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Iron in PDB 6vx1: Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)

Enzymatic activity of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)

All present enzymatic activity of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure):
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure), PDB code: 6vx1 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) 73.45 / 2.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.610, 112.120, 194.430, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.4

Other elements in 6vx1:

The structure of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) (pdb code 6vx1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure), PDB code: 6vx1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 6vx1

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Iron binding site 1 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:40.6
occ:1.00
 FE1 A:SF4701 0.0 40.6 1.0
SG A:CYS51 2.3 36.8 1.0
S2 A:SF4701 2.3 40.5 1.0
S3 A:SF4701 2.3 40.2 1.0
S4 A:SF4701 2.3 32.0 1.0
FE2 A:SF4701 2.7 40.7 1.0
FE4 A:SF4701 2.7 42.5 1.0
FE3 A:SF4701 2.7 33.2 1.0
CB A:CYS51 3.3 40.7 1.0
NH2 A:ARG84 3.5 35.0 1.0
S1 A:SF4701 3.9 35.7 1.0
O A:CYS51 4.3 44.0 1.0
C A:CYS51 4.3 43.6 1.0
N A:ASN53 4.3 33.5 1.0
CB A:ASN53 4.4 35.4 1.0
CA A:CYS51 4.4 45.9 1.0
CZ A:ARG84 4.7 36.8 1.0
SG A:CYS59 4.7 46.2 1.0
CA A:ASN53 4.8 39.9 1.0
N A:ARG52 4.8 41.9 1.0
CB A:CYS59 4.8 45.4 1.0
SG A:CYS74 4.9 38.6 1.0
N A:CYS54 4.9 38.0 1.0
SG A:CYS54 4.9 40.3 1.0
O A:HOH808 5.0 34.0 1.0

Iron binding site 2 out of 16 in 6vx1

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Iron binding site 2 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:40.7
occ:1.00
 FE2 A:SF4701 0.0 40.7 1.0
S1 A:SF4701 2.3 35.7 1.0
SG A:CYS59 2.3 46.2 1.0
S3 A:SF4701 2.3 40.2 1.0
S4 A:SF4701 2.3 32.0 1.0
FE4 A:SF4701 2.7 42.5 1.0
FE1 A:SF4701 2.7 40.6 1.0
FE3 A:SF4701 2.7 33.2 1.0
CB A:CYS59 3.3 45.4 1.0
O A:GLY57 3.4 60.5 1.0
S2 A:SF4701 3.9 40.5 1.0
N A:VAL73 4.0 38.2 1.0
N A:CYS59 4.4 46.7 1.0
CA A:CYS59 4.4 47.0 1.0
CA A:GLY72 4.5 39.6 1.0
C A:GLY57 4.6 54.0 1.0
CB A:VAL73 4.6 35.4 1.0
SG A:CYS51 4.7 36.8 1.0
SG A:CYS54 4.7 40.3 1.0
O A:CYS51 4.7 44.0 1.0
CG2 A:VAL73 4.7 37.5 1.0
SG A:CYS74 4.7 38.6 1.0
N A:CYS74 4.7 37.8 1.0
C A:GLY72 4.8 36.9 1.0
CB A:CYS51 4.8 40.7 1.0
CA A:VAL73 4.9 38.6 1.0

Iron binding site 3 out of 16 in 6vx1

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Iron binding site 3 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:33.2
occ:1.00
 FE3 A:SF4701 0.0 33.2 1.0
SG A:CYS74 2.3 38.6 1.0
S4 A:SF4701 2.3 32.0 1.0
S2 A:SF4701 2.3 40.5 1.0
S1 A:SF4701 2.3 35.7 1.0
FE1 A:SF4701 2.7 40.6 1.0
FE2 A:SF4701 2.7 40.7 1.0
FE4 A:SF4701 2.7 42.5 1.0
CB A:CYS74 3.4 37.8 1.0
S3 A:SF4701 3.9 40.2 1.0
N A:CYS74 3.9 37.8 1.0
NH2 A:ARG84 4.1 35.0 1.0
CA A:CYS74 4.2 36.6 1.0
CG A:MET203 4.3 42.5 1.0
CB A:ALA76 4.7 35.6 1.0
SG A:CYS54 4.7 40.3 1.0
N A:VAL73 4.8 38.2 1.0
SG A:CYS59 4.8 46.2 1.0
O A:HOH824 4.8 34.3 1.0
SG A:CYS51 4.8 36.8 1.0

