Iron in PDB 8bqh: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min, PDB code: 8bqh 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)	90.65 / 1.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.361, 127.456, 128.952, 90, 90, 90
R / Rfree (%)	15.1 / 17.5

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Tungsten	(W)	1 atom

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 - Soaking with Formate 1.5 Min (pdb code 8bqh). 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 - Soaking with Formate 1.5 Min, PDB code: 8bqh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:10.4 occ:1.00 FE1 A:SF41103 0.0 10.4 1.0 S4 A:SF41103 2.2 11.5 1.0 S2 A:SF41103 2.3 10.9 1.0 SG A:CYS53 2.3 10.4 1.0 S3 A:SF41103 2.3 10.7 1.0 FE3 A:SF41103 2.7 10.9 1.0 FE2 A:SF41103 2.7 10.2 1.0 FE4 A:SF41103 2.8 11.0 1.0 CB A:CYS53 3.4 9.8 1.0 N A:CYS53 3.7 11.0 1.0 CA A:CYS53 3.9 11.0 1.0 S1 A:SF41103 3.9 12.2 1.0 O A:CYS53 4.0 10.7 1.0 O A:HOH1422 4.0 11.0 1.0 CB A:VAL55 4.0 11.9 1.0 C A:CYS53 4.1 12.3 1.0 CG2 A:VAL55 4.3 12.3 1.0 N A:VAL55 4.5 10.0 1.0 CD A:PRO234 4.5 10.0 1.0 SG A:CYS50 4.7 10.2 1.0 SG A:CYS57 4.7 11.2 1.0 SG A:CYS88 4.7 11.8 1.0 CA A:VAL55 4.8 10.1 1.0 C A:TYR52 4.9 10.7 1.0 N A:ALA54 4.9 10.8 1.0

Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:10.2 occ:1.00 FE2 A:SF41103 0.0 10.2 1.0 S4 A:SF41103 2.2 11.5 1.0 SG A:CYS57 2.2 11.2 1.0 S3 A:SF41103 2.3 10.7 1.0 S1 A:SF41103 2.3 12.2 1.0 FE3 A:SF41103 2.7 10.9 1.0 FE4 A:SF41103 2.7 11.0 1.0 FE1 A:SF41103 2.7 10.4 1.0 CB A:CYS57 3.2 11.0 1.0 S2 A:SF41103 3.9 10.9 1.0 CD1 A:ILE235 4.2 10.8 1.0 N A:CYS57 4.2 10.7 1.0 CB A:VAL55 4.3 11.9 1.0 CA A:CYS57 4.3 10.3 1.0 CG1 A:ILE235 4.3 11.9 1.0 CB A:ILE235 4.4 10.3 1.0 CG1 A:VAL55 4.4 11.3 1.0 SG A:CYS50 4.6 10.2 1.0 CB A:CYS50 4.6 11.4 1.0 SG A:CYS53 4.8 10.4 1.0 CD2 A:LEU87 4.9 11.2 1.0 SG A:CYS88 4.9 11.8 1.0

Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:10.9 occ:1.00 FE3 A:SF41103 0.0 10.9 1.0 SG A:CYS50 2.3 10.2 1.0 S4 A:SF41103 2.3 11.5 1.0 S2 A:SF41103 2.3 10.9 1.0 S1 A:SF41103 2.3 12.2 1.0 FE2 A:SF41103 2.7 10.2 1.0 FE4 A:SF41103 2.7 11.0 1.0 FE1 A:SF41103 2.7 10.4 1.0 CB A:CYS50 3.1 11.4 1.0 S3 A:SF41103 3.9 10.7 1.0 CB A:TYR52 4.2 9.7 1.0 CA A:GLY91 4.3 9.5 1.0 N A:GLY91 4.3 11.1 1.0 N A:CYS53 4.3 11.0 1.0 SG A:CYS88 4.6 11.8 1.0 CA A:CYS50 4.6 10.2 1.0 SG A:CYS57 4.6 11.2 1.0 CB A:CYS57 4.8 11.0 1.0 N A:TYR52 4.8 9.9 1.0 SG A:CYS53 4.9 10.4 1.0 CA A:TYR52 4.9 10.4 1.0 CD2 A:TYR52 4.9 10.4 1.0 O A:CYS53 4.9 10.7 1.0

Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:11.0 occ:1.00 FE4 A:SF41103 0.0 11.0 1.0 S1 A:SF41103 2.2 12.2 1.0 SG A:CYS88 2.3 11.8 1.0 S3 A:SF41103 2.3 10.7 1.0 S2 A:SF41103 2.3 10.9 1.0 FE3 A:SF41103 2.7 10.9 1.0 FE2 A:SF41103 2.7 10.2 1.0 FE1 A:SF41103 2.8 10.4 1.0 CB A:CYS88 3.3 11.3 1.0 N A:CYS88 3.8 9.5 1.0 S4 A:SF41103 3.9 11.5 1.0 CA A:CYS88 4.1 10.5 1.0 CD A:PRO234 4.4 10.0 1.0 N A:GLY91 4.4 11.1 1.0 CD1 A:ILE235 4.5 10.8 1.0 CG A:PRO234 4.5 10.8 1.0 NZ A:LYS90 4.6 11.8 1.0 O A:HOH1422 4.6 11.0 1.0 C A:CYS88 4.7 12.3 1.0 SG A:CYS53 4.8 10.4 1.0 SG A:CYS57 4.8 11.2 1.0 CB A:PRO234 4.8 11.2 1.0 SG A:CYS50 4.8 10.2 1.0 O A:CYS88 4.9 11.0 1.0 CB A:LYS90 4.9 12.8 1.0 CA A:GLY91 4.9 9.5 1.0

Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:11.1 occ:1.00 FE1 B:SF4301 0.0 11.1 1.0 S3 B:SF4301 2.3 11.3 1.0 SG B:CYS157 2.3 11.7 1.0 S4 B:SF4301 2.3 13.1 1.0 S2 B:SF4301 2.3 11.6 1.0 FE2 B:SF4301 2.7 12.2 1.0 FE4 B:SF4301 2.7 11.6 1.0 FE3 B:SF4301 2.8 12.2 1.0 CB B:CYS157 3.2 11.3 1.0 CA B:CYS157 3.8 11.7 1.0 S1 B:SF4301 3.9 12.2 1.0 OG1 B:THR159 3.9 12.3 1.0 CB B:THR161 4.0 10.3 1.0 CG B:MET162 4.2 13.8 1.0 CD B:PRO158 4.3 12.0 1.0 OG1 B:THR161 4.4 9.9 1.0 C B:CYS157 4.5 11.2 1.0 CG2 B:THR161 4.6 12.0 1.0 N B:PRO158 4.6 12.6 1.0 SG B:CYS15 4.6 13.3 1.0 SG B:CYS18 4.8 10.9 1.0 SG B:CYS12 4.9 12.6 1.0 N B:MET162 4.9 11.8 1.0 N B:THR159 5.0 13.4 1.0

Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:12.2 occ:1.00 FE2 B:SF4301 0.0 12.2 1.0 SG B:CYS18 2.3 10.9 1.0 S3 B:SF4301 2.3 11.3 1.0 S4 B:SF4301 2.3 13.1 1.0 S1 B:SF4301 2.3 12.2 1.0 FE1 B:SF4301 2.7 11.1 1.0 FE3 B:SF4301 2.7 12.2 1.0 FE4 B:SF4301 2.8 11.6 1.0 CB B:CYS18 3.2 10.5 1.0 S2 B:SF4301 3.9 11.6 1.0 N B:CYS18 3.9 11.2 1.0 O B:HOH410 4.0 13.1 1.0 CA B:CYS18 4.2 11.4 1.0 CG B:PRO71 4.4 17.7 1.0 N B:GLY17 4.6 11.4 1.0 SG B:CYS15 4.7 13.3 1.0 CB B:PRO71 4.7 14.3 1.0 N B:ARG16 4.7 10.8 1.0 SG B:CYS12 4.7 12.6 1.0 SG B:CYS157 4.8 11.7 1.0 CA B:ARG16 4.8 12.2 1.0 CG2 B:VAL53 4.9 12.8 1.0 C B:ARG16 5.0 9.9 1.0

Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:12.2 occ:1.00 FE3 B:SF4301 0.0 12.2 1.0 S2 B:SF4301 2.3 11.6 1.0 S4 B:SF4301 2.3 13.1 1.0 SG B:CYS15 2.3 13.3 1.0 S1 B:SF4301 2.3 12.2 1.0 FE2 B:SF4301 2.7 12.2 1.0 FE1 B:SF4301 2.8 11.1 1.0 FE4 B:SF4301 2.8 11.6 1.0 CB B:CYS15 3.5 10.8 1.0 N B:CYS15 3.5 10.4 1.0 N B:ARG16 3.8 10.8 1.0 CA B:CYS15 3.9 11.4 1.0 S3 B:SF4301 3.9 11.3 1.0 N B:GLY17 4.1 11.4 1.0 C B:CYS15 4.2 12.2 1.0 CD B:PRO158 4.3 12.0 1.0 OG1 B:THR13 4.3 11.4 1.0 C B:ALA14 4.5 12.9 1.0 N B:ALA14 4.6 11.0 1.0 CA B:ARG16 4.6 12.2 1.0 SG B:CYS18 4.7 10.9 1.0 SG B:CYS12 4.7 12.6 1.0 SG B:CYS157 4.7 11.7 1.0 CA B:ALA14 4.8 10.9 1.0 CG B:PRO158 4.8 12.7 1.0 C B:ARG16 4.8 9.9 1.0 N B:CYS18 4.9 11.2 1.0 CA B:GLY17 4.9 11.6 1.0

Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:11.6 occ:1.00 FE4 B:SF4301 0.0 11.6 1.0 S2 B:SF4301 2.3 11.6 1.0 SG B:CYS12 2.3 12.6 1.0 S1 B:SF4301 2.3 12.2 1.0 S3 B:SF4301 2.3 11.3 1.0 FE1 B:SF4301 2.7 11.1 1.0 FE2 B:SF4301 2.8 12.2 1.0 FE3 B:SF4301 2.8 12.2 1.0 CB B:CYS12 3.4 11.1 1.0 CA B:CYS12 3.8 13.4 1.0 S4 B:SF4301 3.9 13.1 1.0 N B:ALA14 4.1 11.0 1.0 N B:THR13 4.1 12.6 1.0 OG1 B:THR161 4.3 9.9 1.0 CG B:PRO71 4.3 17.7 1.0 C B:CYS12 4.4 10.5 1.0 CB B:THR161 4.5 10.3 1.0 CG2 B:THR161 4.5 12.0 1.0 CA B:ALA14 4.5 10.9 1.0 SG B:CYS157 4.8 11.7 1.0 N B:CYS15 4.8 10.4 1.0 SG B:CYS18 4.8 10.9 1.0 OG1 B:THR159 4.8 12.3 1.0

Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:16.6 occ:1.00 FE1 B:SF4302 0.0 16.6 1.0 SG B:CYS77 2.3 16.9 1.0 S4 B:SF4302 2.3 14.7 1.0 S3 B:SF4302 2.3 16.5 1.0 S2 B:SF4302 2.3 15.7 1.0 FE4 B:SF4302 2.7 15.8 1.0 FE2 B:SF4302 2.7 16.3 1.0 FE3 B:SF4302 2.8 14.6 1.0 CB B:CYS77 3.3 19.9 1.0 N B:CYS77 3.8 13.7 1.0 S1 B:SF4302 3.9 14.4 1.0 CA B:CYS77 4.2 18.6 1.0 N B:HIS76 4.5 13.5 1.0 CD2 B:TYR123 4.5 18.8 1.0 CB B:PRO80 4.6 19.6 1.0 SG B:CYS121 4.6 15.6 1.0 CD B:PRO81 4.6 26.5 1.0 SG B:CYS74 4.7 14.7 1.0 CB B:ARG75 4.7 13.7 1.0 SG B:CYS82 4.8 16.8 1.0 CE2 B:TYR123 4.8 17.7 1.0 CA B:PRO80 4.8 19.9 1.0 N B:ARG75 4.8 12.4 1.0 C B:HIS76 4.9 13.1 1.0 CA B:HIS76 4.9 13.1 1.0 C B:ARG75 5.0 12.2 1.0

Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 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 - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:16.3 occ:1.00 FE2 B:SF4302 0.0 16.3 1.0 S3 B:SF4302 2.2 16.5 1.0 SG B:CYS82 2.3 16.8 1.0 S4 B:SF4302 2.3 14.7 1.0 S1 B:SF4302 2.4 14.4 1.0 FE4 B:SF4302 2.7 15.8 1.0 FE1 B:SF4302 2.7 16.6 1.0 FE3 B:SF4302 2.7 14.6 1.0 CB B:CYS82 3.1 21.5 1.0 S2 B:SF4302 3.9 15.7 1.0 CB B:PRO80 4.2 19.6 1.0 N B:CYS82 4.2 22.0 1.0 CA B:CYS82 4.2 20.4 1.0 CG1 B:VAL103 4.4 19.0 1.0 SG B:CYS74 4.7 14.7 1.0 SG B:CYS121 4.8 15.6 1.0 CE B:LYS137 4.8 12.6 1.0 SG B:CYS77 4.9 16.9 1.0 CA B:PRO80 4.9 19.9 1.0

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