Iron in PDB 6dc2: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant

All present enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant, PDB code: 6dc2 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) 93.27 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.790, 144.150, 123.690, 90.00, 98.50, 90.00
R / Rfree (%) 16.3 / 21.2

Other elements in 6dc2:

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant (pdb code 6dc2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 40 binding sites of Iron where determined in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant, PDB code: 6dc2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 40 in 6dc2

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Iron binding site 1 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:19.1
occ:1.00
 FE1 A:SF4701 0.0 19.1 1.0
S2 A:SF4701 2.3 18.3 1.0
SG A:CYS51 2.3 22.1 1.0
S4 A:SF4701 2.3 20.6 1.0
S3 A:SF4701 2.3 22.8 1.0
FE4 A:SF4701 2.7 20.3 1.0
FE2 A:SF4701 2.7 20.6 1.0
FE3 A:SF4701 2.7 18.8 1.0
CB A:CYS51 3.1 20.2 1.0
NH2 A:ARG84 3.5 22.3 1.0
S1 A:SF4701 3.9 17.4 1.0
N A:ASN53 4.1 22.0 1.0
CB A:ASN53 4.2 23.8 1.0
CA A:CYS51 4.3 19.7 1.0
C A:CYS51 4.3 20.4 1.0
O A:CYS51 4.6 19.1 1.0
N A:ARG52 4.6 19.6 1.0
CA A:ASN53 4.6 23.8 1.0
CZ A:ARG84 4.6 24.5 1.0
N A:CYS54 4.7 20.6 1.0
SG A:CYS59 4.8 22.7 1.0
SG A:CYS74 4.9 22.8 1.0
O A:HOH1043 4.9 19.2 1.0
SG A:CYS54 4.9 18.5 1.0
C A:ASN53 4.9 20.6 1.0
CG A:ASN53 5.0 23.5 1.0

Iron binding site 2 out of 40 in 6dc2

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Iron binding site 2 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:20.6
occ:1.00
 FE2 A:SF4701 0.0 20.6 1.0
SG A:CYS59 2.3 22.7 1.0
S4 A:SF4701 2.3 20.6 1.0
S1 A:SF4701 2.3 17.4 1.0
S3 A:SF4701 2.3 22.8 1.0
FE1 A:SF4701 2.7 19.1 1.0
FE4 A:SF4701 2.7 20.3 1.0
FE3 A:SF4701 2.8 18.8 1.0
CB A:CYS59 3.4 22.2 1.0
S2 A:SF4701 3.9 18.3 1.0
N A:VAL73 4.0 25.2 1.0
CA A:GLY57 4.1 22.8 1.0
N A:CYS59 4.3 18.4 1.0
N A:GLY57 4.4 20.4 1.0
CA A:GLY72 4.4 24.2 1.0
CA A:CYS59 4.5 19.5 1.0
CB A:CYS51 4.5 20.2 1.0
SG A:CYS51 4.7 22.1 1.0
SG A:CYS54 4.7 18.5 1.0
C A:GLY72 4.7 28.9 1.0
CB A:VAL73 4.7 16.7 1.0
SG A:CYS74 4.8 22.8 1.0
N A:CYS74 4.8 15.9 1.0
O A:CYS51 4.8 19.1 1.0
C A:PRO58 4.9 23.0 1.0
CA A:VAL73 4.9 22.9 1.0
CG2 A:VAL73 4.9 24.2 1.0

Iron binding site 3 out of 40 in 6dc2

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Iron binding site 3 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.8
occ:1.00
 FE3 A:SF4701 0.0 18.8 1.0
S4 A:SF4701 2.3 20.6 1.0
S2 A:SF4701 2.3 18.3 1.0
SG A:CYS74 2.3 22.8 1.0
S1 A:SF4701 2.3 17.4 1.0
FE1 A:SF4701 2.7 19.1 1.0
FE4 A:SF4701 2.8 20.3 1.0
FE2 A:SF4701 2.8 20.6 1.0
CB A:CYS74 3.4 22.5 1.0
S3 A:SF4701 3.9 22.8 1.0
N A:CYS74 3.9 15.9 1.0
NH2 A:ARG84 4.1 22.3 1.0
CA A:CYS74 4.3 18.3 1.0
CG A:MET203 4.3 16.1 1.0
SG A:CYS54 4.6 18.5 1.0
CB A:ALA76 4.6 16.7 1.0
N A:VAL73 4.7 25.2 1.0
O A:HOH901 4.7 16.4 1.0
SG A:CYS59 4.8 22.7 1.0
SG A:CYS51 4.8 22.1 1.0
CA A:GLY72 4.9 24.2 1.0
NH1 A:ARG84 5.0 23.8 1.0
CZ A:ARG84 5.0 24.5 1.0

