Iron in PDB 8rcb: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air (in A Not Degassed Drop) For 34 Min in the Presence of Formate

Enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air (in A Not Degassed Drop) For 34 Min in the Presence of Formate

All present enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air (in A Not Degassed Drop) For 34 Min in the Presence of Formate:
1.2.1.2;

Protein crystallography data

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air (in A Not Degassed Drop) For 34 Min in the Presence of Formate, PDB code: 8rcb was solved by G.Vilela-Alves, R.R.Manuel, I.C.Pereira, M.J.Romao, C.Mota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.67 / 2.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.433, 123.085, 148.138, 90, 90, 90
R / Rfree (%) 19.9 / 24

Other elements in 8rcb:

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Co-Crystallized with Formate and Reoxidized By Exposure to Air (in A Not Degassed Drop) For 34 Min in the Presence of Formate 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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate (pdb code 8rcb). 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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate, PDB code: 8rcb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:25.5
occ:1.00
 FE1 A:SF41103 0.0 25.5 1.0
SG A:CYS53 2.2 24.6 1.0
S3 A:SF41103 2.3 27.9 1.0
S2 A:SF41103 2.3 29.4 1.0
S4 A:SF41103 2.3 23.2 1.0
FE4 A:SF41103 2.7 29.6 1.0
FE2 A:SF41103 2.7 26.3 1.0
FE3 A:SF41103 2.8 25.3 1.0
CB A:CYS53 3.2 19.9 1.0
N A:CYS53 3.8 23.8 1.0
CA A:CYS53 3.8 19.6 1.0
S1 A:SF41103 3.9 25.4 1.0
O A:CYS53 4.1 27.7 1.0
C A:CYS53 4.2 25.8 1.0
CB A:VAL55 4.2 18.2 1.0
CG2 A:VAL55 4.3 18.4 1.0
CD A:PRO234 4.6 21.8 1.0
SG A:CYS88 4.7 25.8 1.0
SG A:CYS57 4.7 25.2 1.0
SG A:CYS50 4.7 24.0 1.0
N A:VAL55 4.8 17.6 1.0
C A:TYR52 5.0 23.6 1.0
CB A:TYR52 5.0 27.6 1.0

Iron binding site 2 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:26.3
occ:1.00
 FE2 A:SF41103 0.0 26.3 1.0
SG A:CYS57 2.2 25.2 1.0
S1 A:SF41103 2.3 25.4 1.0
S3 A:SF41103 2.3 27.9 1.0
S4 A:SF41103 2.3 23.2 1.0
FE3 A:SF41103 2.7 25.3 1.0
FE4 A:SF41103 2.7 29.6 1.0
FE1 A:SF41103 2.7 25.5 1.0
CB A:CYS57 3.2 22.5 1.0
S2 A:SF41103 3.9 29.4 1.0
CD1 A:ILE235 4.1 21.0 1.0
CG1 A:ILE235 4.2 22.4 1.0
N A:CYS57 4.3 22.9 1.0
CB A:VAL55 4.3 18.2 1.0
CB A:ILE235 4.3 23.2 1.0
CA A:CYS57 4.3 24.4 1.0
CG1 A:VAL55 4.4 19.3 1.0
SG A:CYS53 4.6 24.6 1.0
SG A:CYS50 4.6 24.0 1.0
CB A:CYS50 4.7 21.2 1.0
CD2 A:LEU87 4.9 24.4 1.0
CG2 A:VAL55 4.9 18.4 1.0
SG A:CYS88 5.0 25.8 1.0

Iron binding site 3 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:25.3
occ:1.00
 FE3 A:SF41103 0.0 25.3 1.0
S4 A:SF41103 2.2 23.2 1.0
SG A:CYS50 2.3 24.0 1.0
S1 A:SF41103 2.3 25.4 1.0
S2 A:SF41103 2.3 29.4 1.0
FE2 A:SF41103 2.7 26.3 1.0
FE4 A:SF41103 2.7 29.6 1.0
FE1 A:SF41103 2.8 25.5 1.0
CB A:CYS50 3.2 21.2 1.0
S3 A:SF41103 3.9 27.9 1.0
N A:GLY91 4.2 23.5 1.0
CA A:GLY91 4.2 24.6 1.0
CB A:TYR52 4.3 27.6 1.0
SG A:CYS57 4.5 25.2 1.0
N A:CYS53 4.5 23.8 1.0
CB A:CYS57 4.5 22.5 1.0
SG A:CYS88 4.6 25.8 1.0
CA A:CYS50 4.6 21.6 1.0
SG A:CYS53 4.9 24.6 1.0
N A:TYR52 4.9 28.6 1.0
CD2 A:TYR52 4.9 24.1 1.0
CA A:TYR52 5.0 25.6 1.0

