Iron in PDB 8bql: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min

Protein crystallography data

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min, PDB code: 8bql was solved by G.Vilela-Alves, C.Mota, A.R.Oliveira, R.R.Manuel, I.C.Pereira, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.00 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.8, 127.594, 148.622, 90, 90, 90
R / Rfree (%) 18.8 / 22.5

Other elements in 8bql:

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min also contains other interesting chemical elements:

Tungsten (W) 1 atom

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min (pdb code 8bql). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min, PDB code: 8bql:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8bql

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:19.1
occ:1.00
 FE1 A:SF41103 0.0 19.1 1.0
S4 A:SF41103 2.3 19.8 1.0
S2 A:SF41103 2.3 20.8 1.0
S3 A:SF41103 2.3 18.1 1.0
SG A:CYS53 2.3 18.2 1.0
FE3 A:SF41103 2.7 20.6 1.0
FE4 A:SF41103 2.7 19.2 1.0
FE2 A:SF41103 2.8 18.8 1.0
CB A:CYS53 3.4 19.0 1.0
N A:CYS53 3.7 20.9 1.0
CA A:CYS53 3.9 21.0 1.0
S1 A:SF41103 3.9 20.2 1.0
O A:CYS53 4.0 22.3 1.0
C A:CYS53 4.1 20.0 1.0
CB A:VAL55 4.1 19.9 1.0
O A:HOH1364 4.1 15.4 1.0
CG2 A:VAL55 4.3 22.8 1.0
CD A:PRO234 4.5 20.4 1.0
N A:VAL55 4.6 18.8 1.0
SG A:CYS88 4.6 20.8 1.0
SG A:CYS50 4.7 18.8 1.0
SG A:CYS57 4.8 18.5 1.0
CA A:VAL55 4.9 19.3 1.0
C A:TYR52 4.9 20.0 1.0
N A:ALA54 5.0 19.2 1.0

Iron binding site 2 out of 16 in 8bql

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:18.8
occ:1.00
 FE2 A:SF41103 0.0 18.8 1.0
SG A:CYS57 2.2 18.5 1.0
S1 A:SF41103 2.3 20.2 1.0
S4 A:SF41103 2.3 19.8 1.0
S3 A:SF41103 2.3 18.1 1.0
FE3 A:SF41103 2.7 20.6 1.0
FE4 A:SF41103 2.8 19.2 1.0
FE1 A:SF41103 2.8 19.1 1.0
CB A:CYS57 3.1 19.1 1.0
S2 A:SF41103 3.9 20.8 1.0
CD1 A:ILE235 4.1 18.1 1.0
N A:CYS57 4.2 18.0 1.0
CA A:CYS57 4.2 20.6 1.0
CB A:VAL55 4.3 19.9 1.0
CG1 A:ILE235 4.3 17.4 1.0
CG1 A:VAL55 4.4 20.0 1.0
CB A:ILE235 4.4 17.2 1.0
CB A:CYS50 4.6 17.9 1.0
SG A:CYS50 4.6 18.8 1.0
SG A:CYS53 4.8 18.2 1.0
CD2 A:LEU87 4.9 19.2 1.0
SG A:CYS88 4.9 20.8 1.0
CG2 A:VAL55 5.0 22.8 1.0

Iron binding site 3 out of 16 in 8bql

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:20.6
occ:1.00
 FE3 A:SF41103 0.0 20.6 1.0
SG A:CYS50 2.2 18.8 1.0
S4 A:SF41103 2.3 19.8 1.0
S2 A:SF41103 2.3 20.8 1.0
S1 A:SF41103 2.3 20.2 1.0
FE2 A:SF41103 2.7 18.8 1.0
FE1 A:SF41103 2.7 19.1 1.0
FE4 A:SF41103 2.7 19.2 1.0
CB A:CYS50 3.1 17.9 1.0
S3 A:SF41103 3.9 18.1 1.0
CA A:GLY91 4.2 22.5 1.0
N A:GLY91 4.2 22.1 1.0
CB A:TYR52 4.2 20.8 1.0
N A:CYS53 4.3 20.9 1.0
SG A:CYS88 4.5 20.8 1.0
CB A:CYS57 4.5 19.1 1.0
CA A:CYS50 4.6 18.8 1.0
SG A:CYS57 4.6 18.5 1.0
N A:TYR52 4.8 20.8 1.0
CA A:TYR52 4.9 19.8 1.0
SG A:CYS53 4.9 18.2 1.0
O A:CYS53 4.9 22.3 1.0
CD2 A:TYR52 4.9 23.1 1.0
C A:TYR52 5.0 20.0 1.0

