Copper in PDB 6sji: The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Protein crystallography data
The structure of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln, PDB code: 6sji
was solved by
K.M.Polyakov,
T.V.Tikhonova,
T.V.Rakitina,
E.Osipov,
V.O.Popov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
89.97 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.080,
160.410,
90.880,
90.00,
98.11,
90.00
|
R / Rfree (%)
|
15.9 /
19.8
|
Copper Binding Sites:
The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
(pdb code 6sji). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the
The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln, PDB code: 6sji:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Copper binding site 1 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 1 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu601
b:20.5
occ:0.80
|
NE2
|
A:HIS206
|
1.9
|
21.2
|
1.0
|
NE2
|
A:HIS381
|
1.9
|
20.8
|
1.0
|
OD2
|
A:ASP314
|
2.4
|
23.5
|
1.0
|
OD1
|
A:ASP314
|
2.5
|
23.5
|
1.0
|
O
|
A:HOH945
|
2.7
|
24.6
|
0.5
|
CG
|
A:ASP314
|
2.8
|
23.6
|
1.0
|
CD2
|
A:HIS381
|
2.9
|
22.0
|
1.0
|
CD2
|
A:HIS206
|
2.9
|
19.3
|
1.0
|
CE1
|
A:HIS206
|
2.9
|
21.4
|
1.0
|
CE1
|
A:HIS381
|
3.0
|
23.0
|
1.0
|
ND1
|
A:HIS206
|
4.0
|
18.8
|
1.0
|
CG
|
A:HIS206
|
4.0
|
18.8
|
1.0
|
CG
|
A:HIS381
|
4.1
|
21.4
|
1.0
|
ND1
|
A:HIS381
|
4.1
|
21.5
|
1.0
|
O
|
A:HOH789
|
4.1
|
25.3
|
1.0
|
CB
|
A:ASP314
|
4.3
|
21.9
|
1.0
|
O
|
A:HOH715
|
4.3
|
21.8
|
1.0
|
OG1
|
A:THR548
|
4.4
|
25.4
|
1.0
|
O
|
A:HOH725
|
4.6
|
26.9
|
1.0
|
O
|
A:PHE436
|
4.8
|
30.4
|
1.0
|
CG1
|
A:VAL205
|
4.9
|
18.5
|
1.0
|
|
Copper binding site 2 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 2 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu602
b:22.9
occ:0.80
|
ND1
|
A:HIS528
|
1.9
|
19.4
|
1.0
|
NE2
|
A:HIS135
|
1.9
|
16.7
|
1.0
|
O
|
A:HOH824
|
2.0
|
34.1
|
0.8
|
O
|
A:HOH838
|
2.0
|
27.8
|
1.0
|
CD2
|
A:HIS135
|
2.8
|
16.4
|
1.0
|
NZ
|
A:LYS103
|
2.8
|
22.9
|
1.0
|
CE1
|
A:HIS528
|
2.9
|
19.7
|
1.0
|
CG
|
A:HIS528
|
2.9
|
19.3
|
1.0
|
CE1
|
A:HIS135
|
3.0
|
15.9
|
1.0
|
CB
|
A:HIS528
|
3.3
|
17.4
|
1.0
|
O
|
A:HOH789
|
3.6
|
25.3
|
1.0
|
CE
|
A:LYS103
|
3.6
|
22.9
|
1.0
|
CD
|
A:LYS103
|
3.9
|
20.2
|
1.0
|
CG
|
A:HIS135
|
4.0
|
16.0
|
1.0
|
NE2
|
A:HIS528
|
4.0
|
20.5
|
1.0
|
ND1
|
A:HIS135
|
4.0
|
16.0
|
1.0
|
CD2
|
A:HIS528
|
4.0
|
19.3
|
1.0
|
OE1
|
A:GLU288
|
4.2
|
22.8
|
1.0
