Iron in PDB 8cm4: W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen

The structure of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen, PDB code: 8cm4 was solved by G.Vilela-Alves, C.Mota, K.Klymanska, 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)	48.31 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.299, 126.897, 260.94, 90, 90, 90
R / Rfree (%)	20 / 25.6

The structure of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen also contains other interesting chemical elements:

Tungsten

(W)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen (pdb code 8cm4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen, PDB code: 8cm4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:29.2 occ:1.00 FE1 A:SF41103 0.0 29.2 1.0 S4 A:SF41103 2.2 31.1 1.0 SG A:CYS53 2.2 30.8 1.0 S2 A:SF41103 2.3 29.9 1.0 S3 A:SF41103 2.3 28.7 1.0 FE3 A:SF41103 2.6 29.8 1.0 FE2 A:SF41103 2.7 30.5 1.0 FE4 A:SF41103 2.7 27.9 1.0 CB A:CYS53 3.4 31.5 1.0 N A:CYS53 3.6 34.0 1.0 CA A:CYS53 3.8 32.4 1.0 S1 A:SF41103 3.9 32.3 1.0 O A:CYS53 4.0 30.6 1.0 C A:CYS53 4.1 31.9 1.0 CB A:VAL55 4.1 32.4 1.0 O A:HOH1262 4.3 32.3 1.0 CG2 A:VAL55 4.3 32.4 1.0 SG A:CYS50 4.6 36.9 1.0 SG A:CYS88 4.7 28.6 1.0 N A:VAL55 4.7 34.6 1.0 SG A:CYS57 4.7 28.8 1.0 C A:TYR52 4.8 35.1 1.0 CD A:PRO234 4.8 31.1 1.0 CB A:TYR52 4.9 31.8 1.0 N A:ALA54 5.0 31.8 1.0 CA A:VAL55 5.0 34.8 1.0

Iron binding site 2 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:30.5 occ:1.00 FE2 A:SF41103 0.0 30.5 1.0 S3 A:SF41103 2.2 28.7 1.0 SG A:CYS57 2.2 28.8 1.0 S1 A:SF41103 2.3 32.3 1.0 S4 A:SF41103 2.3 31.1 1.0 FE3 A:SF41103 2.7 29.8 1.0 FE4 A:SF41103 2.7 27.9 1.0 FE1 A:SF41103 2.7 29.2 1.0 CB A:CYS57 3.0 31.4 1.0 S2 A:SF41103 3.8 29.9 1.0 CD1 A:ILE235 4.0 32.8 1.0 CA A:CYS57 4.1 30.7 1.0 N A:CYS57 4.2 29.6 1.0 CG1 A:ILE235 4.2 32.3 1.0 CB A:ILE235 4.4 31.1 1.0 CB A:VAL55 4.4 32.4 1.0 CG1 A:VAL55 4.4 31.9 1.0 SG A:CYS53 4.6 30.8 1.0 CB A:CYS50 4.7 35.6 1.0 SG A:CYS50 4.7 36.9 1.0 CD2 A:LEU87 4.8 35.2 1.0 SG A:CYS88 5.0 28.6 1.0

Iron binding site 3 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:29.8 occ:1.00 FE3 A:SF41103 0.0 29.8 1.0 S2 A:SF41103 2.1 29.9 1.0 S4 A:SF41103 2.3 31.1 1.0 S1 A:SF41103 2.3 32.3 1.0 SG A:CYS50 2.3 36.9 1.0 FE1 A:SF41103 2.6 29.2 1.0 FE4 A:SF41103 2.6 27.9 1.0 FE2 A:SF41103 2.7 30.5 1.0 CB A:CYS50 3.1 35.6 1.0 S3 A:SF41103 3.7 28.7 1.0 CB A:TYR52 4.2 31.8 1.0 N A:CYS53 4.2 34.0 1.0 CA A:GLY91 4.2 28.5 1.0 N A:GLY91 4.3 28.1 1.0 CB A:CYS57 4.4 31.4 1.0 CA A:CYS50 4.6 34.0 1.0 SG A:CYS88 4.6 28.6 1.0 SG A:CYS57 4.6 28.8 1.0 SG A:CYS53 4.7 30.8 1.0 N A:TYR52 4.8 34.9 1.0 CA A:TYR52 4.8 33.0 1.0 O A:CYS53 4.9 30.6 1.0 C A:TYR52 4.9 35.1 1.0 CD2 A:TYR52 4.9 29.8 1.0