Iron binding site 4 out of 16 in 6vx1

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Iron binding site 4 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:42.5
occ:1.00
 FE4 A:SF4701 0.0 42.5 1.0
S3 A:SF4701 2.3 40.2 1.0
S1 A:SF4701 2.3 35.7 1.0
SG A:CYS54 2.3 40.3 1.0
S2 A:SF4701 2.3 40.5 1.0
FE2 A:SF4701 2.7 40.7 1.0
FE1 A:SF4701 2.7 40.6 1.0
FE3 A:SF4701 2.7 33.2 1.0
CB A:CYS54 3.5 39.3 1.0
N A:CYS54 3.9 38.0 1.0
S4 A:SF4701 3.9 32.0 1.0
CA A:CYS54 4.1 40.6 1.0
O A:CYS54 4.2 44.3 1.0
O A:GLY57 4.3 60.5 1.0
C A:CYS54 4.3 38.8 1.0
CG A:MET203 4.4 42.5 1.0
C A:ASN53 4.5 40.0 1.0
SG A:CYS74 4.7 38.6 1.0
CB A:MET56 4.8 40.5 1.0
SG A:CYS51 4.8 36.8 1.0
SG A:CYS59 4.8 46.2 1.0
CB A:MET203 4.9 36.6 1.0
N A:ASN53 4.9 33.5 1.0
N A:GLY57 5.0 41.2 1.0

Iron binding site 5 out of 16 in 6vx1

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Iron binding site 5 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:82.4
occ:1.00
 FE1 A:CUV702 0.0 82.4 1.0
SG A:CYS340 2.3 63.5 1.0
S2 A:CUV702 2.5 67.6 1.0
S4 A:CUV702 2.5 67.5 1.0
FE2 A:CUV702 2.9 77.2 1.0
FE3 A:CUV702 3.0 90.2 1.0
CB A:CYS340 3.3 56.4 1.0
NI A:CUV702 3.5 76.8 1.0
OH A:TYR553 3.6 56.3 1.0
NZ A:LYS556 3.9 53.6 1.0
NE2 A:HIS266 4.0 62.6 1.0
FE4 A:CUV702 4.1 78.7 1.0
CE1 A:HIS266 4.2 57.4 1.0
CE A:LYS556 4.3 47.1 1.0
CZ A:TYR553 4.4 53.1 1.0
OG A:SER554 4.4 35.5 1.0
CE2 A:TYR553 4.5 50.6 1.0
S1 A:CUV702 4.6 73.8 1.0
SG A:CYS301 4.7 50.3 0.5
CA A:CYS340 4.8 52.4 1.0
CB A:SER554 4.8 37.8 1.0
SG A:CYS448 4.8 64.5 1.0
SG A:CYS519 4.9 48.9 0.5

Iron binding site 6 out of 16 in 6vx1

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Iron binding site 6 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:77.2
occ:1.00
 FE2 A:CUV702 0.0 77.2 1.0
NI A:CUV702 2.4 76.8 1.0
S3 A:CUV702 2.5 63.2 1.0
SG A:CYS302 2.9 58.7 1.0
FE1 A:CUV702 2.9 82.4 1.0
SG A:CYS301 3.0 50.3 0.5
FE4 A:CUV702 3.1 78.7 1.0
S2 A:CUV702 3.3 67.6 1.0
NE2 A:HIS266 3.5 62.6 1.0
S1 A:CUV702 3.9 73.8 1.0
CB A:CYS302 3.9 49.5 1.0
FE3 A:CUV702 3.9 90.2 1.0
CE1 A:HIS266 3.9 57.4 1.0
N A:CYS302 4.0 49.7 1.0
CB A:CYS301 4.2 49.1 0.5
SG A:CYS519 4.3 48.9 0.5
S4 A:CUV702 4.3 67.5 1.0
CA A:CYS302 4.4 48.2 1.0
CB A:CYS301 4.4 49.0 0.5
CD2 A:HIS266 4.5 58.5 1.0
SG A:CYS301 4.5 54.6 0.5
C A:CYS301 4.6 48.2 0.5
SG A:CYS340 4.7 63.5 1.0
CA A:CYS301 4.7 48.0 0.5
C A:CYS301 4.7 48.2 0.5
CA A:CYS301 4.7 48.1 0.5
CB A:CYS340 4.8 56.4 1.0
NZ A:LYS556 4.8 53.6 1.0
ND1 A:HIS266 5.0 56.9 1.0
CB A:CYS519 5.0 41.4 0.5
CB A:CYS519 5.0 41.4 0.5

Iron binding site 7 out of 16 in 6vx1

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Iron binding site 7 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:90.2
occ:1.00
 FE3 A:CUV702 0.0 90.2 1.0
SG A:CYS448 2.3 64.5 1.0
S4 A:CUV702 2.4 67.5 1.0
S1 A:CUV702 2.5 73.8 1.0
S2 A:CUV702 2.5 67.6 1.0
FE1 A:CUV702 3.0 82.4 1.0
FE4 A:CUV702 3.0 78.7 1.0
CB A:CYS448 3.2 59.4 1.0
CA A:CYS448 3.9 58.6 1.0
FE2 A:CUV702 3.9 77.2 1.0
SG A:CYS519 4.1 48.9 0.5
OG A:SER554 4.2 35.5 1.0
CE2 A:TYR553 4.2 50.6 1.0
N A:CYS448 4.4 55.6 1.0
O A:GLY447 4.6 49.4 1.0
SG A:CYS478 4.7 67.2 1.0
C A:GLY447 4.7 58.3 1.0
CD2 A:TYR553 4.8 43.5 1.0
NI A:CUV702 4.8 76.8 1.0
S3 A:CUV702 4.8 63.2 1.0
CZ A:TYR553 4.9 53.1 1.0
OH A:TYR553 5.0 56.3 1.0
SG A:CYS340 5.0 63.5 1.0