|
O
|
A:HOH815
|
4.2
|
22.0
|
0.5
|
NE2
|
A:HIS136
|
4.2
|
17.2
|
1.0
|
OH
|
A:TYR164
|
4.3
|
25.5
|
1.0
|
OE1
|
A:GLN156
|
4.5
|
21.1
|
1.0
|
CE1
|
A:HIS136
|
4.6
|
18.2
|
1.0
|
CA
|
A:HIS528
|
4.8
|
17.0
|
1.0
|
OE2
|
A:GLU288
|
4.9
|
23.6
|
1.0
|
CD
|
A:GLU288
|
5.0
|
22.2
|
1.0
|
|
Copper binding site 3 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 3 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu601
b:17.4
occ:0.80
|
NE2
|
B:HIS206
|
1.9
|
20.3
|
1.0
|
NE2
|
B:HIS381
|
1.9
|
22.9
|
1.0
|
O
|
B:HOH890
|
2.1
|
22.6
|
0.5
|
OD2
|
B:ASP314
|
2.4
|
20.9
|
1.0
|
OD1
|
B:ASP314
|
2.5
|
23.9
|
1.0
|
CG
|
B:ASP314
|
2.8
|
23.8
|
1.0
|
CD2
|
B:HIS206
|
2.8
|
22.2
|
1.0
|
CE1
|
B:HIS381
|
2.9
|
23.1
|
1.0
|
CE1
|
B:HIS206
|
2.9
|
18.6
|
1.0
|
CD2
|
B:HIS381
|
3.0
|
24.0
|
1.0
|
CG
|
B:HIS206
|
4.0
|
16.7
|
1.0
|
ND1
|
B:HIS206
|
4.0
|
19.1
|
1.0
|
ND1
|
B:HIS381
|
4.0
|
22.8
|
1.0
|
CG
|
B:HIS381
|
4.1
|
21.6
|
1.0
|
O
|
B:HOH776
|
4.2
|
28.3
|
1.0
|
CB
|
B:ASP314
|
4.3
|
21.0
|
1.0
|
O
|
B:HOH709
|
4.3
|
21.6
|
1.0
|
OG1
|
B:THR548
|
4.5
|
24.7
|
1.0
|
O
|
B:HOH716
|
4.6
|
23.6
|
1.0
|
O
|
B:PHE436
|
4.7
|
29.5
|
1.0
|
CG1
|
B:VAL205
|
4.9
|
15.6
|
1.0
|
|
Copper binding site 4 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 4 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu602
b:22.6
occ:0.80
|
O
|
B:HOH738
|
2.0
|
42.0
|
0.8
|
ND1
|
B:HIS528
|
2.0
|
16.8
|
1.0
|
NE2
|
B:HIS135
|
2.0
|
18.4
|
1.0
|
O
|
B:HOH894
|
2.0
|
22.0
|
1.0
|
NZ
|
B:LYS103
|
2.7
|
22.7
|
1.0
|
CD2
|
B:HIS135
|
2.9
|
16.9
|
1.0
|
CG
|
B:HIS528
|
2.9
|
16.5
|
1.0
|
CE1
|
B:HIS528
|
3.0
|
17.1
|
1.0
|
CE1
|
B:HIS135
|
3.1
|
16.5
|
1.0
|
CB
|
B:HIS528
|
3.2
|
16.8
|
1.0
|
O
|
B:HOH776
|
3.5
|
28.3
|
1.0
|
CE
|
B:LYS103
|
3.6
|
21.7
|
1.0
|
CD
|
B:LYS103
|
4.0
|
20.3
|
1.0
|
NE2
|
B:HIS528
|
4.0
|
16.1
|
1.0
|
CG
|
B:HIS135
|
4.1
|
17.6
|
1.0
|
CD2
|
B:HIS528
|
4.1
|
17.4
|
1.0
|
ND1
|
B:HIS135
|
4.2
|
15.5
|
1.0
|
NE2
|
B:HIS136
|
4.2
|
19.4
|
1.0
|
OE1
|
B:GLU288
|
4.2
|
21.5
|
1.0
|
O
|
B:HOH729
|
4.4
|
19.4
|
0.5
|
OH
|
B:TYR164
|
4.4
|
29.0
|
1.0
|
CE1
|
B:HIS136
|
4.6
|
18.5
|
1.0
|
OE1
|
B:GLN156
|
4.6
|
20.3
|
1.0
|
CA
|
B:HIS528
|
4.8
|
15.7
|
1.0
|
CD2
|
B:HIS136
|
5.0
|
18.4
|
1.0
|
OE2
|
B:GLU288
|
5.0
|
20.8
|
1.0
|
|
Copper binding site 5 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 5 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Cu601
b:21.0
occ:0.80
|
NE2
