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Iron in PDB 6ons: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated

All present enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated, PDB code: 6ons was solved by S.E.Cohen, 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) 45.42 / 2.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.544, 100.609, 65.343, 90.00, 124.75, 90.00
R / Rfree (%) 20.7 / 24.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated (pdb code 6ons). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated, PDB code: 6ons:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6ons

Go back to Iron Binding Sites List in 6ons
Iron binding site 1 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated


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 with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:44.7
occ:1.00
 FE1 A:SF4701 0.0 44.7 1.0
SG A:CYS51 2.3 35.6 1.0
S3 A:SF4701 2.3 34.8 1.0
S4 A:SF4701 2.3 36.4 1.0
S2 A:SF4701 2.3 32.6 1.0
FE2 A:SF4701 2.7 45.9 1.0
FE4 A:SF4701 2.7 44.8 1.0
FE3 A:SF4701 2.7 44.0 1.0
CB A:CYS51 3.2 35.9 1.0
NH2 A:ARG84 3.6 34.5 1.0
S1 A:SF4701 3.9 35.6 1.0
N A:ASN53 4.2 33.8 1.0
C A:CYS51 4.3 38.7 1.0
CA A:CYS51 4.3 39.5 1.0
CB A:ASN53 4.4 34.5 1.0
O A:CYS51 4.5 38.4 1.0
CZ A:ARG84 4.6 34.4 1.0
N A:ARG52 4.7 37.9 1.0
SG A:CYS59 4.8 38.9 1.0
N A:CYS54 4.8 34.5 1.0
CA A:ASN53 4.8 35.9 1.0
SG A:CYS74 4.8 39.9 1.0
SG A:CYS54 4.9 37.7 1.0
ND2 A:ASN53 4.9 36.6 1.0
NH1 A:ARG84 5.0 34.5 1.0
CG A:ASN53 5.0 34.8 1.0

Iron binding site 2 out of 8 in 6ons

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Iron binding site 2 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated


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 with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:45.9
occ:1.00
 FE2 A:SF4701 0.0 45.9 1.0
S4 A:SF4701 2.3 36.4 1.0
SG A:CYS59 2.3 38.9 1.0
S1 A:SF4701 2.3 35.6 1.0
S3 A:SF4701 2.3 34.8 1.0
FE1 A:SF4701 2.7 44.7 1.0
FE3 A:SF4701 2.7 44.0 1.0
FE4 A:SF4701 2.7 44.8 1.0
CB A:CYS59 3.4 42.7 1.0
S2 A:SF4701 3.9 32.6 1.0
N A:VAL73 3.9 36.7 1.0
CA A:GLY57 4.0 39.9 1.0
N A:GLY57 4.1 38.9 1.0
N A:CYS59 4.2 39.4 1.0
CA A:CYS59 4.4 40.8 1.0
CA A:GLY72 4.4 41.1 1.0
CB A:VAL73 4.6 42.3 1.0
SG A:CYS51 4.7 35.6 1.0
C A:GLY72 4.7 40.2 1.0
CB A:CYS51 4.7 35.9 1.0
SG A:CYS54 4.7 37.7 1.0
SG A:CYS74 4.8 39.9 1.0
N A:CYS74 4.8 40.3 1.0
CG2 A:VAL73 4.8 40.7 1.0
CA A:VAL73 4.8 43.1 1.0
O A:CYS51 4.9 38.4 1.0
C A:MET56 4.9 40.4 1.0
C A:PRO58 5.0 41.7 1.0

Iron binding site 3 out of 8 in 6ons

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Iron binding site 3 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated


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 with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:44.0
occ:1.00
 FE3 A:SF4701 0.0 44.0 1.0
S1 A:SF4701 2.3 35.6 1.0
SG A:CYS74 2.3 39.9 1.0
S4 A:SF4701 2.3 36.4 1.0
S2 A:SF4701 2.3 32.6 1.0
FE4 A:SF4701 2.7 44.8 1.0
FE2 A:SF4701 2.7 45.9 1.0
FE1 A:SF4701 2.7 44.7 1.0
CB A:CYS74 3.4 40.1 1.0
N A:CYS74 3.9 40.3 1.0
S3 A:SF4701 3.9 34.8 1.0
NH2 A:ARG84 4.1 34.5 1.0
CA A:CYS74 4.2 38.2 1.0
CG A:MET203 4.3 36.1 1.0
N A:VAL73 4.6 36.7 1.0
SG A:CYS54 4.7 37.7 1.0
CB A:ALA76 4.7 35.3 1.0
O A:HOH810 4.7 35.0 1.0
SG A:CYS59 4.8 38.9 1.0
SG A:CYS51 4.8 35.6 1.0
NH1 A:ARG84 4.9 34.5 1.0
CA A:GLY72 5.0 41.1 1.0

Iron binding site 4 out of 8 in 6ons

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Iron binding site 4 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated


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 with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:44.8
occ:1.00
 FE4 A:SF4701 0.0 44.8 1.0
S2 A:SF4701 2.3 32.6 1.0
S1 A:SF4701 2.3 35.6 1.0
SG A:CYS54 2.3 37.7 1.0
S3 A:SF4701 2.3 34.8 1.0
FE3 A:SF4701 2.7 44.0 1.0
FE1 A:SF4701 2.7 44.7 1.0
FE2 A:SF4701 2.7 45.9 1.0
CB A:CYS54 3.5 37.1 1.0
N A:CYS54 3.9 34.5 1.0
S4 A:SF4701 3.9 36.4 1.0
O A:CYS54 4.0 36.9 1.0
CA A:CYS54 4.1 37.8 1.0
N A:GLY57 4.1 38.9 1.0
C A:CYS54 4.2 36.1 1.0
CB A:MET56 4.5 37.7 1.0
CG A:MET203 4.6 36.1 1.0
C A:ASN53 4.7 34.6 1.0
SG A:CYS74 4.7 39.9 1.0
CA A:GLY57 4.8 39.9 1.0
CE A:MET56 4.8 38.4 1.0
N A:MET56 4.8 37.1 1.0
SG A:CYS51 4.8 35.6 1.0
SG A:CYS59 4.8 38.9 1.0
C A:MET56 4.9 40.4 1.0
N A:ASN53 5.0 33.8 1.0
CA A:MET56 5.0 37.8 1.0
CB A:MET203 5.0 34.2 1.0

Iron binding site 5 out of 8 in 6ons

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Iron binding site 5 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated


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 with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:52.0
occ:1.00
 FE1 A:XCC702 0.0 52.0 1.0
S2 A:XCC702 2.3 40.9 1.0
S4 A:XCC702 2.3 38.5 1.0
S3 A:XCC702 2.4 40.7 1.0
SG A:CYS340 2.5 42.0 1.0
FE3 A:XCC702 2.6 55.0 1.0
FE4 A:XCC702 2.8 46.0 1.0
FE2 A:XCC702 3.2 49.9 1.0
CB A:CYS340 3.5 38.6 1.0
O A:HOH814 3.5 42.2 1.0
S1 A:XCC702 3.8 38.5 1.0
CE1 A:HIS266 4.1 41.8 1.0
CE2 A:TYR553 4.2 37.9 1.0
NE2 A:HIS266 4.2 42.4 1.0
NZ A:LYS556 4.4 40.3 1.0
OH A:TYR553 4.6 40.7 1.0
CE A:LYS556 4.6 38.9 1.0
SG A:CYS448 4.8 41.8 1.0
CZ A:TYR553 4.9 39.6 1.0
OG A:SER554 4.9 32.0 1.0
CA A:CYS340 4.9 37.1 1.0

Iron binding site 6 out of 8 in 6ons

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Iron binding site 6 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated


