Copper in PDB 5fej: Copm in the Cu(I)-Bound Form
Protein crystallography data
The structure of Copm in the Cu(I)-Bound Form, PDB code: 5fej
was solved by
S.Zhao,
X.Wang,
L.Liu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.94 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.824,
86.082,
74.971,
90.00,
106.26,
90.00
|
R / Rfree (%)
|
21.1 /
25.9
|
Copper Binding Sites:
The binding sites of Copper atom in the Copm in the Cu(I)-Bound Form
(pdb code 5fej). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the
Copm in the Cu(I)-Bound Form, PDB code: 5fej:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Copper binding site 1 out
of 8 in 5fej
Go back to
Copper Binding Sites List in 5fej
Copper binding site 1 out
of 8 in the Copm in the Cu(I)-Bound Form
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu201
b:11.8
occ:1.00
|
ND1
|
A:HIS56
|
1.8
|
8.0
|
1.0
|
ND1
|
A:HIS57
|
1.8
|
10.0
|
1.0
|
CE1
|
A:HIS57
|
2.5
|
10.5
|
1.0
|
CE1
|
A:HIS56
|
2.7
|
8.1
|
1.0
|
CG
|
A:HIS56
|
2.9
|
8.1
|
1.0
|
N
|
A:HIS57
|
3.0
|
9.2
|
1.0
|
CG
|
A:HIS57
|
3.0
|
10.7
|
1.0
|
SD
|
A:MET53
|
3.1
|
9.2
|
1.0
|
C
|
A:HIS56
|
3.2
|
8.7
|
1.0
|
CA
|
A:HIS57
|
3.3
|
9.4
|
1.0
|
CB
|
A:HIS56
|
3.4
|
9.0
|
1.0
|
O
|
A:HOH311
|
3.5
|
12.2
|
1.0
|
O
|
A:HIS56
|
3.6
|
11.7
|
1.0
|
CB
|
A:HIS57
|
3.6
|
8.8
|
1.0
|
O
|
A:MET53
|
3.7
|
9.9
|
1.0
|
NE2
|
A:HIS57
|
3.8
|
10.0
|
1.0
|
NE2
|
A:HIS56
|
3.8
|
8.2
|
1.0
|
OE1
|
A:GLN87
|
3.9
|
13.1
|
1.0
|
CA
|
A:HIS56
|
3.9
|
8.4
|
1.0
|
CD2
|
A:HIS56
|
4.0
|
6.4
|
1.0
|
CD2
|
A:HIS57
|
4.0
|
9.9
|
1.0
|
CG
|
A:MET53
|
4.0
|
10.0
|
1.0
|
CE1
|
A:HIS148
|
4.4
|
9.7
|
1.0
|
NE2
|
A:HIS148
|
4.6
|
10.1
|
1.0
|
CB
|
A:ALA152
|
4.6
|
9.2
|
1.0
|
C
|
A:MET53
|
4.6
|
9.6
|
1.0
|
NE2
|
A:GLN179
|
4.7
|
12.7
|
1.0
|
CE
|
A:MET53
|
4.7
|
11.1
|
1.0
|
C
|
A:HIS57
|
4.8
|
10.2
|
1.0
|
CA
|
A:MET53
|
4.8
|
7.6
|
1.0
|
N
|
A:HIS56
|
4.9
|
9.9
|
1.0
|
|
Copper binding site 2 out
of 8 in 5fej
Go back to
Copper Binding Sites List in 5fej
Copper binding site 2 out
of 8 in the Copm in the Cu(I)-Bound Form
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu202
b:10.3
occ:1.00
|
ND1
|
A:HIS148
|
1.8
|
10.1
|
1.0
|
ND1
|
A:HIS149
|
1.8
|
11.6
|
1.0
|
CE1
|
A:HIS149
|
2.5
|
9.9
|
1.0
|
CE1
|
A:HIS148
|
2.7
|
9.7
|
1.0
|
CG
|
A:HIS148
|
2.9
|
9.4
|
1.0
|
