Nickel in PDB 6vwy: Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)
Enzymatic activity of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)
All present enzymatic activity of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic):
1.2.7.4;
Protein crystallography data
The structure of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic), PDB code: 6vwy
was solved by
E.C.Wittenborn,
C.L.Drennan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
73.68 /
1.83
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.560,
147.360,
66.050,
90.00,
110.78,
90.00
|
R / Rfree (%)
|
14.7 /
17.8
|
Other elements in 6vwy:
The structure of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)
(pdb code 6vwy). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the
Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic), PDB code: 6vwy:
Jump to Nickel binding site number:
1;
2;
3;
4;
Nickel binding site 1 out
of 4 in 6vwy
Go back to
Nickel Binding Sites List in 6vwy
Nickel binding site 1 out
of 4 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni703
b:42.7
occ:0.20
|
NI
|
A:XCC703
|
0.0
|
42.7
|
0.2
|
SG
|
A:CYS519
|
2.2
|
28.0
|
0.5
|
S1
|
A:XCC703
|
2.3
|
23.1
|
0.8
|
S4
|
A:CUV704
|
2.3
|
26.5
|
0.2
|
FE2
|
A:XCC703
|
2.4
|
50.2
|
0.8
|
S4
|
A:XCC703
|
2.4
|
26.2
|
0.8
|
S1
|
A:CUV704
|
2.4
|
25.9
|
0.2
|
FE3
|
A:CUV704
|
2.5
|
16.8
|
0.2
|
FE3
|
A:XCC703
|
2.5
|
29.2
|
0.8
|
FE1
|
A:CUV704
|
2.6
|
24.1
|
0.2
|
NI
|
A:CUV704
|
2.8
|
16.5
|
0.2
|
FE1
|
A:XCC703
|
2.9
|
30.1
|
0.8
|
FE4
|
A:XCC703
|
3.0
|
36.0
|
0.8
|
S3
|
A:XCC703
|
3.0
|
48.9
|
0.8
|
FE2
|
A:CUV704
|
3.1
|
17.0
|
0.2
|
FE4
|
A:CUV704
|
3.1
|
17.2
|
0.2
|
CB
|
A:CYS519
|
3.6
|
25.3
|
0.5
|
S2
|
A:CUV704
|
3.6
|
28.5
|
0.2
|
CB
|
A:CYS519
|
3.7
|
25.6
|
0.5
|
SG
|
A:CYS302
|
3.8
|
29.2
|
0.5
|
S3
|
A:CUV704
|
3.8
|
17.4
|
0.2
|
SG
|
A:CYS302
|
3.9
|
30.2
|
0.5
|
S2
|
A:XCC703
|
3.9
|
25.4
|
0.8
|
NZ
|
A:LYS556
|
4.1
|
27.0
|
0.5
|
SG
|
A:CYS519
|
4.3
|
30.9
|
0.5
|
NE2
|
A:HIS266
|
4.3
|
22.8
|
0.5
|
SG
|
A:CYS448
|
4.6
|
25.8
|
0.5
|
NE2
|
A:HIS266
|
4.6
|
26.6
|
0.5