Iron binding site 4 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:29.6
occ:1.00
 FE4 A:SF41103 0.0 29.6 1.0
S1 A:SF41103 2.3 25.4 1.0
S2 A:SF41103 2.3 29.4 1.0
S3 A:SF41103 2.3 27.9 1.0
SG A:CYS88 2.3 25.8 1.0
FE2 A:SF41103 2.7 26.3 1.0
FE1 A:SF41103 2.7 25.5 1.0
FE3 A:SF41103 2.7 25.3 1.0
CB A:CYS88 3.2 30.5 1.0
N A:CYS88 3.8 30.1 1.0
S4 A:SF41103 3.9 23.2 1.0
CA A:CYS88 4.0 27.9 1.0
CD A:PRO234 4.3 21.8 1.0
CD1 A:ILE235 4.5 21.0 1.0
CG A:PRO234 4.5 19.6 1.0
C A:CYS88 4.5 30.1 1.0
N A:GLY91 4.6 23.5 1.0
NZ A:LYS90 4.6 28.4 1.0
O A:CYS88 4.6 29.8 1.0
SG A:CYS57 4.7 25.2 1.0
SG A:CYS53 4.8 24.6 1.0
CB A:PRO234 4.8 21.3 1.0
SG A:CYS50 4.9 24.0 1.0
C A:LEU87 5.0 30.5 1.0

Iron binding site 5 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:29.5
occ:1.00
 FE1 B:SF4301 0.0 29.5 1.0
S4 B:SF4301 2.3 32.3 1.0
S3 B:SF4301 2.3 27.7 1.0
S2 B:SF4301 2.3 32.5 1.0
SG B:CYS157 2.3 26.4 1.0
FE2 B:SF4301 2.7 30.6 1.0
FE3 B:SF4301 2.7 30.6 1.0
FE4 B:SF4301 2.8 29.9 1.0
CB B:CYS157 3.3 27.2 1.0
CA B:CYS157 3.8 26.1 1.0
S1 B:SF4301 3.9 30.1 1.0
OG1 B:THR159 4.0 30.9 1.0
CB B:THR161 4.1 34.3 1.0
CD B:PRO158 4.2 29.4 1.0
CG B:MET162 4.4 37.1 1.0
OG1 B:THR161 4.5 29.4 1.0
C B:CYS157 4.6 25.4 1.0
SG B:CYS15 4.6 32.9 1.0
CG2 B:THR161 4.6 33.9 1.0
N B:PRO158 4.6 26.0 1.0
SG B:CYS18 4.8 32.1 1.0
SG B:CYS12 5.0 27.4 1.0
N B:CYS157 5.0 27.6 1.0

Iron binding site 6 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.6
occ:1.00
 FE2 B:SF4301 0.0 30.6 1.0
SG B:CYS18 2.2 32.1 1.0
S4 B:SF4301 2.3 32.3 1.0
S3 B:SF4301 2.3 27.7 1.0
S1 B:SF4301 2.3 30.1 1.0
FE1 B:SF4301 2.7 29.5 1.0
FE3 B:SF4301 2.7 30.6 1.0
FE4 B:SF4301 2.8 29.9 1.0
CB B:CYS18 3.2 41.7 1.0
N B:CYS18 3.8 29.7 1.0
S2 B:SF4301 3.9 32.5 1.0
CA B:CYS18 4.2 34.5 1.0
N B:ARG16 4.5 27.9 1.0
N B:GLY17 4.6 33.2 1.0
SG B:CYS15 4.6 32.9 1.0
CA B:ARG16 4.7 27.6 1.0
CB B:PRO71 4.8 34.4 1.0
CG2 B:VAL53 4.8 37.6 1.0
SG B:CYS157 4.8 26.4 1.0
CG B:PRO71 4.9 45.3 1.0
C B:ARG16 4.9 28.9 1.0
SG B:CYS12 4.9 27.4 1.0
C B:GLY17 5.0 29.2 1.0

Iron binding site 7 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.6
occ:1.00
 FE3 B:SF4301 0.0 30.6 1.0
S1 B:SF4301 2.3 30.1 1.0
S2 B:SF4301 2.3 32.5 1.0
S4 B:SF4301 2.3 32.3 1.0
SG B:CYS15 2.3 32.9 1.0
FE2 B:SF4301 2.7 30.6 1.0
FE1 B:SF4301 2.7 29.5 1.0
FE4 B:SF4301 2.7 29.9 1.0
N B:CYS15 3.4 25.8 1.0
CB B:CYS15 3.5 32.6 1.0
N B:ARG16 3.6 27.9 1.0
CA B:CYS15 3.8 30.6 1.0
S3 B:SF4301 3.9 27.7 1.0
C B:CYS15 4.1 28.1 1.0
N B:GLY17 4.2 33.2 1.0
CD B:PRO158 4.4 29.4 1.0
C B:ALA14 4.4 25.3 1.0
OG1 B:THR13 4.4 32.0 1.0
N B:ALA14 4.5 25.2 1.0
CA B:ARG16 4.5 27.6 1.0
SG B:CYS18 4.6 32.1 1.0
CA B:ALA14 4.7 25.9 1.0
SG B:CYS12 4.8 27.4 1.0
SG B:CYS157 4.8 26.4 1.0
C B:ARG16 4.9 28.9 1.0
N B:THR13 4.9 28.3 1.0
N B:CYS18 4.9 29.7 1.0
CA B:GLY17 5.0 32.0 1.0