N
|
A:HIS149
|
2.9
|
10.2
|
1.0
|
CG
|
A:HIS149
|
3.0
|
11.2
|
1.0
|
C
|
A:HIS148
|
3.2
|
9.4
|
1.0
|
CA
|
A:HIS149
|
3.2
|
9.3
|
1.0
|
O
|
A:HOH311
|
3.3
|
12.2
|
1.0
|
SD
|
A:MET145
|
3.4
|
10.1
|
1.0
|
CB
|
A:HIS148
|
3.4
|
9.3
|
1.0
|
O
|
A:MET145
|
3.6
|
9.5
|
1.0
|
CB
|
A:HIS149
|
3.6
|
9.7
|
1.0
|
O
|
A:HIS148
|
3.6
|
9.9
|
1.0
|
NE2
|
A:HIS149
|
3.7
|
7.6
|
1.0
|
NE2
|
A:HIS148
|
3.8
|
10.1
|
1.0
|
OE1
|
A:GLN179
|
3.8
|
10.8
|
1.0
|
CD2
|
A:HIS148
|
3.9
|
9.6
|
1.0
|
CA
|
A:HIS148
|
3.9
|
9.8
|
1.0
|
CD2
|
A:HIS149
|
4.0
|
9.5
|
1.0
|
CG
|
A:MET145
|
4.2
|
8.4
|
1.0
|
CE1
|
A:HIS56
|
4.3
|
8.1
|
1.0
|
CB
|
A:ALA60
|
4.5
|
10.6
|
1.0
|
C
|
A:MET145
|
4.5
|
8.6
|
1.0
|
C
|
A:HIS149
|
4.7
|
10.9
|
1.0
|
NE2
|
A:HIS56
|
4.7
|
8.2
|
1.0
|
CA
|
A:MET145
|
4.8
|
8.7
|
1.0
|
N
|
A:HIS148
|
4.8
|
10.0
|
1.0
|
CD
|
A:GLN179
|
4.9
|
12.1
|
1.0
|
NE2
|
A:GLN87
|
5.0
|
12.8
|
1.0
|
|
Copper binding site 3 out
of 8 in 5fej
Go back to
Copper Binding Sites List in 5fej
Copper binding site 3 out
of 8 in the Copm in the Cu(I)-Bound Form
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu201
b:15.8
occ:1.00
|
ND1
|
B:HIS57
|
1.8
|
13.7
|
1.0
|
ND1
|
B:HIS56
|
1.8
|
12.4
|
1.0
|
CE1
|
B:HIS57
|
2.6
|
13.3
|
1.0
|
CE1
|
B:HIS56
|
2.6
|
11.7
|
1.0
|
SD
|
B:MET53
|
2.9
|
13.6
|
1.0
|
CG
|
B:HIS56
|
3.0
|
11.7
|
1.0
|
CG
|
B:HIS57
|
3.0
|
14.3
|
1.0
|
N
|
B:HIS57
|
3.0
|
12.3
|
1.0
|
CA
|
B:HIS57
|
3.2
|
12.0
|
1.0
|
C
|
B:HIS56
|
3.2
|
12.5
|
1.0
|
O
|
B:MET53
|
3.5
|
12.4
|
1.0
|
CB
|
B:HIS56
|
3.5
|
11.9
|
1.0
|
O
|
B:HIS56
|
3.5
|
13.6
|
1.0
|
O
|
B:HOH302
|
3.5
|
15.1
|
1.0
|
CB
|
B:HIS57
|
3.6
|
12.7
|
1.0
|
NE2
|
B:HIS57
|
3.7
|
13.6
|
1.0
|
NE2
|
B:HIS56
|
3.8
|
13.0
|
1.0
|
CD2
|
B:HIS57
|
4.0
|
12.6
|
1.0
|
OE1
|
B:GLN87
|
4.0
|
14.5
|
1.0
|
CG
|
B:MET53
|
4.0
|
14.0
|
1.0
|
CD2
|
B:HIS56
|
4.0
|
11.2
|
1.0
|
CA
|
B:HIS56
|
4.0
|
11.4
|
1.0
|
CE1
|
B:HIS148
|
4.4
|
12.7
|
1.0
|
CB
|
B:ALA152
|
4.5
|
12.9
|
1.0
|
C
|
B:MET53
|
4.5
|
12.5
|
1.0
|
CE
|
B:MET53
|
4.5
|
16.5
|
1.0
|
NE2
|
B:HIS148
|
4.6
|
13.1
|
1.0
|
C
|
B:HIS57
|
4.7
|
13.0
|
1.0
|
NE2
|
B:GLN179
|
4.7
|
13.3
|
1.0
|
CA
|
B:MET53
|
4.8
|
10.8
|
1.0
|
N
|
B:HIS56
|
4.8
|
11.9
|
1.0
|
CB
|
B:MET53
|
5.0
|
11.9
|
1.0
|
|
Copper binding site 4 out
of 8 in 5fej
Go back to
Copper Binding Sites List in 5fej