Iron binding site 4 out of 16 in 8bql

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:19.2
occ:1.00
 FE4 A:SF41103 0.0 19.2 1.0
SG A:CYS88 2.2 20.8 1.0
S2 A:SF41103 2.3 20.8 1.0
S1 A:SF41103 2.3 20.2 1.0
S3 A:SF41103 2.3 18.1 1.0
FE3 A:SF41103 2.7 20.6 1.0
FE1 A:SF41103 2.7 19.1 1.0
FE2 A:SF41103 2.8 18.8 1.0
CB A:CYS88 3.3 23.4 1.0
N A:CYS88 3.9 18.4 1.0
S4 A:SF41103 3.9 19.8 1.0
CA A:CYS88 4.1 20.6 1.0
CD A:PRO234 4.3 20.4 1.0
N A:GLY91 4.4 22.1 1.0
CG A:PRO234 4.5 22.8 1.0
CD1 A:ILE235 4.5 18.1 1.0
NZ A:LYS90 4.5 21.6 1.0
O A:HOH1364 4.6 15.4 1.0
C A:CYS88 4.7 22.9 1.0
SG A:CYS53 4.7 18.2 1.0
SG A:CYS50 4.8 18.8 1.0
O A:CYS88 4.8 23.1 1.0
CB A:PRO234 4.8 19.1 1.0
SG A:CYS57 4.9 18.5 1.0
CA A:GLY91 4.9 22.5 1.0
CE A:LYS90 5.0 23.3 1.0

Iron binding site 5 out of 16 in 8bql

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.7
occ:1.00
 FE1 B:SF4301 0.0 21.7 1.0
S3 B:SF4301 2.2 20.9 1.0
S4 B:SF4301 2.3 22.2 1.0
SG B:CYS157 2.3 21.7 1.0
S2 B:SF4301 2.3 21.8 1.0
FE3 B:SF4301 2.7 21.8 1.0
FE2 B:SF4301 2.7 23.0 1.0
FE4 B:SF4301 2.7 21.9 1.0
CB B:CYS157 3.2 24.2 1.0
CA B:CYS157 3.8 20.3 1.0
OG1 B:THR159 3.9 16.3 1.0
S1 B:SF4301 3.9 23.3 1.0
CB B:THR161 4.1 22.9 1.0
CD B:PRO158 4.1 25.3 1.0
CG B:MET162 4.2 22.8 1.0
OG1 B:THR161 4.4 22.5 1.0
C B:CYS157 4.5 20.8 1.0
CG2 B:THR161 4.6 23.8 1.0
N B:PRO158 4.6 21.2 1.0
SG B:CYS15 4.6 23.8 1.0
SG B:CYS18 4.8 24.1 1.0
SG B:CYS12 4.9 22.9 1.0
N B:THR159 5.0 21.7 1.0
N B:MET162 5.0 22.7 1.0

Iron binding site 6 out of 16 in 8bql

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:23.0
occ:1.00
 FE2 B:SF4301 0.0 23.0 1.0
SG B:CYS18 2.2 24.1 1.0
S4 B:SF4301 2.3 22.2 1.0
S3 B:SF4301 2.3 20.9 1.0
S1 B:SF4301 2.3 23.3 1.0
FE3 B:SF4301 2.7 21.8 1.0
FE1 B:SF4301 2.7 21.7 1.0
FE4 B:SF4301 2.8 21.9 1.0
CB B:CYS18 3.2 22.6 1.0
S2 B:SF4301 3.9 21.8 1.0
O B:HOH414 3.9 22.1 1.0
N B:CYS18 3.9 22.5 1.0
CA B:CYS18 4.2 21.5 1.0
CG B:PRO71 4.4 23.8 1.0
SG B:CYS15 4.6 23.8 1.0
N B:ARG16 4.7 22.9 1.0
CB B:PRO71 4.7 23.6 1.0
N B:GLY17 4.7 20.3 1.0
SG B:CYS12 4.8 22.9 1.0
CG2 B:VAL53 4.8 29.4 1.0
CA B:ARG16 4.8 23.4 1.0
SG B:CYS157 4.8 21.7 1.0

Iron binding site 7 out of 16 in 8bql

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.8
occ:1.00
 FE3 B:SF4301 0.0 21.8 1.0
S2 B:SF4301 2.3 21.8 1.0
SG B:CYS15 2.3 23.8 1.0
S1 B:SF4301 2.3 23.3 1.0
S4 B:SF4301 2.3 22.2 1.0
FE2 B:SF4301 2.7 23.0 1.0
FE1 B:SF4301 2.7 21.7 1.0
FE4 B:SF4301 2.7 21.9 1.0
N B:CYS15 3.5 21.6 1.0
CB B:CYS15 3.6 23.3 1.0
N B:ARG16 3.7 22.9 1.0
S3 B:SF4301 3.9 20.9 1.0
CA B:CYS15 3.9 23.0 1.0
N B:GLY17 4.2 20.3 1.0
CD B:PRO158 4.2 25.3 1.0
C B:CYS15 4.2 21.5 1.0
OG1 B:THR13 4.4 23.7 1.0
C B:ALA14 4.5 21.7 1.0
SG B:CYS18 4.6 24.1 1.0
N B:ALA14 4.6 21.5 1.0
CA B:ARG16 4.6 23.4 1.0
CA B:ALA14 4.7 22.8 1.0
SG B:CYS157 4.7 21.7 1.0
SG B:CYS12 4.7 22.9 1.0
CG B:PRO158 4.8 23.5 1.0
C B:ARG16 4.9 20.0 1.0
N B:CYS18 4.9 22.5 1.0
CA B:GLY17 5.0 20.8 1.0