Iron binding site 4 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:27.9 occ:1.00 FE4 A:SF41103 0.0 27.9 1.0 S2 A:SF41103 2.2 29.9 1.0 S1 A:SF41103 2.2 32.3 1.0 S3 A:SF41103 2.3 28.7 1.0 SG A:CYS88 2.4 28.6 1.0 FE3 A:SF41103 2.6 29.8 1.0 FE2 A:SF41103 2.7 30.5 1.0 FE1 A:SF41103 2.7 29.2 1.0 CB A:CYS88 3.3 30.2 1.0 N A:CYS88 3.8 32.0 1.0 S4 A:SF41103 3.8 31.1 1.0 CA A:CYS88 4.0 30.4 1.0 N A:GLY91 4.2 28.1 1.0 CD1 A:ILE235 4.3 32.8 1.0 NZ A:LYS90 4.5 28.8 1.0 CG A:PRO234 4.6 30.3 1.0 C A:CYS88 4.6 29.5 1.0 SG A:CYS53 4.6 30.8 1.0 CA A:GLY91 4.7 28.5 1.0 CD A:PRO234 4.7 31.1 1.0 O A:CYS88 4.7 31.3 1.0 SG A:CYS50 4.7 36.9 1.0 O A:HOH1262 4.8 32.3 1.0 SG A:CYS57 4.8 28.8 1.0 CB A:PRO234 4.9 30.1 1.0 C A:LEU87 4.9 33.5 1.0 CE A:LYS90 4.9 28.5 1.0 CB A:LYS90 5.0 26.3 1.0

Iron binding site 5 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:28.8 occ:1.00 FE1 B:SF4301 0.0 28.8 1.0 S2 B:SF4301 2.2 26.6 1.0 S3 B:SF4301 2.3 26.6 1.0 S4 B:SF4301 2.3 28.1 1.0 SG B:CYS157 2.3 28.0 1.0 FE4 B:SF4301 2.7 26.1 1.0 FE3 B:SF4301 2.7 26.9 1.0 FE2 B:SF4301 2.7 27.0 1.0 CB B:CYS157 3.4 31.8 1.0 OG1 B:THR159 3.8 28.8 1.0 S1 B:SF4301 3.8 27.7 1.0 CA B:CYS157 3.9 31.9 1.0 CB B:THR161 4.0 32.0 1.0 CG B:MET162 4.2 33.5 1.0 CD B:PRO158 4.2 34.5 1.0 OG1 B:THR161 4.4 31.1 1.0 CG2 B:THR161 4.6 31.8 1.0 C B:CYS157 4.7 32.1 1.0 SG B:CYS12 4.7 26.2 1.0 SG B:CYS15 4.7 27.4 1.0 N B:PRO158 4.8 34.0 1.0 SG B:CYS18 4.8 27.3 1.0 N B:MET162 5.0 33.2 1.0

Iron binding site 6 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.0 occ:1.00 FE2 B:SF4301 0.0 27.0 1.0 S1 B:SF4301 2.2 27.7 1.0 SG B:CYS18 2.3 27.3 1.0 S4 B:SF4301 2.3 28.1 1.0 S3 B:SF4301 2.3 26.6 1.0 FE3 B:SF4301 2.7 26.9 1.0 FE4 B:SF4301 2.7 26.1 1.0 FE1 B:SF4301 2.7 28.8 1.0 CB B:CYS18 3.3 27.9 1.0 S2 B:SF4301 3.8 26.6 1.0 N B:CYS18 3.8 27.6 1.0 O B:HOH419 3.9 18.3 1.0 CA B:CYS18 4.2 27.3 1.0 CG B:PRO71 4.3 27.7 1.0 SG B:CYS12 4.4 26.2 1.0 N B:GLY17 4.6 29.6 1.0 SG B:CYS15 4.6 27.4 1.0 N B:ARG16 4.7 31.7 1.0 CB B:PRO71 4.7 28.2 1.0 CA B:ARG16 4.8 29.8 1.0 CG2 B:VAL53 4.8 29.7 1.0 SG B:CYS157 4.9 28.0 1.0 C B:GLY17 5.0 30.1 1.0

Iron binding site 7 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.9 occ:1.00 FE3 B:SF4301 0.0 26.9 1.0 S4 B:SF4301 2.2 28.1 1.0 S1 B:SF4301 2.3 27.7 1.0 S2 B:SF4301 2.3 26.6 1.0 SG B:CYS15 2.3 27.4 1.0 FE2 B:SF4301 2.7 27.0 1.0 FE1 B:SF4301 2.7 28.8 1.0 FE4 B:SF4301 2.8 26.1 1.0 CB B:CYS15 3.6 25.8 1.0 N B:CYS15 3.8 25.0 1.0 N B:ARG16 3.8 31.7 1.0 S3 B:SF4301 3.9 26.6 1.0 N B:GLY17 4.0 29.6 1.0 CA B:CYS15 4.1 26.6 1.0 CD B:PRO158 4.3 34.5 1.0 C B:CYS15 4.3 29.6 1.0 OG1 B:THR13 4.4 26.4 1.0 SG B:CYS18 4.6 27.3 1.0 SG B:CYS12 4.6 26.2 1.0 CA B:ARG16 4.7 29.8 1.0 N B:CYS18 4.7 27.6 1.0 N B:ALA14 4.7 25.4 1.0 C B:ALA14 4.7 25.0 1.0 SG B:CYS157 4.7 28.0 1.0 CA B:GLY17 4.7 29.1 1.0 C B:ARG16 4.8 28.1 1.0 CG B:PRO158 4.8 36.0 1.0 CA B:ALA14 4.9 25.3 1.0

