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Iron in PDB 7tsj: Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris

Enzymatic activity of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris

All present enzymatic activity of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris:
1.2.7.4;

Protein crystallography data

The structure of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris, PDB code: 7tsj was solved by A.Biester, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.72 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.892, 100.87, 65.384, 90, 124.88, 90
R / Rfree (%) 16.7 / 20.6

Other elements in 7tsj:

The structure of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Xenon (Xe) 12 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris (pdb code 7tsj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris, PDB code: 7tsj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7tsj

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Iron binding site 1 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

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

b:40.9
occ:1.00
 FE1 A:SF4701 0.0 40.9 1.0
S4 A:SF4701 2.2 40.6 1.0
S3 A:SF4701 2.3 41.4 1.0
S2 A:SF4701 2.3 38.8 1.0
SG A:CYS51 2.4 38.8 1.0
FE4 A:SF4701 2.7 40.8 1.0
FE2 A:SF4701 2.7 45.4 1.0
FE3 A:SF4701 2.7 41.7 1.0
CB A:CYS51 3.1 38.6 1.0
NH2 A:ARG84 3.6 41.2 1.0
S1 A:SF4701 3.8 40.5 1.0
N A:ASN53 4.2 35.6 1.0
C A:CYS51 4.3 44.0 1.0
CA A:CYS51 4.3 42.7 1.0
CB A:ASN53 4.3 38.2 1.0
O A:CYS51 4.5 43.9 1.0
N A:ARG52 4.6 41.9 1.0
N A:CYS54 4.6 36.0 1.0
CA A:ASN53 4.7 40.2 1.0
CZ A:ARG84 4.7 43.7 1.0
SG A:CYS59 4.8 42.9 1.0
CB A:CYS59 4.9 43.2 1.0
C A:ASN53 4.9 38.9 1.0

Iron binding site 2 out of 9 in 7tsj

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Iron binding site 2 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

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

b:45.4
occ:1.00
 FE2 A:SF4701 0.0 45.4 1.0
S1 A:SF4701 2.3 40.5 1.0
S4 A:SF4701 2.3 40.6 1.0
S3 A:SF4701 2.3 41.4 1.0
SG A:CYS59 2.4 42.9 1.0
FE1 A:SF4701 2.7 40.9 1.0
FE4 A:SF4701 2.7 40.8 1.0
FE3 A:SF4701 2.7 41.7 1.0
CB A:CYS59 3.3 43.2 1.0
S2 A:SF4701 3.9 38.8 1.0
N A:VAL73 4.0 44.5 1.0
CA A:GLY57 4.1 48.0 1.0
N A:GLY57 4.2 47.5 1.0
N A:CYS59 4.3 42.6 1.0
CA A:CYS59 4.4 44.6 1.0
CA A:GLY72 4.4 45.9 1.0
CB A:CYS51 4.5 38.6 1.0
C A:GLY72 4.7 44.5 1.0
CB A:VAL73 4.7 49.1 1.0
SG A:CYS51 4.8 38.8 1.0
O A:CYS51 4.8 43.9 1.0
N A:CYS74 4.8 43.9 1.0
C A:PRO58 4.9 46.2 1.0
SG A:CYS54 4.9 40.4 1.0
CA A:VAL73 4.9 49.0 1.0
CG2 A:VAL73 4.9 48.8 1.0

Iron binding site 3 out of 9 in 7tsj

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Iron binding site 3 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

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

b:41.7
occ:1.00
 FE3 A:SF4701 0.0 41.7 1.0
S1 A:SF4701 2.3 40.5 1.0
S2 A:SF4701 2.3 38.8 1.0
S4 A:SF4701 2.3 40.6 1.0
SG A:CYS74 2.6 47.8 1.0
FE1 A:SF4701 2.7 40.9 1.0
FE4 A:SF4701 2.7 40.8 1.0
FE2 A:SF4701 2.7 45.4 1.0
CB A:CYS74 3.3 43.4 1.0
S3 A:SF4701 3.9 41.4 1.0
N A:CYS74 3.9 43.9 1.0
NH2 A:ARG84 4.2 41.2 1.0
CA A:CYS74 4.2 45.7 1.0
N A:VAL73 4.6 44.5 1.0
CB A:ALA76 4.6 43.4 1.0
SG A:CYS54 4.7 40.4 1.0
CA A:GLY72 4.8 45.9 1.0
CB A:MET203 4.8 49.4 1.0
SG A:CYS59 4.9 42.9 1.0
C A:GLY72 4.9 44.5 1.0
SG A:CYS51 4.9 38.8 1.0