Iron binding site 4 out of 40 in 6dc2

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Iron binding site 4 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:20.3
occ:1.00
 FE4 A:SF4701 0.0 20.3 1.0
SG A:CYS54 2.3 18.5 1.0
S3 A:SF4701 2.3 22.8 1.0
S1 A:SF4701 2.3 17.4 1.0
S2 A:SF4701 2.3 18.3 1.0
FE1 A:SF4701 2.7 19.1 1.0
FE2 A:SF4701 2.7 20.6 1.0
FE3 A:SF4701 2.8 18.8 1.0
CB A:CYS54 3.4 14.7 1.0
N A:CYS54 3.6 20.6 1.0
S4 A:SF4701 3.9 20.6 1.0
CA A:CYS54 3.9 21.1 1.0
O A:CYS54 4.1 20.1 1.0
C A:CYS54 4.2 20.8 1.0
N A:GLY57 4.2 20.4 1.0
C A:ASN53 4.4 20.6 1.0
CG A:MET203 4.5 16.1 1.0
CA A:GLY57 4.7 22.8 1.0
N A:ASN53 4.7 22.0 1.0
CB A:MET56 4.8 20.3 1.0
SG A:CYS51 4.8 22.1 1.0
SG A:CYS74 4.8 22.8 1.0
SG A:CYS59 4.8 22.7 1.0
CA A:ASN53 4.9 23.8 1.0
CB A:MET203 5.0 14.5 1.0

Iron binding site 5 out of 40 in 6dc2

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Iron binding site 5 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:22.1
occ:1.00
 FE1 A:FES702 0.0 22.1 1.0
S1 A:FES702 2.2 24.4 1.0
S2 A:FES702 2.2 22.1 1.0
SG B:CYS42 2.3 25.9 1.0
SG B:CYS45 2.3 21.8 1.0
FE2 A:FES702 2.9 21.1 1.0
CB B:CYS42 3.2 19.6 1.0
CB B:CYS45 3.4 24.2 1.0
N B:CYS45 3.7 26.4 1.0
CA B:CYS45 4.1 25.0 1.0
O A:HOH1000 4.2 19.5 1.0
SG A:CYS45 4.5 24.2 1.0
OG1 A:THR50 4.5 17.8 1.0
CB B:PHE44 4.6 22.5 1.0
CA B:CYS42 4.6 26.3 1.0
SG A:CYS42 4.6 24.0 1.0
C B:PHE44 4.7 27.1 1.0
OG1 B:THR50 4.7 29.5 1.0
CG2 B:THR50 4.8 18.0 1.0
CD A:ARG60 4.9 17.2 1.0
CB B:THR50 4.9 22.0 1.0
C B:CYS42 5.0 25.8 1.0

Iron binding site 6 out of 40 in 6dc2

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Iron binding site 6 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:21.1
occ:1.00
 FE2 A:FES702 0.0 21.1 1.0
S1 A:FES702 2.2 24.4 1.0
S2 A:FES702 2.2 22.1 1.0
SG A:CYS42 2.3 24.0 1.0
SG A:CYS45 2.3 24.2 1.0
FE1 A:FES702 2.9 22.1 1.0
CB A:CYS42 3.2 17.5 1.0
CB A:CYS45 3.4 22.4 1.0
N A:CYS45 3.6 18.9 1.0
CA A:CYS45 4.1 21.7 1.0
O B:HOH986 4.2 21.9 1.0
OG1 B:THR50 4.5 29.5 1.0
CB A:PHE44 4.5 22.2 1.0
SG B:CYS45 4.5 21.8 1.0
CA A:CYS42 4.6 24.4 1.0
C A:PHE44 4.6 23.1 1.0
SG B:CYS42 4.7 25.9 1.0
CG2 A:THR50 4.8 15.7 1.0
OG1 A:THR50 4.8 17.8 1.0
CA A:PHE44 4.9 20.8 1.0
N A:PHE44 4.9 25.6 1.0
C A:CYS42 4.9 20.0 1.0
CB A:THR50 5.0 21.6 1.0

Iron binding site 7 out of 40 in 6dc2

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Iron binding site 7 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:23.3
occ:1.00
 FE1 A:XCC703 0.0 23.3 1.0
S2 A:XCC703 2.3 23.4 1.0
S3 A:XCC703 2.3 27.7 1.0
S4 A:XCC703 2.3 25.8 1.0
SG A:CYS340 2.5 22.8 1.0
FE3 A:XCC703 2.6 23.8 1.0
FE4 A:XCC703 2.8 23.7 1.0
FE A:FE704 3.0 29.8 0.3
FE2 A:XCC703 3.3 30.6 0.7
CB A:CYS340 3.4 23.9 1.0
S1 A:XCC703 3.8 23.9 1.0
NZ A:LYS556 4.0 27.3 1.0
CE2 A:TYR553 4.1 25.9 1.0
NE2 A:HIS266 4.2 22.2 1.0
O A:HOH848 4.3 32.2 0.7
CE1 A:HIS266 4.3 21.1 1.0
OH A:TYR553 4.5 28.7 1.0
O A:HOH855 4.6 41.2 1.0
CE A:LYS556 4.7 27.7 1.0
SG A:CYS448 4.7 20.2 1.0
OG A:SER554 4.7 22.5 1.0
CA A:CYS340 4.8 17.5 1.0
CZ A:TYR553 4.8 25.4 1.0