|
CE1
|
A:HIS266
|
4.7
|
25.6
|
0.5
|
SG
|
A:CYS448
|
4.8
|
21.7
|
0.5
|
CA
|
A:GLY477
|
4.8
|
24.4
|
1.0
|
NZ
|
A:LYS556
|
4.8
|
25.6
|
0.5
|
CA
|
A:CYS519
|
4.8
|
24.3
|
0.5
|
SG
|
A:CYS340
|
4.8
|
23.1
|
0.5
|
O
|
A:HOH901
|
4.8
|
22.1
|
1.0
|
CA
|
A:CYS519
|
4.8
|
24.4
|
0.5
|
CE
|
A:LYS556
|
4.9
|
23.1
|
0.5
|
SG
|
A:CYS340
|
4.9
|
24.3
|
0.5
|
|
Nickel binding site 2 out
of 4 in 6vwy
Go back to
Nickel Binding Sites List in 6vwy
Nickel binding site 2 out
of 4 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni704
b:16.5
occ:0.20
|
NI
|
A:CUV704
|
0.0
|
16.5
|
0.2
|
FE2
|
A:XCC703
|
1.2
|
50.2
|
0.8
|
NE2
|
A:HIS266
|
1.6
|
22.8
|
0.5
|
NE2
|
A:HIS266
|
2.2
|
26.6
|
0.5
|
CE1
|
A:HIS266
|
2.4
|
25.6
|
0.5
|
CD2
|
A:HIS266
|
2.6
|
23.9
|
0.5
|
SG
|
A:CYS302
|
2.7
|
30.2
|
0.5
|
NZ
|
A:LYS556
|
2.7
|
27.0
|
0.5
|
CD2
|
A:HIS266
|
2.8
|
20.9
|
0.5
|
NI
|
A:XCC703
|
2.8
|
42.7
|
0.2
|
SG
|
A:CYS519
|
2.8
|
30.9
|
0.5
|
FE2
|
A:CUV704
|
2.9
|
17.0
|
0.2
|
SG
|
A:CYS302
|
2.9
|
29.2
|
0.5
|
NZ
|
A:LYS556
|
3.0
|
25.6
|
0.5
|
SG
|
A:CYS519
|
3.2
|
28.0
|
0.5
|
CE
|
A:LYS556
|
3.3
|
23.1
|
0.5
|
FE1
|
A:CUV704
|
3.3
|
24.1
|
0.2
|
S3
|
A:XCC703
|
3.4
|
48.9
|
0.8
|
CB
|
A:CYS519
|
3.4
|
25.6
|
0.5
|
CB
|
A:CYS519
|
3.4
|
25.3
|
0.5
|
CE1
|
A:HIS266
|
3.5
|
24.9
|
0.5
|
ND1
|
A:HIS266
|
3.5
|
23.5
|
0.5
|
FE1
|
A:XCC703
|
3.6
|
30.1
|
0.8
|
S4
|
A:XCC703
|
3.7
|
26.2
|
0.8
|
CB
|
A:CYS302
|
3.7
|
27.5
|
0.5
|
CG
|
A:HIS266
|
3.8
|
23.8
|
0.5
|
S4
|
A:CUV704
|
3.8
|
26.5
|
0.2
|
CB
|
A:CYS302
|
3.9
|
27.2
|
0.5
|
CG
|
A:HIS266
|
3.9
|
24.5
|
0.5
|
O
|
A:HOH912
|
4.1
|
37.1
|
1.0
|
CE
|
A:LYS556
|
4.2
|
22.4
|
0.5
|
ND1
|
A:HIS266
|
4.3
|
24.6
|
0.5
|
SG
|
A:CYS340
|
4.5
|
23.1
|
0.5
|
SG
|
A:CYS301
|
4.6
|
18.4
|
0.3
|
SG
|
A:CYS340
|
4.6
|
24.3
|
0.5
|
CA
|
A:CYS519
|
4.6
|
24.3
|
0.5
|
CA
|
A:CYS519
|
4.6
|
24.4
|
0.5
|
CD
|
A:LYS556
|
4.7
|
25.3
|
0.5
|
N
|
A:CYS519
|
4.7
|
21.8
|
0.5
|
N
|
A:CYS519
|
4.7
|
21.9
|
0.5
|
O
|
A:HOH971
|
4.7
|
34.2
|
1.0
|
OE1
|
A:GLN339
|
4.7
|
36.7
|
1.0
|
CD
|
A:LYS556
|
4.8
|
25.4
|
0.5
|
S3
|
A:CUV704