Iron binding site 4 out of 9 in 7tsj

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Iron binding site 4 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

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

b:40.8
occ:1.00
 FE4 A:SF4701 0.0 40.8 1.0
S1 A:SF4701 2.3 40.5 1.0
S2 A:SF4701 2.3 38.8 1.0
S3 A:SF4701 2.3 41.4 1.0
SG A:CYS54 2.5 40.4 1.0
FE1 A:SF4701 2.7 40.9 1.0
FE3 A:SF4701 2.7 41.7 1.0
FE2 A:SF4701 2.7 45.4 1.0
CB A:CYS54 3.5 40.0 1.0
N A:CYS54 3.6 36.0 1.0
S4 A:SF4701 3.9 40.6 1.0
O A:CYS54 3.9 40.6 1.0
CA A:CYS54 3.9 38.1 1.0
C A:CYS54 4.1 38.2 1.0
N A:GLY57 4.1 47.5 1.0
C A:ASN53 4.4 38.9 1.0
CB A:MET56 4.6 44.5 1.0
CB A:MET203 4.7 49.4 1.0
CA A:GLY57 4.7 48.0 1.0
N A:ASN53 4.8 35.6 1.0
N A:MET56 4.9 42.3 1.0
SG A:CYS59 4.9 42.9 1.0
SG A:CYS51 4.9 38.8 1.0
CA A:ASN53 5.0 40.2 1.0

Iron binding site 5 out of 9 in 7tsj

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Iron binding site 5 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

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

b:48.1
occ:1.00
 FE1 A:FES702 0.0 48.1 1.0
S2 A:FES702 2.3 47.3 1.0
SG A:CYS45 2.5 47.7 1.0
SG A:CYS42 2.5 49.2 1.0
CB A:CYS42 3.2 51.2 1.0
CB A:CYS45 3.6 44.3 1.0
N A:CYS45 3.7 45.9 1.0
CA A:CYS45 4.2 45.6 1.0
CB A:PHE44 4.5 47.3 1.0
CA A:CYS42 4.6 54.2 1.0
C A:PHE44 4.6 46.5 1.0
OG1 A:THR50 4.8 49.2 1.0
CG2 A:THR50 4.8 44.9 1.0
N A:PHE44 4.9 47.3 1.0
CB A:THR50 4.9 48.0 1.0
CA A:PHE44 4.9 48.1 1.0
C A:CYS42 5.0 51.6 1.0

Iron binding site 6 out of 9 in 7tsj

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Iron binding site 6 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:52.8
occ:0.90
 FE1 A:CUV703 0.0 52.8 0.9
SG A:CYS340 2.4 52.7 1.0
S2 A:CUV703 2.7 54.0 0.9
S4 A:CUV703 2.7 53.2 0.9
FE2 A:CUV703 2.9 55.6 0.9
NI A:CUV703 3.0 52.5 0.9
FE3 A:CUV703 3.0 49.8 0.9
CB A:CYS340 3.5 53.2 1.0
FE4 A:CUV703 3.6 53.5 0.9
CE A:LYS556 4.0 52.5 1.0
SG A:CYS301 4.1 55.4 1.0
NE2 A:HIS266 4.2 53.4 1.0
CE1 A:HIS266 4.2 51.7 1.0
S1 A:CUV703 4.4 46.3 0.9
OG A:SER554 4.6 41.4 1.0
OH A:TYR553 4.6 51.1 1.0
CE2 A:TYR553 4.7 47.6 1.0
NZ A:LYS556 4.8 55.7 1.0
S3 A:CUV703 4.9 62.1 0.9
SG A:CYS302 4.9 48.2 1.0
CA A:CYS340 4.9 53.0 1.0
SG A:CYS448 4.9 46.5 1.0

Iron binding site 7 out of 9 in 7tsj

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Iron binding site 7 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

