|
CB
|
A:THR37
|
4.8
|
10.6
|
1.0
|
|
CG
|
A:ARG36
|
4.8
|
19.4
|
0.3
|
|
C
|
A:TYR35
|
4.9
|
13.4
|
1.0
|
|
O
|
A:HOH1340
|
4.9
|
16.0
|
0.1
|
|
Copper binding site 14 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 14 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 14 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu311
b:47.9
occ:0.34
|
O
|
A:HOH1265
|
1.6
|
21.1
|
0.3
|
|
O
|
A:HOH1264
|
2.5
|
41.2
|
0.6
|
|
CB
|
A:ASN48
|
3.5
|
17.0
|
1.0
|
|
CA
|
A:ASN48
|
3.7
|
12.9
|
1.0
|
|
N
|
A:ASN48
|
3.7
|
14.7
|
1.0
|
|
O
|
A:EOH1201
|
3.7
|
15.7
|
0.5
|
|
O
|
A:HOH1304
|
3.9
|
17.9
|
0.5
|
|
O
|
A:HOH1319
|
3.9
|
49.5
|
1.0
|
|
CG
|
A:ASN48
|
4.0
|
19.2
|
1.0
|
|
OD1
|
A:ASN48
|
4.4
|
34.6
|
1.0
|
|
C
|
A:LYS47
|
4.5
|
14.1
|
1.0
|
|
C1
|
A:EOH1201
|
4.6
|
18.4
|
0.5
|
|
ND2
|
A:ASN48
|
4.7
|
28.5
|
1.0
|
|
O
|
A:HOH1251
|
4.9
|
17.3
|
0.9
|
|
Copper binding site 15 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 15 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 15 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu312
b:7.7
occ:0.25
|
O
|
A:GLY19
|
2.3
|
9.4
|
1.0
|
|
O
|
A:HOH1237
|
2.4
|
14.0
|
1.0
|
|
O
|
A:HOH1203
|
2.5
|
9.1
|
1.0
|
|
C
|
A:GLY19
|
3.4
|
8.9
|
1.0
|
|
O
|
A:HOH1298
|
3.8
|
9.4
|
0.3
|
|
N
|
A:LEU1
|
3.9
|
10.7
|
1.0
|
|
O
|
A:GLU21
|
4.0
|
8.9
|
1.0
|
|
CA
|
A:GLY19
|
4.1
|
9.4
|
1.0
|
|
N
|
A:GLY20
|
4.4
|
9.3
|
1.0
|
|
O
|
A:HOH1204
|
4.4
|
15.2
|
1.0
|
|
O
|
A:HOH1300
|
4.5
|
24.7
|
0.4
|
|
O
|
A:SER18
|
4.5
|
8.8
|
1.0
|
|
CA
|
A:GLY20
|
4.6
|
8.9
|
1.0
|
|
C
|
A:GLY20
|
4.7
|
8.6
|
1.0
|
|
N
|
A:GLU21
|
4.8
|
8.7
|
1.0
|
|
Copper binding site 16 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 16 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 16 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu301
b:8.5
occ:0.76
|
CU
|
B:CU301
|
0.0
|
8.5
|
0.8
|
|
CU
|
B:CU301
|
0.7
|
19.2
|
0.2
|
|
OE1
|
A:GLU38
|
1.9
|
11.5
|
1.0
|
|
NE2
|
B:HIS4
|
1.9
|
9.5
|
1.0
|
|
CL
|
A:CL401
|
2.1
|
9.4
|
0.3
|
|
OD1
|
B:ASN62
|
2.2
|
11.4
|
1.0
|
|
O
|
B:ARG59
|
2.4
|
8.6
|
1.0
|
|
CD
|
A:GLU38
|
2.7
|
9.7
|
1.0
|
|
OE2
|
A:GLU38
|
2.9
|
11.4
|
1.0
|
|
CD2
|
B:HIS4
|
2.9
|
8.4
|
1.0
|
|
CE1
|
B:HIS4
|
3.0
|
9.4
|
1.0
|
|
CG
|
B:ASN62
|
3.2
|
10.0
|
1.0
|
|
ND2
|
B:ASN62
|
3.4
|
12.0
|
1.0
|
|
O
|
A:HOH1241
|
3.4
|
16.6
|
1.0
|
|
CB
|
B:ARG59
|
3.4
|
10.1
|
1.0
|
|
C
|
B:ARG59
|
3.5
|
7.8
|
1.0
|
|
O
|
B:HOH325
|
4.0
|
14.9
|
1.0
|
|
CA
|
B:ARG59
|
4.0
|
8.8
|
1.0
|
|
CG
|
B:HIS4
|
4.1
|
7.8
|
1.0
|
|
ND1
|
B:HIS4
|
4.1
|
8.8
|
1.0
|
|
CG
|
A:GLU38
|
4.1
|
9.5
|
1.0
|
|
O
|
A:HOH1258
|
4.1
|
22.8
|
1.0
|
|
NZ
|
A:LYS27
|
4.5
|
13.8
|
0.4
|
|
CB
|
B:ASN62
|
4.6
|
10.5
|
1.0
|
|
N
|
B:CYS60
|
4.7
|
7.5
|
1.0
|
|
CG
|
B:ARG59
|