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 with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:49.9
occ:1.00
 FE2 A:XCC702 0.0 49.9 1.0
O A:HOH814 2.0 42.2 1.0
NE2 A:HIS266 2.3 42.4 1.0
S3 A:XCC702 2.3 40.7 1.0
SG A:CYS302 2.4 37.3 1.0
CE1 A:HIS266 3.0 41.8 1.0
FE1 A:XCC702 3.2 52.0 1.0
SG A:CYS519 3.2 43.8 1.0
CD2 A:HIS266 3.2 40.1 1.0
CB A:CYS302 3.5 38.0 1.0
FE4 A:XCC702 3.5 46.0 1.0
S4 A:XCC702 3.8 38.5 1.0
O A:HOH818 3.9 41.8 1.0
S1 A:XCC702 3.9 38.5 1.0
CB A:CYS519 4.0 39.0 1.0
ND1 A:HIS266 4.1 40.9 1.0
CG A:HIS266 4.2 40.1 1.0
NZ A:LYS556 4.3 40.3 1.0
FE3 A:XCC702 4.4 55.0 1.0
N A:CYS302 4.4 37.4 1.0
O A:HOH824 4.4 37.9 1.0
CA A:CYS302 4.5 39.4 1.0
CE A:LYS556 4.7 38.9 1.0
SG A:CYS340 4.8 42.0 1.0
S2 A:XCC702 4.9 40.9 1.0
N A:CYS519 4.9 35.5 1.0

Iron binding site 7 out of 8 in 6ons

Go back to Iron Binding Sites List in 6ons
Iron binding site 7 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated


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 with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:55.0
occ:1.00
 FE3 A:XCC702 0.0 55.0 1.0
S4 A:XCC702 2.2 38.5 1.0
S1 A:XCC702 2.2 38.5 1.0
S2 A:XCC702 2.3 40.9 1.0
SG A:CYS448 2.5 41.8 1.0
FE1 A:XCC702 2.6 52.0 1.0
FE4 A:XCC702 2.7 46.0 1.0
CB A:CYS448 3.1 40.5 1.0
CA A:CYS448 3.7 41.0 1.0
S3 A:XCC702 4.0 40.7 1.0
N A:CYS448 4.0 39.7 1.0
CE2 A:TYR553 4.1 37.9 1.0
O A:HOH824 4.2 37.9 1.0
OG A:SER554 4.2 32.0 1.0
O A:HOH814 4.2 42.2 1.0
C A:GLY447 4.3 40.4 1.0
CD2 A:TYR553 4.4 36.7 1.0
FE2 A:XCC702 4.4 49.9 1.0
O A:GLY447 4.5 39.3 1.0
SG A:CYS519 4.6 43.8 1.0
SG A:CYS340 4.7 42.0 1.0
SG A:CYS478 4.8 40.7 1.0
CB A:SER554 5.0 32.3 1.0

Iron binding site 8 out of 8 in 6ons

Go back to Iron Binding Sites List in 6ons
Iron binding site 8 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated


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 with the D-Cluster Ligating Cysteines Mutated to Alanines, Coexpressed with Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:46.0
occ:1.00
 FE4 A:XCC702 0.0 46.0 1.0
S3 A:XCC702 2.3 40.7 1.0
S1 A:XCC702 2.3 38.5 1.0
S2 A:XCC702 2.3 40.9 1.0
SG A:CYS478 2.5 40.7 1.0
FE3 A:XCC702 2.7 55.0 1.0
FE1 A:XCC702 2.8 52.0 1.0
CB A:CYS478 3.5 39.3 1.0
FE2 A:XCC702 3.5 49.9 1.0
S4 A:XCC702 4.0 38.5 1.0
N A:CYS478 4.1 37.6 1.0
CA A:CYS478 4.3 38.6 1.0
CA A:CYS448 4.5 41.0 1.0
O A:HOH814 4.6 42.2 1.0
CB A:CYS448 4.6 40.5 1.0
SG A:CYS301 4.6 44.8 1.0
O A:GLY447 4.7 39.3 1.0
CB A:HIS319 4.7 40.1 1.0
SG A:CYS519 4.7 43.8 1.0
SG A:CYS448 4.8 41.8 1.0
CB A:CYS301 4.8 40.5 1.0
SG A:CYS302 4.9 37.3 1.0

Reference:

E.C.Wittenborn, S.E.Cohen, M.Merrouch, C.Leger, V.Fourmond, S.Dementin, C.L.Drennan. Structural Insight Into Metallocofactor Maturation in Carbon Monoxide Dehydrogenase. J.Biol.Chem. V. 294 13017 2019.
ISSN: ESSN 1083-351X
PubMed: 31296570
DOI: 10.1074/JBC.RA119.009610
Page generated: Wed Aug 7 05:02:08 2024

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