Copper binding site 4 out
of 8 in the Copm in the Cu(I)-Bound Form
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu202
b:12.9
occ:1.00
|
ND1
|
B:HIS148
|
1.8
|
13.5
|
1.0
|
ND1
|
B:HIS149
|
1.8
|
13.4
|
1.0
|
CE1
|
B:HIS149
|
2.5
|
13.1
|
1.0
|
CE1
|
B:HIS148
|
2.7
|
12.7
|
1.0
|
CG
|
B:HIS148
|
2.9
|
12.4
|
1.0
|
N
|
B:HIS149
|
2.9
|
12.4
|
1.0
|
CG
|
B:HIS149
|
3.0
|
12.1
|
1.0
|
O
|
B:HOH302
|
3.1
|
15.1
|
1.0
|
CA
|
B:HIS149
|
3.2
|
12.9
|
1.0
|
C
|
B:HIS148
|
3.2
|
12.7
|
1.0
|
SD
|
B:MET145
|
3.4
|
13.4
|
1.0
|
CB
|
B:HIS148
|
3.4
|
11.5
|
1.0
|
O
|
B:MET145
|
3.6
|
10.5
|
1.0
|
CB
|
B:HIS149
|
3.6
|
11.5
|
1.0
|
O
|
B:HIS148
|
3.7
|
12.9
|
1.0
|
NE2
|
B:HIS149
|
3.7
|
11.6
|
1.0
|
NE2
|
B:HIS148
|
3.8
|
13.1
|
1.0
|
CA
|
B:HIS148
|
3.9
|
13.0
|
1.0
|
CD2
|
B:HIS148
|
4.0
|
13.2
|
1.0
|
CD2
|
B:HIS149
|
4.0
|
10.9
|
1.0
|
CG
|
B:MET145
|
4.3
|
12.0
|
1.0
|
NE2
|
B:GLN179
|
4.3
|
13.3
|
1.0
|
CE1
|
B:HIS56
|
4.4
|
11.7
|
1.0
|
CB
|
B:ALA60
|
4.5
|
13.6
|
1.0
|
C
|
B:MET145
|
4.6
|
11.0
|
1.0
|
OE1
|
B:GLN179
|
4.6
|
15.6
|
1.0
|
NE2
|
B:HIS56
|
4.6
|
13.0
|
1.0
|
C
|
B:HIS149
|
4.7
|
14.1
|
1.0
|
CD
|
B:GLN179
|
4.8
|
13.2
|
1.0
|
CA
|
B:MET145
|
4.8
|
10.1
|
1.0
|
N
|
B:HIS148
|
4.9
|
12.2
|
1.0
|
CE
|
B:MET145
|
4.9
|
12.6
|
1.0
|
|
Copper binding site 5 out
of 8 in 5fej
Go back to
Copper Binding Sites List in 5fej
Copper binding site 5 out
of 8 in the Copm in the Cu(I)-Bound Form
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu201
b:9.4
occ:1.00
|
ND1
|
C:HIS57
|
1.8
|
10.4
|
1.0
|
ND1
|
C:HIS56
|
1.8
|
12.2
|
1.0
|
CE1
|
C:HIS57
|
2.6
|
11.5
|
1.0
|
CE1
|
C:HIS56
|
2.6
|
11.6
|
1.0
|
CG
|
C:HIS57
|
2.9
|
12.4
|
1.0
|
N
|
C:HIS57
|
2.9
|
10.2
|
1.0
|
CG
|
C:HIS56
|
3.0
|
11.2
|
1.0
|
SD
|
C:MET53
|
3.1
|
12.6
|
1.0
|
CA
|
C:HIS57
|
3.1
|
10.0
|
1.0
|
C
|
C:HIS56
|
3.4
|
10.9
|
1.0
|
CB
|
C:HIS57
|
3.4
|
11.2
|
1.0
|
CB
|
C:HIS56
|
3.5
|
9.3
|
1.0
|
O
|
C:MET53
|
3.6
|
10.3
|
1.0
|
NE2
|
C:HIS57
|
3.7
|
11.8
|
1.0
|
NE2
|
C:HIS56
|
3.8
|
11.6
|
1.0
|
O
|
C:HIS56
|
3.8
|
12.2
|
1.0
|
NE2
|
C:GLN87
|
3.9
|
15.4
|
1.0
|
CD2
|
C:HIS57
|
3.9
|
12.0
|
1.0
|
CD2
|
C:HIS56
|
4.0
|
10.0
|
1.0
|
CG
|
C:MET53
|
4.0
|
11.4
|
1.0
|
CA
|
C:HIS56
|
4.1
|
9.6
|
1.0
|
CE1
|
C:HIS148
|
4.5
|
11.6
|
1.0
|
C
|
C:HIS57
|
4.6
|
11.2
|
1.0
|
C
|
C:MET53
|