Iron binding site 8 out of 16 in 6vx1

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Iron binding site 8 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:78.7
occ:1.00
 FE4 A:CUV702 0.0 78.7 1.0
SG A:CYS478 2.3 67.2 1.0
S3 A:CUV702 2.4 63.2 1.0
S1 A:CUV702 2.4 73.8 1.0
S2 A:CUV702 2.5 67.6 1.0
FE3 A:CUV702 3.0 90.2 1.0
FE2 A:CUV702 3.1 77.2 1.0
CB A:CYS478 3.4 58.9 1.0
N A:CYS478 3.6 47.4 1.0
CA A:CYS478 3.9 53.0 1.0
FE1 A:CUV702 4.1 82.4 1.0
CB A:CYS448 4.1 59.4 1.0
CA A:CYS448 4.1 58.6 1.0
O A:GLY447 4.5 49.4 1.0
C A:GLY477 4.5 44.5 1.0
SG A:CYS448 4.5 64.5 1.0
CB A:HIS319 4.7 55.0 1.0
CA A:GLY477 4.8 44.9 1.0
SG A:CYS301 4.9 54.6 0.5
S4 A:CUV702 4.9 67.5 1.0
SG A:CYS301 4.9 50.3 0.5

Iron binding site 9 out of 16 in 6vx1

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Iron binding site 9 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:49.4
occ:1.00
 FE1 B:SF4701 0.0 49.4 1.0
S2 B:SF4701 2.3 44.3 1.0
SG B:CYS51 2.3 48.6 1.0
S4 B:SF4701 2.3 43.7 1.0
S3 B:SF4701 2.3 41.7 1.0
FE4 B:SF4701 2.7 43.4 1.0
FE3 B:SF4701 2.7 41.5 1.0
FE2 B:SF4701 2.7 44.5 1.0
CB B:CYS51 3.2 46.7 1.0
NH2 B:ARG84 3.6 42.5 1.0
S1 B:SF4701 3.9 45.1 1.0
N B:ASN53 4.2 41.2 1.0
CB B:ASN53 4.3 38.5 1.0
C B:CYS51 4.3 46.0 1.0
CA B:CYS51 4.4 46.9 1.0
O B:CYS51 4.4 46.5 1.0
CZ B:ARG84 4.7 42.7 1.0
CA B:ASN53 4.7 43.3 1.0
SG B:CYS59 4.7 46.5 1.0
N B:ARG52 4.8 48.6 1.0
N B:CYS54 4.9 40.1 1.0
SG B:CYS74 4.9 42.2 1.0
SG B:CYS54 4.9 43.5 1.0

Iron binding site 10 out of 16 in 6vx1

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Iron binding site 10 out of 16 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)


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 Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:44.5
occ:1.00
 FE2 B:SF4701 0.0 44.5 1.0
S1 B:SF4701 2.3 45.1 1.0
SG B:CYS59 2.3 46.5 1.0
S3 B:SF4701 2.3 41.7 1.0
S4 B:SF4701 2.3 43.7 1.0
FE3 B:SF4701 2.7 41.5 1.0
FE1 B:SF4701 2.7 49.4 1.0
FE4 B:SF4701 2.7 43.4 1.0
CB B:CYS59 3.3 44.8 1.0
S2 B:SF4701 3.9 44.3 1.0
N B:VAL73 4.0 48.2 1.0
N B:CYS59 4.2 50.5 1.0
N B:GLY57 4.3 47.4 1.0
CA B:GLY57 4.4 44.9 1.0
CA B:GLY72 4.4 47.4 1.0
CA B:CYS59 4.4 48.6 1.0
SG B:CYS51 4.7 48.6 1.0
C B:GLY72 4.7 50.8 1.0
CB B:VAL73 4.7 45.9 1.0
SG B:CYS54 4.7 43.5 1.0
CB B:CYS51 4.7 46.7 1.0
SG B:CYS74 4.7 42.2 1.0
N B:CYS74 4.7 43.6 1.0
C B:PRO58 4.8 47.8 1.0
CG2 B:VAL73 4.9 43.0 1.0
O B:CYS51 4.9 46.5 1.0
CA B:VAL73 4.9 45.6 1.0
C B:MET56 4.9 46.4 1.0

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: Wed Aug 7 13:38:21 2024

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