Iron in PDB 8bqj: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 5 Min

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 5 Min, PDB code: 8bqj 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)	95.60 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.351, 150.55, 64.941, 90, 90, 90
R / Rfree (%)	21.4 / 24.5

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 5 Min also contains other interesting chemical elements:

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 5 Min (pdb code 8bqj). 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 5 Min, PDB code: 8bqj:
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 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:23.8 occ:1.00 FE1 A:SF41103 0.0 23.8 1.0 S2 A:SF41103 2.3 22.7 1.0 SG A:CYS53 2.3 24.3 1.0 S4 A:SF41103 2.3 24.5 1.0 S3 A:SF41103 2.3 23.2 1.0 FE3 A:SF41103 2.7 27.2 1.0 FE4 A:SF41103 2.7 23.0 1.0 FE2 A:SF41103 2.8 22.1 1.0 CB A:CYS53 3.3 24.3 1.0 N A:CYS53 3.8 24.6 1.0 CA A:CYS53 3.8 24.4 1.0 O A:CYS53 3.8 22.7 1.0 S1 A:SF41103 3.9 23.8 1.0 C A:CYS53 4.0 24.0 1.0 CB A:VAL55 4.0 20.4 1.0 CG2 A:VAL55 4.1 20.1 1.0 N A:VAL55 4.6 20.9 1.0 SG A:CYS50 4.6 23.2 1.0 CD A:PRO234 4.7 23.4 1.0 SG A:CYS57 4.7 26.2 1.0 SG A:CYS88 4.8 20.7 1.0 N A:ALA54 4.8 23.1 1.0 CA A:VAL55 4.9 21.1 1.0 C A:TYR52 5.0 26.1 1.0

Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:22.1 occ:1.00 FE2 A:SF41103 0.0 22.1 1.0 S1 A:SF41103 2.2 23.8 1.0 SG A:CYS57 2.3 26.2 1.0 S4 A:SF41103 2.3 24.5 1.0 S3 A:SF41103 2.3 23.2 1.0 FE3 A:SF41103 2.7 27.2 1.0 FE4 A:SF41103 2.7 23.0 1.0 FE1 A:SF41103 2.8 23.8 1.0 CB A:CYS57 3.2 23.8 1.0 S2 A:SF41103 3.9 22.7 1.0 CD1 A:ILE235 4.0 23.2 1.0 N A:CYS57 4.2 22.9 1.0 CG1 A:ILE235 4.3 23.4 1.0 CB A:VAL55 4.3 20.4 1.0 CA A:CYS57 4.3 23.8 1.0 CB A:ILE235 4.3 23.8 1.0 CG1 A:VAL55 4.4 20.1 1.0 SG A:CYS50 4.6 23.2 1.0 CB A:CYS50 4.6 24.1 1.0 CD2 A:LEU87 4.8 26.6 1.0 SG A:CYS53 4.8 24.3 1.0 CG2 A:VAL55 4.9 20.1 1.0 SG A:CYS88 4.9 20.7 1.0 N A:CYS88 5.0 22.6 1.0

Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:27.2 occ:1.00 FE3 A:SF41103 0.0 27.2 1.0 SG A:CYS50 2.2 23.2 1.0 S4 A:SF41103 2.3 24.5 1.0 S2 A:SF41103 2.3 22.7 1.0 S1 A:SF41103 2.3 23.8 1.0 FE1 A:SF41103 2.7 23.8 1.0 FE2 A:SF41103 2.7 22.1 1.0 FE4 A:SF41103 2.8 23.0 1.0 CB A:CYS50 3.1 24.1 1.0 S3 A:SF41103 3.9 23.2 1.0 CB A:TYR52 4.2 28.4 1.0 CA A:GLY91 4.2 22.8 1.0 N A:GLY91 4.3 22.8 1.0 N A:CYS53 4.4 24.6 1.0 CA A:CYS50 4.5 25.0 1.0 SG A:CYS88 4.6 20.7 1.0 CB A:CYS57 4.6 23.8 1.0 SG A:CYS57 4.6 26.2 1.0 O A:CYS53 4.8 22.7 1.0 SG A:CYS53 4.8 24.3 1.0 N A:TYR52 4.8 28.4 1.0 CA A:TYR52 4.9 28.2 1.0 CD2 A:TYR52 4.9 28.4 1.0 C A:CYS50 4.9 25.2 1.0

Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:23.0 occ:1.00 FE4 A:SF41103 0.0 23.0 1.0 S3 A:SF41103 2.2 23.2 1.0 S1 A:SF41103 2.3 23.8 1.0 S2 A:SF41103 2.3 22.7 1.0 SG A:CYS88 2.3 20.7 1.0 FE1 A:SF41103 2.7 23.8 1.0 FE2 A:SF41103 2.7 22.1 1.0 FE3 A:SF41103 2.8 27.2 1.0 CB A:CYS88 3.3 22.1 1.0 S4 A:SF41103 3.9 24.5 1.0 N A:CYS88 3.9 22.6 1.0 CA A:CYS88 4.1 23.0 1.0 CD A:PRO234 4.3 23.4 1.0 NZ A:LYS90 4.4 26.4 1.0 CD1 A:ILE235 4.5 23.2 1.0 N A:GLY91 4.5 22.8 1.0 CG A:PRO234 4.6 23.1 1.0 SG A:CYS53 4.7 24.3 1.0 C A:CYS88 4.7 23.1 1.0 SG A:CYS50 4.8 23.2 1.0 CE A:LYS90 4.9 26.0 1.0 O A:CYS88 4.9 23.3 1.0 CB A:PRO234 4.9 23.2 1.0 SG A:CYS57 4.9 26.2 1.0 CA A:GLY91 5.0 22.8 1.0 CB A:LYS90 5.0 24.9 1.0

Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.4 occ:1.00 FE1 B:SF4301 0.0 27.4 1.0 SG B:CYS157 2.2 26.9 1.0 S4 B:SF4301 2.2 26.2 1.0 S3 B:SF4301 2.3 26.4 1.0 S2 B:SF4301 2.3 27.1 1.0 FE2 B:SF4301 2.7 26.7 1.0 FE3 B:SF4301 2.7 27.0 1.0 FE4 B:SF4301 2.8 28.7 1.0 CB B:CYS157 3.2 26.0 1.0 CA B:CYS157 3.7 26.4 1.0 OG1 B:THR159 3.8 27.2 1.0 S1 B:SF4301 3.9 26.6 1.0 CD B:PRO158 4.0 26.9 1.0 CB B:THR161 4.2 25.8 1.0 CG B:MET162 4.2 28.8 1.0 C B:CYS157 4.5 27.4 1.0 N B:PRO158 4.5 27.5 1.0 SG B:CYS15 4.5 24.4 1.0 CG2 B:THR161 4.6 26.0 1.0 OG1 B:THR161 4.6 24.0 1.0 SG B:CYS18 4.8 25.4 1.0 N B:CYS157 4.9 27.2 1.0 N B:THR159 4.9 26.7 1.0 N B:MET162 5.0 30.3 1.0

Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.7 occ:1.00 FE2 B:SF4301 0.0 26.7 1.0 SG B:CYS18 2.2 25.4 1.0 S3 B:SF4301 2.3 26.4 1.0 S4 B:SF4301 2.3 26.2 1.0 S1 B:SF4301 2.3 26.6 1.0 FE1 B:SF4301 2.7 27.4 1.0 FE4 B:SF4301 2.7 28.7 1.0 FE3 B:SF4301 2.8 27.0 1.0 CB B:CYS18 3.2 26.6 1.0 S2 B:SF4301 3.9 27.1 1.0 N B:CYS18 3.9 26.3 1.0 CA B:CYS18 4.2 26.6 1.0 CG B:PRO71 4.5 35.5 1.0 SG B:CYS15 4.6 24.4 1.0 CB B:PRO71 4.7 34.5 1.0 N B:ARG16 4.7 28.2 1.0 N B:GLY17 4.7 28.6 1.0 SG B:CYS157 4.7 26.9 1.0 CA B:ARG16 4.8 28.4 1.0 SG B:CYS12 4.8 36.0 1.0 CG B:MET162 4.9 28.8 1.0 CG2 B:VAL53 5.0 37.4 1.0

Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.0 occ:1.00 FE3 B:SF4301 0.0 27.0 1.0 SG B:CYS15 2.2 24.4 1.0 S2 B:SF4301 2.3 27.1 1.0 S1 B:SF4301 2.3 26.6 1.0 S4 B:SF4301 2.3 26.2 1.0 FE4 B:SF4301 2.7 28.7 1.0 FE1 B:SF4301 2.7 27.4 1.0 FE2 B:SF4301 2.8 26.7 1.0 N B:CYS15 3.4 27.0 1.0 CB B:CYS15 3.5 25.3 1.0 N B:ARG16 3.6 28.2 1.0 CA B:CYS15 3.8 25.5 1.0 S3 B:SF4301 3.9 26.4 1.0 C B:CYS15 4.1 25.8 1.0 N B:GLY17 4.1 28.6 1.0 CD B:PRO158 4.2 26.9 1.0 OG1 B:THR13 4.3 30.0 1.0 C B:ALA14 4.4 27.8 1.0 N B:ALA14 4.5 29.7 1.0 CA B:ARG16 4.5 28.4 1.0 SG B:CYS18 4.5 25.4 1.0 CA B:ALA14 4.6 28.9 1.0 SG B:CYS157 4.8 26.9 1.0 SG B:CYS12 4.8 36.0 1.0 C B:ARG16 4.8 27.8 1.0 N B:CYS18 4.9 26.3 1.0 CG B:PRO158 4.9 27.4 1.0 CA B:GLY17 4.9 27.9 1.0

Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:28.7 occ:1.00 FE4 B:SF4301 0.0 28.7 1.0 S1 B:SF4301 2.2 26.6 1.0 S2 B:SF4301 2.3 27.1 1.0 S3 B:SF4301 2.3 26.4 1.0 SG B:CYS12 2.4 36.0 1.0 FE2 B:SF4301 2.7 26.7 1.0 FE3 B:SF4301 2.7 27.0 1.0 FE1 B:SF4301 2.8 27.4 1.0 CB B:CYS12 3.6 32.9 1.0 CA B:CYS12 3.8 31.6 1.0 S4 B:SF4301 3.9 26.2 1.0 N B:ALA14 4.1 29.7 1.0 N B:THR13 4.2 30.6 1.0 CG2 B:THR161 4.3 26.0 1.0 CA B:ALA14 4.4 28.9 1.0 C B:CYS12 4.4 31.1 1.0 CB B:THR161 4.5 25.8 1.0 CG B:PRO71 4.5 35.5 1.0 OG1 B:THR161 4.5 24.0 1.0 N B:CYS15 4.7 27.0 1.0 SG B:CYS18 4.7 25.4 1.0 SG B:CYS157 4.7 26.9 1.0 OG1 B:THR159 4.8 27.2 1.0 SG B:CYS15 4.9 24.4 1.0

Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:52.0 occ:1.00 FE1 B:SF4302 0.0 52.0 1.0 SG B:CYS77 2.0 41.3 1.0 S3 B:SF4302 2.3 53.0 1.0 S4 B:SF4302 2.3 53.9 1.0 S2 B:SF4302 2.3 56.6 1.0 FE2 B:SF4302 2.7 56.3 1.0 FE4 B:SF4302 2.7 52.5 1.0 FE3 B:SF4302 2.8 50.7 1.0 CB B:CYS77 3.6 44.4 1.0 S1 B:SF4302 3.9 51.7 1.0 N B:CYS77 4.0 46.7 1.0 CD2 B:TYR123 4.5 44.5 1.0 CA B:CYS77 4.5 46.1 1.0 CD B:PRO81 4.5 56.0 1.0 SG B:CYS74 4.5 44.4 1.0 N B:HIS76 4.6 46.0 1.0 SG B:CYS121 4.7 50.8 1.0 CE2 B:TYR123 4.7 45.7 1.0 SG B:CYS82 4.7 62.5 1.0 CB B:ARG75 4.8 40.2 1.0 N B:ARG75 4.8 41.5 1.0 CA B:PRO80 4.9 56.8 1.0 CB B:PRO80 5.0 58.6 1.0

Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:56.3 occ:1.00 FE2 B:SF4302 0.0 56.3 1.0 S3 B:SF4302 2.3 53.0 1.0 S4 B:SF4302 2.3 53.9 1.0 S1 B:SF4302 2.3 51.7 1.0 SG B:CYS82 2.3 62.5 1.0 FE1 B:SF4302 2.7 52.0 1.0 FE4 B:SF4302 2.7 52.5 1.0 FE3 B:SF4302 2.7 50.7 1.0 CB B:CYS82 3.0 59.0 1.0 S2 B:SF4302 3.9 56.6 1.0 N B:CYS82 4.0 57.1 1.0 CA B:CYS82 4.1 58.0 1.0 CG1 B:VAL103 4.4 38.0 1.0 CB B:PRO80 4.4 58.6 1.0 SG B:CYS77 4.5 41.3 1.0 SG B:CYS74 4.6 44.4 1.0 SG B:CYS121 4.6 50.8 1.0 CZ B:PHE105 4.8 51.3 1.0 CE1 B:PHE105 4.9 52.6 1.0 CA B:PRO80 4.9 56.8 1.0 CE B:LYS137 5.0 41.7 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