Iron binding site 8 out of 40 in 6dc2

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Iron binding site 8 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:30.6
occ:0.70
 FE2 A:XCC703 0.0 30.6 0.7
FE A:FE704 1.9 29.8 0.3
O A:HOH848 2.0 32.2 0.7
NE2 A:HIS266 2.2 22.2 1.0
S3 A:XCC703 2.3 27.7 1.0
SG A:CYS302 2.4 23.8 1.0
CD2 A:HIS266 3.0 18.6 1.0
CE1 A:HIS266 3.3 21.1 1.0
CB A:CYS302 3.3 25.6 1.0
FE1 A:XCC703 3.3 23.3 1.0
SG A:CYS519 3.4 30.1 1.0
NZ A:LYS556 3.5 27.3 1.0
S4 A:XCC703 3.6 25.8 1.0
FE4 A:XCC703 3.9 23.7 1.0
CB A:CYS519 4.0 20.0 1.0
S1 A:XCC703 4.0 23.9 1.0
CG A:HIS266 4.2 26.4 1.0
ND1 A:HIS266 4.3 20.8 1.0
O A:HOH1067 4.4 22.8 1.0
CA A:CYS302 4.4 21.4 1.0
N A:CYS302 4.5 20.1 1.0
FE3 A:XCC703 4.5 23.8 1.0
O A:HOH994 4.6 24.5 1.0
SG A:CYS340 4.6 22.8 1.0
CE A:LYS556 4.8 27.7 1.0
N A:CYS519 4.9 21.4 1.0

Iron binding site 9 out of 40 in 6dc2

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Iron binding site 9 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:23.8
occ:1.00
 FE3 A:XCC703 0.0 23.8 1.0
S4 A:XCC703 2.2 25.8 1.0
S1 A:XCC703 2.3 23.9 1.0
S2 A:XCC703 2.4 23.4 1.0
SG A:CYS448 2.5 20.2 1.0
FE1 A:XCC703 2.6 23.3 1.0
FE4 A:XCC703 2.7 23.7 1.0
FE A:FE704 2.9 29.8 0.3
CB A:CYS448 3.2 14.8 1.0
CA A:CYS448 3.7 21.1 1.0
S3 A:XCC703 3.9 27.7 1.0
N A:CYS448 3.9 24.2 1.0
OG A:SER554 4.0 22.5 1.0
C A:GLY447 4.2 25.1 1.0
CE2 A:TYR553 4.3 25.9 1.0
FE2 A:XCC703 4.5 30.6 0.7
CA A:GLY447 4.5 27.8 1.0
CD2 A:TYR553 4.5 28.4 1.0
SG A:CYS519 4.6 30.1 1.0
O A:GLY447 4.7 22.4 1.0
SG A:CYS340 4.7 22.8 1.0
CB A:SER554 4.8 23.8 1.0
SG A:CYS478 4.9 21.8 1.0

Iron binding site 10 out of 40 in 6dc2

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Iron binding site 10 out of 40 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:23.7
occ:1.00
 FE4 A:XCC703 0.0 23.7 1.0
S1 A:XCC703 2.2 23.9 1.0
S2 A:XCC703 2.3 23.4 1.0
S3 A:XCC703 2.3 27.7 1.0
SG A:CYS478 2.5 21.8 1.0
FE3 A:XCC703 2.7 23.8 1.0
FE1 A:XCC703 2.8 23.3 1.0
FE A:FE704 2.9 29.8 0.3
CB A:CYS478 3.5 23.4 1.0
O A:HOH1067 3.6 22.8 1.0
FE2 A:XCC703 3.9 30.6 0.7
S4 A:XCC703 4.0 25.8 1.0
N A:CYS478 4.0 20.0 1.0
CA A:CYS478 4.3 24.9 1.0
CA A:CYS448 4.4 21.1 1.0
CB A:HIS319 4.5 19.4 1.0
O A:HOH855 4.5 41.2 1.0
CB A:CYS448 4.6 14.8 1.0
SG A:CYS448 4.8 20.2 1.0
O A:GLY447 4.8 22.4 1.0
SG A:CYS302 4.9 23.8 1.0
CB A:SER301 4.9 28.1 1.0
SG A:CYS519 4.9 30.1 1.0
C A:GLY447 4.9 25.1 1.0
OG A:SER301 4.9 27.7 1.0
C A:GLY477 4.9 19.6 1.0

Reference:

E.C.Wittenborn, M.Merrouch, C.Ueda, L.Fradale, C.Leger, V.Fourmond, M.E.Pandelia, S.Dementin, C.L.Drennan. Redox-Dependent Rearrangements of the Nifes Cluster of Carbon Monoxide Dehydrogenase. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30277213
DOI: 10.7554/ELIFE.39451
Page generated: Sun Dec 13 16:24:14 2020

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