|
4.9
|
17.4
|
0.2
|
FE3
|
A:CUV704
|
4.9
|
16.8
|
0.2
|
FE4
|
A:XCC703
|
4.9
|
36.0
|
0.8
|
FE3
|
A:XCC703
|
4.9
|
29.2
|
0.8
|
S1
|
A:XCC703
|
4.9
|
23.1
|
0.8
|
NE2
|
A:HIS97
|
5.0
|
25.6
|
1.0
|
|
Nickel binding site 3 out
of 4 in 6vwy
Go back to
Nickel Binding Sites List in 6vwy
Nickel binding site 3 out
of 4 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni702
b:36.8
occ:0.20
|
NI
|
B:XCC702
|
0.0
|
36.8
|
0.2
|
S1
|
B:XCC702
|
2.2
|
23.4
|
0.8
|
SG
|
B:CYS519
|
2.3
|
28.5
|
0.5
|
S4
|
B:CUV703
|
2.4
|
28.8
|
0.2
|
S4
|
B:XCC702
|
2.4
|
28.2
|
0.8
|
FE2
|
B:XCC702
|
2.5
|
50.6
|
0.8
|
S1
|
B:CUV703
|
2.5
|
29.5
|
0.2
|
FE3
|
B:CUV703
|
2.5
|
26.3
|
0.2
|
FE1
|
B:CUV703
|
2.6
|
31.4
|
0.2
|
FE3
|
B:XCC702
|
2.6
|
25.5
|
0.8
|
NI
|
B:CUV703
|
2.7
|
19.9
|
0.2
|
FE1
|
B:XCC702
|
2.8
|
30.8
|
0.8
|
S3
|
B:XCC702
|
2.8
|
33.8
|
0.8
|
FE4
|
B:XCC702
|
2.9
|
31.5
|
0.8
|
FE2
|
B:CUV703
|
3.0
|
27.2
|
0.2
|
FE4
|
B:CUV703
|
3.1
|
23.4
|
0.2
|
S2
|
B:CUV703
|
3.6
|
30.6
|
0.2
|
SG
|
B:CYS302
|
3.6
|
31.1
|
0.5
|
CB
|
B:CYS519
|
3.7
|
26.3
|
0.5
|
CB
|
B:CYS519
|
3.7
|
26.2
|
0.5
|
SG
|
B:CYS302
|
3.7
|
30.5
|
0.5
|
S3
|
B:CUV703
|
3.7
|
18.7
|
0.2
|
S2
|
B:XCC702
|
3.9
|
24.3
|
0.8
|
NZ
|
B:LYS556
|
4.2
|
24.6
|
0.5
|
SG
|
B:CYS519
|
4.3
|
33.6
|
0.5
|
NE2
|
B:HIS266
|
4.5
|
22.3
|
0.5
|
NE2
|
B:HIS266
|
4.6
|
24.1
|
0.5
|
SG
|
B:CYS448
|
4.7
|
25.8
|
0.5
|
CA
|
B:GLY477
|
4.7
|
28.2
|
1.0
|
O
|
B:HOH948
|
4.8
|
26.2
|
1.0
|
CA
|
B:CYS519
|
4.8
|
22.4
|
0.5
|
SG
|
B:CYS340
|
4.9
|
25.1
|
0.5
|
CA
|
B:CYS519
|
4.9
|
22.4
|
0.5
|
SG
|
B:CYS448
|
4.9
|
26.3
|
0.5
|
SG
|
B:CYS340
|
4.9
|
24.0
|
0.5
|
N
|
B:CYS478
|
4.9
|
27.7
|
0.5
|
SG
|
B:CYS478
|
4.9
|
20.9
|
0.5
|
CE
|
B:LYS556
|
5.0
|
21.0
|
0.5
|
N
|
B:CYS478
|
5.0
|
27.6
|
0.5
|
NZ
|
B:LYS556
|
5.0
|
21.9
|
0.5
|
|
Nickel binding site 4 out
of 4 in 6vwy
Go back to
Nickel Binding Sites List in 6vwy
Nickel binding site 4 out
of 4 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni703
b:19.9
occ:0.20
|
NI
|
B:CUV703
|
0.0
|
19.9
|
0.2
|
FE2
|
B:XCC702
|
1.0
|
50.6
|
0.8
|
NE2
|