|
J:HIS381
|
2.0
|
23.0
|
1.0
|
NE2
|
J:HIS206
|
2.0
|
21.7
|
1.0
|
OD2
|
J:ASP314
|
2.4
|
22.7
|
1.0
|
OD1
|
J:ASP314
|
2.5
|
21.4
|
1.0
|
CG
|
J:ASP314
|
2.8
|
23.0
|
1.0
|
CD2
|
J:HIS381
|
2.9
|
21.1
|
1.0
|
CD2
|
J:HIS206
|
2.9
|
22.4
|
1.0
|
CE1
|
J:HIS206
|
3.0
|
19.8
|
1.0
|
CE1
|
J:HIS381
|
3.0
|
21.6
|
1.0
|
CG
|
J:HIS206
|
4.1
|
19.6
|
1.0
|
CG
|
J:HIS381
|
4.1
|
21.0
|
1.0
|
ND1
|
J:HIS206
|
4.1
|
19.3
|
1.0
|
ND1
|
J:HIS381
|
4.1
|
20.9
|
1.0
|
O
|
J:HOH785
|
4.2
|
25.0
|
1.0
|
CB
|
J:ASP314
|
4.3
|
22.1
|
1.0
|
O
|
J:HOH743
|
4.4
|
21.7
|
1.0
|
OG1
|
J:THR548
|
4.5
|
26.1
|
1.0
|
O
|
J:HOH726
|
4.6
|
26.8
|
1.0
|
O
|
J:PHE436
|
4.6
|
29.4
|
1.0
|
CG1
|
J:VAL205
|
4.9
|
19.1
|
1.0
|
|
Copper binding site 6 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 6 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Cu602
b:23.6
occ:0.80
|
NE2
|
J:HIS135
|
1.9
|
17.7
|
1.0
|
ND1
|
J:HIS528
|
1.9
|
18.6
|
1.0
|
O
|
J:HOH821
|
2.0
|
47.2
|
0.8
|
O
|
J:HOH807
|
2.0
|
25.4
|
1.0
|
NZ
|
J:LYS103
|
2.8
|
21.2
|
1.0
|
CD2
|
J:HIS135
|
2.8
|
15.0
|
1.0
|
CE1
|
J:HIS528
|
2.9
|
18.1
|
1.0
|
CG
|
J:HIS528
|
3.0
|
17.9
|
1.0
|
CE1
|
J:HIS135
|
3.0
|
17.2
|
1.0
|
CB
|
J:HIS528
|
3.3
|
17.5
|
1.0
|
O
|
J:HOH785
|
3.6
|
25.0
|
1.0
|
CE
|
J:LYS103
|
3.7
|
20.5
|
1.0
|
CD
|
J:LYS103
|
3.8
|
19.5
|
1.0
|
CG
|
J:HIS135
|
4.0
|
16.0
|
1.0
|
NE2
|
J:HIS528
|
4.0
|
19.9
|
1.0
|
ND1
|
J:HIS135
|
4.0
|
17.4
|
1.0
|
CD2
|
J:HIS528
|
4.1
|
18.6
|
1.0
|
O
|
J:HOH780
|
4.2
|
24.1
|
0.5
|
NE2
|
J:HIS136
|
4.2
|
20.9
|
1.0
|
OE1
|
J:GLU288
|
4.2
|
22.1
|
1.0
|
OH
|
J:TYR164
|
4.3
|
31.1
|
1.0
|
OE1
|
J:GLN156
|
4.6
|
22.4
|
1.0
|
CE1
|
J:HIS136
|
4.6
|
19.2
|
1.0
|
CA
|
J:HIS528
|
4.8
|
17.3
|
1.0
|
CD2
|
J:HIS136
|
4.9
|
20.0
|
1.0
|
|
Copper binding site 7 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 7 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 7 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Cu601
b:20.4
occ:0.80
|
NE2
|
K:HIS206
|
1.9
|
21.0
|
1.0
|
NE2
|
K:HIS381
|
1.9
|
27.2
|
1.0
|
OD2
|
K:ASP314
|
2.4
|
27.0
|
1.0
|
OD1
|
K:ASP314
|
2.5
|
22.5
|
1.0
|
CG
|
K:ASP314
|
2.8
|
24.5
|
1.0
|
O
|
K:HOH948
|
2.8
|
25.3
|
0.5
|
CD2
|
K:HIS206
|
2.9
|
19.7
|
1.0
|
CE1
|
K:HIS381
|
2.9
|
27.6
|
1.0
|
CD2
|
K:HIS381
|
3.0
|
25.3
|
1.0
|
CE1
|
K:HIS206
|
3.0
|
20.1
|
1.0
|
ND1
|
K:HIS381
|
4.0
|
28.1
|
1.0
|
CG
|
K:HIS206
|
4.0
|
16.7
|
1.0
|
ND1
|
K:HIS206
|
4.0
|
19.4
|
1.0
|