4.7
|
13.4
|
1.0
|
|
CB
|
A:GLU38
|
4.8
|
8.0
|
1.0
|
|
CD
|
B:ARG59
|
4.8
|
15.3
|
1.0
|
|
CH2
|
A:TRP29
|
4.9
|
18.2
|
1.0
|
|
NZ
|
A:LYS27
|
4.9
|
13.2
|
0.6
|
|
Copper binding site 17 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 17 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 17 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu301
b:19.2
occ:0.24
|
CU
|
B:CU301
|
0.0
|
19.2
|
0.2
|
|
CU
|
B:CU301
|
0.7
|
8.5
|
0.8
|
|
CL
|
A:CL401
|
1.5
|
9.4
|
0.3
|
|
NE2
|
B:HIS4
|
1.9
|
9.5
|
1.0
|
|
OE1
|
A:GLU38
|
2.1
|
11.5
|
1.0
|
|
OD1
|
B:ASN62
|
2.7
|
11.4
|
1.0
|
|
CE1
|
B:HIS4
|
2.7
|
9.4
|
1.0
|
|
CD
|
A:GLU38
|
2.8
|
9.7
|
1.0
|
|
OE2
|
A:GLU38
|
2.8
|
11.4
|
1.0
|
|
O
|
B:ARG59
|
3.0
|
8.6
|
1.0
|
|
O
|
A:HOH1241
|
3.1
|
16.6
|
1.0
|
|
CD2
|
B:HIS4
|
3.2
|
8.4
|
1.0
|
|
CB
|
B:ARG59
|
3.5
|
10.1
|
1.0
|
|
CG
|
B:ASN62
|
3.7
|
10.0
|
1.0
|
|
NZ
|
A:LYS27
|
3.9
|
13.8
|
0.4
|
|
ND1
|
B:HIS4
|
4.0
|
8.8
|
1.0
|
|
C
|
B:ARG59
|
4.0
|
7.8
|
1.0
|
|
ND2
|
B:ASN62
|
4.0
|
12.0
|
1.0
|
|
O
|
B:HOH325
|
4.1
|
14.9
|
1.0
|
|
CG
|
B:HIS4
|
4.2
|
7.8
|
1.0
|
|
CG
|
A:GLU38
|
4.2
|
9.5
|
1.0
|
|
NZ
|
A:LYS27
|
4.2
|
13.2
|
0.6
|
|
CA
|
B:ARG59
|
4.3
|
8.8
|
1.0
|
|
O
|
A:HOH1258
|
4.5
|
22.8
|
1.0
|
|
CD
|
B:ARG59
|
4.5
|
15.3
|
1.0
|
|
CE
|
A:LYS27
|
4.5
|
14.3
|
0.4
|
|
CE
|
A:LYS27
|
4.6
|
13.9
|
0.6
|
|
CU
|
A:CU308
|
4.6
|
28.9
|
0.3
|
|
CG
|
B:ARG59
|
4.6
|
13.4
|
1.0
|
|
CH2
|
A:TRP29
|
4.6
|
18.2
|
1.0
|
|
CB
|
A:GLU38
|
4.7
|
8.0
|
1.0
|
|
CD
|
A:LYS27
|
4.8
|
12.1
|
0.6
|
|
CZ3
|
A:TRP29
|
4.9
|
17.2
|
1.0
|
|
CD
|
A:LYS27
|
4.9
|
13.4
|
0.4
|
|
Copper binding site 18 out
of 18 in 1v6p
Go back to
Copper Binding Sites List in 1v6p
Copper binding site 18 out
of 18 in the Crystal Structure of Cobrotoxin
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 18 of Crystal Structure of Cobrotoxin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu309
b:10.2
occ:0.26
|
NE1
|
B:TRP29
|
3.2
|
8.0
|
1.0
|
|
O
|
B:HOH392
|
3.2
|
14.0
|
1.0
|
|
CE2
|
B:TRP29
|
4.1
|
7.7
|
1.0
|
|
CG
|
B:ARG36
|
4.2
|
9.4
|
1.0
|
|
CD1
|
B:TRP29
|
4.2
|
8.2
|
1.0
|
|
CG
|
B:ASP31
|
4.2
|
13.4
|
1.0
|
|
CB
|
B:ASP31
|
4.2
|
11.7
|
1.0
|
|
CZ2
|
B:TRP29
|
4.3
|
9.1
|
1.0
|
|
OD1
|
B:ASP31
|
4.4
|
16.2
|
1.0
|
|
OD2
|
B:ASP31
|
4.6
|
18.6
|
1.0
|
|
CD
|
B:ARG36
|
4.7
|
11.1
|
1.0
|
|
NE
|
B:ARG36
|
4.7
|
12.5
|
1.0
|
|
CB
|
B:ARG36
|
4.9
|
8.7
|
1.0
|
|
Reference:
X.Lou,
Q.Liu,
X.Tu,
J.Wang,
M.Teng,
L.Niu,
D.J.Schuller,
Q.Huang,
Q.Hao.
The Atomic Resolution Crystal Structure of Atratoxin Determined By Single Wavelength Anomalous Diffraction Phasing J.Biol.Chem. V. 279 39094 2004.
ISSN: ISSN 0021-9258
PubMed: 15252034
DOI: 10.1074/JBC.M403863200
Page generated: Thu Sep 3 16:22:41 2020
|