Iron binding site 8 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:29.9
occ:1.00
 FE4 B:SF4301 0.0 29.9 1.0
S1 B:SF4301 2.3 30.1 1.0
S2 B:SF4301 2.3 32.5 1.0
S3 B:SF4301 2.3 27.7 1.0
SG B:CYS12 2.4 27.4 1.0
FE3 B:SF4301 2.7 30.6 1.0
FE1 B:SF4301 2.8 29.5 1.0
FE2 B:SF4301 2.8 30.6 1.0
CB B:CYS12 3.5 22.9 1.0
CA B:CYS12 3.8 24.9 1.0
S4 B:SF4301 3.9 32.3 1.0
N B:ALA14 4.1 25.2 1.0
N B:THR13 4.2 28.3 1.0
C B:CYS12 4.4 26.1 1.0
CA B:ALA14 4.5 25.9 1.0
CG2 B:THR161 4.5 33.9 1.0
OG1 B:THR161 4.5 29.4 1.0
CB B:THR161 4.6 34.3 1.0
N B:CYS15 4.7 25.8 1.0
SG B:CYS18 4.7 32.1 1.0
CG B:PRO71 4.8 45.3 1.0
SG B:CYS157 4.8 26.4 1.0
OG1 B:THR159 5.0 30.9 1.0

Iron binding site 9 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:62.9
occ:1.00
 FE1 B:SF4302 0.0 62.9 1.0
SG B:CYS77 2.2 45.3 1.0
S3 B:SF4302 2.3 62.7 1.0
S2 B:SF4302 2.3 53.9 1.0
S4 B:SF4302 2.3 57.5 1.0
FE4 B:SF4302 2.7 53.8 1.0
FE2 B:SF4302 2.8 64.2 1.0
FE3 B:SF4302 2.8 52.2 1.0
CB B:CYS77 3.5 49.7 1.0
N B:CYS77 3.9 43.5 1.0
S1 B:SF4302 3.9 47.5 1.0
CA B:CYS77 4.3 46.3 1.0
CD2 B:TYR123 4.5 46.4 1.0
CD B:PRO81 4.5 69.9 1.0
N B:HIS76 4.5 46.4 1.0
SG B:CYS74 4.6 45.9 1.0
SG B:CYS121 4.7 57.8 1.0
CE2 B:TYR123 4.8 46.8 1.0
N B:ARG75 4.9 45.4 1.0
CB B:ARG75 4.9 42.0 1.0
C B:HIS76 4.9 39.8 1.0
CA B:HIS76 4.9 47.6 1.0
SG B:CYS82 5.0 63.8 1.0

Iron binding site 10 out of 16 in 8rcb

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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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate


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 (in A Not Degassed Drop) For 34 Min in the Presence of Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:64.2
occ:1.00
 FE2 B:SF4302 0.0 64.2 1.0
S4 B:SF4302 2.3 57.5 1.0
S1 B:SF4302 2.3 47.5 1.0
S3 B:SF4302 2.3 62.7 1.0
SG B:CYS82 2.5 63.8 1.0
FE3 B:SF4302 2.7 52.2 1.0
FE4 B:SF4302 2.7 53.8 1.0
FE1 B:SF4302 2.8 62.9 1.0
CB B:CYS82 3.1 68.7 1.0
S2 B:SF4302 3.9 53.9 1.0
N B:CYS82 4.2 64.5 1.0
CA B:CYS82 4.3 67.1 1.0
CG1 B:VAL103 4.3 54.4 1.0
CE B:LYS137 4.7 45.0 1.0
SG B:CYS77 4.7 45.3 1.0
CB B:PRO80 4.8 64.1 1.0
SG B:CYS121 4.8 57.8 1.0
SG B:CYS74 4.8 45.9 1.0
CZ B:PHE105 4.9 62.0 1.0
CE1 B:PHE105 4.9 66.1 1.0

Reference:

G.Vilela-Alves, R.R.Manuel, A.Viegas, P.Carpentier, F.Biaso, B.Guigliarelli, I.C.Pereira, M.J.Romao, C.Mota. Substrate-Dependent Oxidative Inactivation of A W-Dependent Formate Dehydrogenase Involving Selenocysteine Displacement Chem Sci 2024.
ISSN: ESSN 2041-6539
Page generated: Sat Aug 10 16:38:31 2024

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