CG
|
K:HIS381
|
4.1
|
25.9
|
1.0
|
O
|
K:HOH821
|
4.3
|
23.9
|
1.0
|
CB
|
K:ASP314
|
4.3
|
20.9
|
1.0
|
O
|
K:HOH710
|
4.4
|
26.4
|
1.0
|
OG1
|
K:THR548
|
4.6
|
25.5
|
1.0
|
O
|
K:HOH739
|
4.6
|
26.6
|
1.0
|
O
|
K:PHE436
|
4.8
|
25.3
|
1.0
|
CE1
|
K:HIS437
|
4.9
|
27.4
|
1.0
|
CG1
|
K:VAL205
|
4.9
|
17.7
|
1.0
|
O
|
K:HOH971
|
4.9
|
35.7
|
0.5
|
|
Copper binding site 8 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 8 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 8 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Cu602
b:21.6
occ:0.80
|
ND1
|
K:HIS528
|
1.9
|
19.7
|
1.0
|
O
|
K:HOH734
|
2.0
|
25.5
|
0.8
|
NE2
|
K:HIS135
|
2.0
|
18.6
|
1.0
|
O
|
K:HOH790
|
2.0
|
25.5
|
1.0
|
NZ
|
K:LYS103
|
2.6
|
26.3
|
1.0
|
CD2
|
K:HIS135
|
2.8
|
18.1
|
1.0
|
CE1
|
K:HIS528
|
2.9
|
17.8
|
1.0
|
CG
|
K:HIS528
|
3.0
|
19.0
|
1.0
|
CE1
|
K:HIS135
|
3.0
|
18.6
|
1.0
|
CB
|
K:HIS528
|
3.4
|
16.6
|
1.0
|
CE
|
K:LYS103
|
3.5
|
23.4
|
1.0
|
O
|
K:HOH821
|
3.5
|
23.9
|
1.0
|
CD
|
K:LYS103
|
3.8
|
20.9
|
1.0
|
CG
|
K:HIS135
|
4.0
|
16.9
|
1.0
|
NE2
|
K:HIS528
|
4.0
|
18.1
|
1.0
|
ND1
|
K:HIS135
|
4.1
|
17.0
|
1.0
|
CD2
|
K:HIS528
|
4.1
|
17.7
|
1.0
|
OH
|
K:TYR164
|
4.1
|
29.9
|
1.0
|
OE1
|
K:GLU288
|
4.1
|
20.8
|
1.0
|
NE2
|
K:HIS136
|
4.3
|
19.0
|
1.0
|
OE1
|
K:GLN156
|
4.4
|
17.8
|
1.0
|
O
|
K:HOH769
|
4.6
|
21.8
|
0.5
|
CE1
|
K:HIS136
|
4.8
|
17.6
|
1.0
|
CA
|
K:HIS528
|
4.9
|
17.4
|
1.0
|
O
|
K:HOH845
|
4.9
|
23.1
|
1.0
|
CD2
|
K:HIS136
|
5.0
|
17.5
|
1.0
|
|
Copper binding site 9 out
of 9 in 6sji
Go back to
Copper Binding Sites List in 6sji
Copper binding site 9 out
of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 9 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Cu603
b:29.7
occ:0.50
|
ND1
|
K:HIS411
|
1.9
|
30.0
|
1.0
|
CE1
|
K:HIS411
|
2.8
|
32.2
|
1.0
|
CG
|
K:HIS411
|
3.1
|
29.9
|
1.0
|
CB
|
K:HIS411
|
3.6
|
26.8
|
1.0
|
NE2
|
K:HIS411
|
4.0
|
30.1
|
1.0
|
CD2
|
K:HIS411
|
4.1
|
30.0
|
1.0
|
O
|
K:HIS411
|
4.6
|
27.7
|
1.0
|
C
|
K:HIS411
|
4.6
|
27.1
|
1.0
|
CA
|
K:HIS411
|
4.7
|
24.8
|
1.0
|
OD2
|
K:ASP412
|
4.8
|
36.2
|
0.5
|
OD1
|
K:ASP412
|
5.0
|
35.9
|
0.5
|
|
Reference:
T.V.Tikhonova,
D.Y.Sorokin,
W.R.Hagen,
M.G.Khrenova,
G.Mauser,
T.V.Rakitina,
K.M.Polyakov,
I.G.Shabalin,
A.A.Trofimov,
S.I.Tsalallagov,
V.O.Popov.
A Novel Copper Biocatalytic Center Forms An Active Site of the Thiocyanate Dehydrogenase To Be Published.
Page generated: Wed Jul 31 07:30:17 2024
|