4.6
|
10.8
|
1.0
|
CB
|
C:ALA152
|
4.7
|
11.4
|
1.0
|
NE2
|
C:HIS148
|
4.7
|
12.0
|
1.0
|
CE
|
C:MET53
|
4.7
|
15.3
|
1.0
|
CD
|
C:GLN87
|
4.8
|
13.7
|
1.0
|
CA
|
C:MET53
|
4.8
|
11.2
|
1.0
|
OE1
|
C:GLN87
|
5.0
|
15.2
|
1.0
|
N
|
C:HIS56
|
5.0
|
9.4
|
1.0
|
|
Copper binding site 6 out
of 8 in 5fej
Go back to
Copper Binding Sites List in 5fej
Copper binding site 6 out
of 8 in the Copm in the Cu(I)-Bound Form
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu202
b:14.9
occ:1.00
|
ND1
|
C:HIS148
|
1.8
|
11.2
|
1.0
|
ND1
|
C:HIS149
|
1.8
|
11.3
|
1.0
|
CE1
|
C:HIS149
|
2.5
|
11.5
|
1.0
|
CE1
|
C:HIS148
|
2.6
|
11.6
|
1.0
|
CG
|
C:HIS148
|
2.9
|
11.9
|
1.0
|
CG
|
C:HIS149
|
3.0
|
11.4
|
1.0
|
N
|
C:HIS149
|
3.0
|
11.8
|
1.0
|
SD
|
C:MET145
|
3.2
|
12.3
|
1.0
|
CA
|
C:HIS149
|
3.3
|
11.9
|
1.0
|
C
|
C:HIS148
|
3.3
|
11.9
|
1.0
|
CB
|
C:HIS148
|
3.4
|
11.6
|
1.0
|
O
|
C:MET145
|
3.5
|
10.8
|
1.0
|
CB
|
C:HIS149
|
3.7
|
12.1
|
1.0
|
O
|
C:HIS148
|
3.7
|
11.6
|
1.0
|
NE2
|
C:HIS149
|
3.7
|
10.8
|
1.0
|
OE1
|
C:GLN179
|
3.8
|
16.2
|
1.0
|
NE2
|
C:HIS148
|
3.8
|
12.0
|
1.0
|
CD2
|
C:HIS148
|
3.9
|
12.1
|
1.0
|
CD2
|
C:HIS149
|
4.0
|
10.9
|
1.0
|
CA
|
C:HIS148
|
4.0
|
12.4
|
1.0
|
CG
|
C:MET145
|
4.0
|
10.3
|
1.0
|
CE1
|
C:HIS56
|
4.4
|
11.6
|
1.0
|
C
|
C:MET145
|
4.5
|
10.5
|
1.0
|
CB
|
C:ALA60
|
4.5
|
11.7
|
1.0
|
NE2
|
C:HIS56
|
4.6
|
11.6
|
1.0
|
CA
|
C:MET145
|
4.7
|
9.5
|
1.0
|
C
|
C:HIS149
|
4.7
|
12.7
|
1.0
|
CE
|
C:MET145
|
4.9
|
10.7
|
1.0
|
N
|
C:HIS148
|
4.9
|
11.6
|
1.0
|
OE1
|
C:GLN87
|
4.9
|
15.2
|
1.0
|
CD
|
C:GLN179
|
5.0
|
17.1
|
1.0
|
CB
|
C:MET145
|
5.0
|
10.4
|
1.0
|
|
Copper binding site 7 out
of 8 in 5fej
Go back to
Copper Binding Sites List in 5fej
Copper binding site 7 out
of 8 in the Copm in the Cu(I)-Bound Form
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 7 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu201
b:13.2
occ:1.00
|
ND1
|
D:HIS57
|
1.8
|
11.5
|
1.0
|
ND1
|
D:HIS56
|
1.8
|
12.6
|
1.0
|
CE1
|
D:HIS57
|
2.4
|
11.4
|
1.0
|
CE1
|
D:HIS56
|
2.7
|
12.2
|
1.0
|
CG
|
D:HIS56
|
2.9
|
11.8
|
1.0
|
SD
|
D:MET53
|
3.0
|
12.3
|
1.0
|
CG
|
D:HIS57
|
3.0
|
12.5
|
1.0
|
N
|
D:HIS57
|
3.0
|
10.8
|
1.0
|
C
|
D:HIS56
|
3.3
|
12.0
|
1.0
|
CA
|
D:HIS57
|
3.3
|
10.5
|
1.0
|
CB
|
D:HIS56
|
3.4
|
11.4
|
1.0
|
NE2
|
D:HIS57
|
3.7
|
13.3
|