B:HIS266
|
1.8
|
22.3
|
0.5
|
NE2
|
B:HIS266
|
2.2
|
24.1
|
0.5
|
CE1
|
B:HIS266
|
2.6
|
24.4
|
0.5
|
CD2
|
B:HIS266
|
2.7
|
22.4
|
0.5
|
NI
|
B:XCC702
|
2.7
|
36.8
|
0.2
|
SG
|
B:CYS302
|
2.8
|
31.1
|
0.5
|
SG
|
B:CYS302
|
2.8
|
30.5
|
0.5
|
SG
|
B:CYS519
|
2.8
|
33.6
|
0.5
|
NZ
|
B:LYS556
|
2.9
|
21.9
|
0.5
|
CD2
|
B:HIS266
|
3.0
|
21.3
|
0.5
|
FE2
|
B:CUV703
|
3.0
|
27.2
|
0.2
|
NZ
|
B:LYS556
|
3.0
|
24.6
|
0.5
|
S3
|
B:XCC702
|
3.2
|
33.8
|
0.8
|
CE
|
B:LYS556
|
3.3
|
21.0
|
0.5
|
FE1
|
B:CUV703
|
3.3
|
31.4
|
0.2
|
SG
|
B:CYS519
|
3.4
|
28.5
|
0.5
|
CB
|
B:CYS519
|
3.4
|
26.2
|
0.5
|
CE1
|
B:HIS266
|
3.4
|
21.0
|
0.5
|
CB
|
B:CYS519
|
3.5
|
26.3
|
0.5
|
FE1
|
B:XCC702
|
3.5
|
30.8
|
0.8
|
S4
|
B:XCC702
|
3.6
|
28.2
|
0.8
|
CB
|
B:CYS302
|
3.7
|
26.2
|
0.5
|
CB
|
B:CYS302
|
3.8
|
27.2
|
0.5
|
S4
|
B:CUV703
|
3.8
|
28.8
|
0.2
|
ND1
|
B:HIS266
|
3.8
|
22.6
|
0.5
|
CG
|
B:HIS266
|
4.0
|
22.7
|
0.5
|
CG
|
B:HIS266
|
4.0
|
24.1
|
0.5
|
O
|
B:HOH914
|
4.1
|
32.1
|
1.0
|
ND1
|
B:HIS266
|
4.3
|
19.6
|
0.5
|
CE
|
B:LYS556
|
4.3
|
19.7
|
0.5
|
SG
|
B:CYS340
|
4.4
|
24.0
|
0.5
|
SG
|
B:CYS301
|
4.5
|
18.2
|
0.3
|
SG
|
B:CYS340
|
4.6
|
25.1
|
0.5
|
CA
|
B:CYS519
|
4.7
|
22.4
|
0.5
|
N
|
B:CYS519
|
4.7
|
19.9
|
0.5
|
N
|
B:CYS519
|
4.7
|
20.0
|
0.5
|
CA
|
B:CYS519
|
4.7
|
22.4
|
0.5
|
CD
|
B:LYS556
|
4.8
|
25.9
|
0.5
|
CD
|
B:LYS556
|
4.8
|
25.6
|
0.5
|
FE4
|
B:XCC702
|
4.8
|
31.5
|
0.8
|
O
|
B:HOH868
|
4.9
|
31.9
|
1.0
|
FE3
|
B:XCC702
|
4.9
|
25.5
|
0.8
|
OE1
|
B:GLN339
|
4.9
|
36.5
|
1.0
|
S1
|
B:XCC702
|
4.9
|
23.4
|
0.8
|
S3
|
B:CUV703
|
4.9
|
18.7
|
0.2
|
FE3
|
B:CUV703
|
4.9
|
26.3
|
0.2
|
CA
|
B:CYS302
|
5.0
|
25.4
|
0.5
|
|
Reference:
E.C.Wittenborn,
C.Guendon,
M.Merrouch,
M.Benvenuti,
V.Fourmond,
C.Leger,
C.L.Drennan,
S.Dementin.
The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance Indesulfovibrio Vulgarisni-Fe Carbon Monoxide Dehydrogenase. Acs Catalysis V. 10 7328 2020.
ISSN: ESSN 2155-5435
PubMed: 32655979
DOI: 10.1021/ACSCATAL.0C00934
Page generated: Thu Oct 10 08:55:34 2024
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