Iron binding site 8 out of 16 in 8bql

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Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.9
occ:1.00
 FE4 B:SF4301 0.0 21.9 1.0
S2 B:SF4301 2.2 21.8 1.0
SG B:CYS12 2.3 22.9 1.0
S1 B:SF4301 2.3 23.3 1.0
S3 B:SF4301 2.3 20.9 1.0
FE1 B:SF4301 2.7 21.7 1.0
FE3 B:SF4301 2.7 21.8 1.0
FE2 B:SF4301 2.8 23.0 1.0
CB B:CYS12 3.5 21.9 1.0
CA B:CYS12 3.8 22.8 1.0
S4 B:SF4301 3.9 22.2 1.0
N B:ALA14 4.1 21.5 1.0
N B:THR13 4.2 25.3 1.0
OG1 B:THR161 4.4 22.5 1.0
CG B:PRO71 4.4 23.8 1.0
C B:CYS12 4.4 25.7 1.0
CG2 B:THR161 4.4 23.8 1.0
CA B:ALA14 4.4 22.8 1.0
CB B:THR161 4.5 22.9 1.0
N B:CYS15 4.7 21.6 1.0
SG B:CYS18 4.8 24.1 1.0
SG B:CYS157 4.8 21.7 1.0
OG1 B:THR159 4.8 16.3 1.0
SG B:CYS15 4.9 23.8 1.0

Iron binding site 9 out of 16 in 8bql

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:35.4
occ:1.00
 FE1 B:SF4302 0.0 35.4 1.0
S3 B:SF4302 2.2 33.8 1.0
SG B:CYS77 2.3 32.8 1.0
S4 B:SF4302 2.3 29.0 1.0
S2 B:SF4302 2.3 29.0 1.0
FE4 B:SF4302 2.7 34.3 1.0
FE2 B:SF4302 2.7 34.4 1.0
FE3 B:SF4302 2.8 31.3 1.0
CB B:CYS77 3.4 33.3 1.0
N B:CYS77 3.8 31.1 1.0
S1 B:SF4302 3.9 31.9 1.0
CA B:CYS77 4.3 34.5 1.0
N B:HIS76 4.5 28.6 1.0
CD2 B:TYR123 4.5 32.3 1.0
SG B:CYS121 4.6 32.8 1.0
CB B:PRO80 4.6 36.0 1.0
CD B:PRO81 4.7 36.0 1.0
SG B:CYS74 4.7 30.2 1.0
CB B:ARG75 4.7 31.0 1.0
N B:ARG75 4.7 26.5 1.0
CA B:PRO80 4.8 36.3 1.0
CE2 B:TYR123 4.8 32.2 1.0
SG B:CYS82 4.9 34.0 1.0
C B:HIS76 4.9 27.4 1.0
C B:ARG75 5.0 26.7 1.0
CA B:HIS76 5.0 28.6 1.0

Iron binding site 10 out of 16 in 8bql

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Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air For 12 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:34.4
occ:1.00
 FE2 B:SF4302 0.0 34.4 1.0
S4 B:SF4302 2.2 29.0 1.0
S3 B:SF4302 2.3 33.8 1.0
S1 B:SF4302 2.3 31.9 1.0
SG B:CYS82 2.4 34.0 1.0
FE1 B:SF4302 2.7 35.4 1.0
FE4 B:SF4302 2.7 34.3 1.0
FE3 B:SF4302 2.8 31.3 1.0
CB B:CYS82 3.2 33.8 1.0
S2 B:SF4302 3.9 29.0 1.0
CB B:PRO80 4.1 36.0 1.0
N B:CYS82 4.3 38.4 1.0
CG1 B:VAL103 4.3 29.1 1.0
CA B:CYS82 4.3 37.3 1.0
CE B:LYS137 4.6 29.1 1.0
SG B:CYS74 4.7 30.2 1.0
CA B:PRO80 4.8 36.3 1.0
SG B:CYS121 4.8 32.8 1.0
SG B:CYS77 4.8 32.8 1.0
CD B:LYS137 5.0 32.5 1.0

Reference:

G.Vilela-Alves, R.R.Manuel, A.R.Oliveira, I.C.Pereira, M.J.Romao, C.Mota. Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation. Int J Mol Sci V. 24 2022.
ISSN: ESSN 1422-0067
PubMed: 36613918
DOI: 10.3390/IJMS24010476
Page generated: Wed Apr 5 08:12:25 2023

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