1.0
|
CB
|
D:HIS57
|
3.7
|
11.2
|
1.0
|
O
|
D:MET53
|
3.7
|
12.5
|
1.0
|
O
|
D:HIS56
|
3.7
|
13.8
|
1.0
|
NE2
|
D:HIS56
|
3.8
|
12.8
|
1.0
|
CD2
|
D:HIS57
|
3.9
|
12.6
|
1.0
|
CD2
|
D:HIS56
|
4.0
|
11.8
|
1.0
|
CA
|
D:HIS56
|
4.0
|
10.5
|
1.0
|
CG
|
D:MET53
|
4.0
|
10.2
|
1.0
|
NE2
|
D:GLN87
|
4.1
|
12.2
|
1.0
|
CE1
|
D:HIS148
|
4.4
|
12.1
|
1.0
|
NE2
|
D:HIS148
|
4.5
|
12.5
|
1.0
|
CE
|
D:MET53
|
4.6
|
13.9
|
1.0
|
CB
|
D:ALA152
|
4.6
|
12.1
|
1.0
|
C
|
D:MET53
|
4.7
|
12.2
|
1.0
|
C
|
D:HIS57
|
4.8
|
11.3
|
1.0
|
N
|
D:HIS56
|
4.9
|
12.3
|
1.0
|
CD
|
D:GLN87
|
4.9
|
11.4
|
1.0
|
CA
|
D:MET53
|
4.9
|
10.8
|
1.0
|
OE1
|
D:GLN87
|
4.9
|
13.7
|
1.0
|
|
Copper binding site 8 out
of 8 in 5fej
Go back to
Copper Binding Sites List in 5fej
Copper binding site 8 out
of 8 in the Copm in the Cu(I)-Bound Form
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 8 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu202
b:10.7
occ:1.00
|
ND1
|
D:HIS149
|
1.8
|
11.8
|
1.0
|
ND1
|
D:HIS148
|
1.8
|
11.7
|
1.0
|
CE1
|
D:HIS149
|
2.5
|
12.2
|
1.0
|
CE1
|
D:HIS148
|
2.6
|
12.1
|
1.0
|
CG
|
D:HIS148
|
3.0
|
12.0
|
1.0
|
CG
|
D:HIS149
|
3.0
|
9.7
|
1.0
|
N
|
D:HIS149
|
3.1
|
9.5
|
1.0
|
SD
|
D:MET145
|
3.2
|
12.3
|
1.0
|
CA
|
D:HIS149
|
3.3
|
10.4
|
1.0
|
C
|
D:HIS148
|
3.4
|
10.5
|
1.0
|
O
|
D:MET145
|
3.5
|
11.1
|
1.0
|
CB
|
D:HIS148
|
3.5
|
11.4
|
1.0
|
CB
|
D:HIS149
|
3.7
|
11.2
|
1.0
|
NE2
|
D:HIS149
|
3.7
|
11.9
|
1.0
|
O
|
D:HIS148
|
3.7
|
11.5
|
1.0
|
NE2
|
D:HIS148
|
3.8
|
12.5
|
1.0
|
NE2
|
D:GLN179
|
3.9
|
17.4
|
1.0
|
CD2
|
D:HIS148
|
4.0
|
12.3
|
1.0
|
CD2
|
D:HIS149
|
4.0
|
9.6
|
1.0
|
CA
|
D:HIS148
|
4.1
|
11.2
|
1.0
|
CG
|
D:MET145
|
4.1
|
11.2
|
1.0
|
CE1
|
D:HIS56
|
4.5
|
12.2
|
1.0
|
C
|
D:MET145
|
4.5
|
10.4
|
1.0
|
CB
|
D:ALA60
|
4.6
|
10.5
|
1.0
|
NE2
|
D:HIS56
|
4.7
|
12.8
|
1.0
|
CA
|
D:MET145
|
4.8
|
10.0
|
1.0
|
C
|
D:HIS149
|
4.8
|
11.6
|
1.0
|
CE
|
D:MET145
|
4.9
|
10.5
|
1.0
|
N
|
D:HIS148
|
4.9
|
11.4
|
1.0
|
CD
|
D:GLN179
|
4.9
|
16.2
|
1.0
|
|
Reference:
S.Zhao,
X.Wang,
G.Niu,
W.Dong,
J.Wang,
Y.Fang,
Y.Lin,
L.Liu.
Structural Basis For Copper/Silver Binding By the Synechocystis Metallochaperone Copm Acta Crystallogr.,Sect.D V. 72 997 2016.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798316011943
Page generated: Wed Jul 31 04:05:09 2024
|