Iron binding site 8 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.1 occ:1.00 FE4 B:SF4301 0.0 26.1 1.0 SG B:CYS12 2.1 26.2 1.0 S2 B:SF4301 2.2 26.6 1.0 S3 B:SF4301 2.2 26.6 1.0 S1 B:SF4301 2.3 27.7 1.0 FE1 B:SF4301 2.7 28.8 1.0 FE2 B:SF4301 2.7 27.0 1.0 FE3 B:SF4301 2.8 26.9 1.0 CB B:CYS12 3.4 28.0 1.0 CA B:CYS12 3.7 29.3 1.0 S4 B:SF4301 3.9 28.1 1.0 N B:THR13 4.1 28.5 1.0 N B:ALA14 4.1 25.4 1.0 OG1 B:THR161 4.2 31.1 1.0 CG2 B:THR161 4.3 31.8 1.0 C B:CYS12 4.3 28.2 1.0 CB B:THR161 4.4 32.0 1.0 CG B:PRO71 4.4 27.7 1.0 CA B:ALA14 4.5 25.3 1.0 SG B:CYS157 4.7 28.0 1.0 SG B:CYS18 4.8 27.3 1.0 N B:CYS15 4.8 25.0 1.0 OG1 B:THR159 4.9 28.8 1.0 SG B:CYS15 5.0 27.4 1.0 N B:CYS12 5.0 29.0 1.0

Iron binding site 9 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:31.5 occ:1.00 FE1 B:SF4302 0.0 31.5 1.0 S4 B:SF4302 2.2 31.8 1.0 S2 B:SF4302 2.3 30.6 1.0 S3 B:SF4302 2.3 30.9 1.0 SG B:CYS77 2.4 34.1 1.0 FE2 B:SF4302 2.7 29.9 1.0 FE3 B:SF4302 2.8 29.1 1.0 FE4 B:SF4302 2.8 29.5 1.0 CB B:CYS77 3.3 31.7 1.0 N B:CYS77 3.8 27.7 1.0 S1 B:SF4302 3.9 33.6 1.0 CA B:CYS77 4.2 31.3 1.0 N B:HIS76 4.4 27.5 1.0 SG B:CYS74 4.5 23.8 1.0 SG B:CYS121 4.5 29.0 1.0 CB B:PRO80 4.6 35.0 1.0 CD B:PRO81 4.7 29.3 1.0 CD2 B:TYR123 4.7 26.6 1.0 CB B:ARG75 4.7 26.8 1.0 N B:ARG75 4.8 27.5 1.0 CA B:PRO80 4.8 34.5 1.0 C B:HIS76 4.9 27.2 1.0 SG B:CYS82 4.9 28.2 1.0 CE2 B:TYR123 4.9 28.3 1.0 CA B:HIS76 4.9 26.9 1.0

Iron binding site 10 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - Exposed to Oxygen


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 C872A From Desulfovibrio Vulgaris - Exposed to Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:29.9 occ:1.00 FE2 B:SF4302 0.0 29.9 1.0 S3 B:SF4302 2.2 30.9 1.0 S4 B:SF4302 2.3 31.8 1.0 S1 B:SF4302 2.3 33.6 1.0 SG B:CYS82 2.4 28.2 1.0 FE1 B:SF4302 2.7 31.5 1.0 FE4 B:SF4302 2.7 29.5 1.0 FE3 B:SF4302 2.8 29.1 1.0 CB B:CYS82 3.1 28.6 1.0 S2 B:SF4302 3.8 30.6 1.0 N B:CYS82 4.1 27.5 1.0 CA B:CYS82 4.2 29.6 1.0 CB B:PRO80 4.2 35.0 1.0 SG B:CYS74 4.6 23.8 1.0 SG B:CYS121 4.6 29.0 1.0 CG1 B:VAL103 4.8 33.2 1.0 CA B:PRO80 4.8 34.5 1.0 SG B:CYS77 4.8 34.1 1.0 CE B:LYS137 4.9 30.8 1.0 CB B:CYS121 5.0 30.0 1.0

A.R.Oliveira, C.Mota, R.R.Manuel, G.Vilela-Alves, N.Pedrosa, V.Fourmond, K.Klymanska, C.Leger, B.Guigliarelli, M.J.Romao, I.C.Pereira. W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469