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

b:55.6
occ:0.90
 FE2 A:CUV703 0.0 55.6 0.9
SG A:CYS301 2.4 55.4 1.0
S3 A:CUV703 2.6 62.1 0.9
SG A:CYS302 2.8 48.2 1.0
NI A:CUV703 2.8 52.5 0.9
FE1 A:CUV703 2.9 52.8 0.9
FE4 A:CUV703 3.2 53.5 0.9
N A:CYS302 3.4 44.6 1.0
CB A:CYS302 3.6 47.2 1.0
NE2 A:HIS266 3.7 53.4 1.0
CB A:CYS301 3.8 49.4 1.0
CE1 A:HIS266 3.9 51.7 1.0
C A:CYS301 3.9 49.6 1.0
S2 A:CUV703 3.9 54.0 0.9
CA A:CYS302 3.9 46.8 1.0
CA A:CYS301 4.0 51.1 1.0
S1 A:CUV703 4.5 46.3 0.9
SG A:CYS340 4.6 52.7 1.0
FE3 A:CUV703 4.7 49.8 0.9
CD2 A:HIS266 4.7 47.0 1.0
CB A:CYS340 4.7 53.2 1.0
O A:CYS301 4.8 51.7 1.0
ND1 A:HIS266 4.9 49.3 1.0
S4 A:CUV703 4.9 53.2 0.9

Iron binding site 8 out of 9 in 7tsj

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Iron binding site 8 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

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

b:49.8
occ:0.90
 FE3 A:CUV703 0.0 49.8 0.9
SG A:CYS448 2.3 46.5 1.0
S4 A:CUV703 2.6 53.2 0.9
S1 A:CUV703 2.6 46.3 0.9
CB A:CYS448 2.7 45.0 1.0
S2 A:CUV703 2.8 54.0 0.9
FE4 A:CUV703 2.9 53.5 0.9
FE1 A:CUV703 3.0 52.8 0.9
CA A:CYS448 3.3 47.5 1.0
N A:CYS448 3.5 49.7 1.0
C A:GLY447 4.0 59.6 1.0
OG A:SER554 4.0 41.4 1.0
CA A:GLY447 4.3 60.0 1.0
CE2 A:TYR553 4.3 47.6 1.0
SG A:CYS478 4.4 49.8 1.0
CD2 A:TYR553 4.6 43.2 1.0
O A:GLY447 4.7 55.8 1.0
FE2 A:CUV703 4.7 55.6 0.9
C A:CYS448 4.7 48.0 1.0
CB A:ALA557 4.9 34.6 1.0
SG A:CYS340 4.9 52.7 1.0
CB A:SER554 4.9 36.9 1.0

Iron binding site 9 out of 9 in 7tsj

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Iron binding site 9 out of 9 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

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

b:53.5
occ:0.90
 FE4 A:CUV703 0.0 53.5 0.9
SG A:CYS478 2.3 49.8 1.0
S1 A:CUV703 2.6 46.3 0.9
S2 A:CUV703 2.6 54.0 0.9
S3 A:CUV703 2.6 62.1 0.9
FE3 A:CUV703 2.9 49.8 0.9
FE2 A:CUV703 3.2 55.6 0.9
N A:CYS478 3.4 46.2 1.0
CB A:CYS478 3.4 48.6 1.0
FE1 A:CUV703 3.6 52.8 0.9
CA A:CYS478 3.9 49.4 1.0
CA A:CYS448 3.9 47.5 1.0
CB A:CYS448 4.1 45.0 1.0
C A:GLY477 4.2 50.5 1.0
CA A:GLY477 4.5 46.8 1.0
O A:GLY447 4.6 55.8 1.0
N A:CYS448 4.6 49.7 1.0
CB A:HIS319 4.7 49.3 1.0
C A:GLY447 4.7 59.6 1.0
SG A:CYS301 4.7 55.4 1.0
S4 A:CUV703 4.8 53.2 0.9
SG A:CYS448 4.9 46.5 1.0
C A:CYS448 5.0 48.0 1.0

Reference:

A.Biester, S.Dementin, C.L.Drennan. Visualizing the Gas Channel of A Monofunctional Carbon Monoxide Dehydrogenase. J.Inorg.Biochem. V. 230 11774 2022.
ISSN: ISSN 0162-0134
PubMed: 35278753
DOI: 10.1016/J.JINORGBIO.2022.111774
Page generated: Fri Aug 9 02:28:13 2024

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