Magnesium in PDB 8j3o: Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh

All present enzymatic activity of Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh:
1.17.1.9;

The structure of Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh, PDB code: 8j3o was solved by W.Ma, Y.C.Zheng, Q.Geng, C.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.58 / 2.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.402, 60.156, 120.482, 90, 90, 111.02
R / Rfree (%)	22.6 / 27.8

The binding sites of Magnesium atom in the Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh (pdb code 8j3o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh, PDB code: 8j3o:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:38.4 occ:1.00 O B:LEU136 2.7 33.3 1.0 O B:ASP160 2.7 38.6 1.0 OH B:TYR266 3.0 37.4 1.0 O B:LEU137 3.2 32.2 1.0 OD1 B:ASP160 3.3 39.1 1.0 CG B:ASP160 3.4 40.1 1.0 CE2 B:TYR266 3.4 36.7 1.0 OD2 B:ASP160 3.5 41.2 1.0 C B:LEU137 3.7 35.6 1.0 CZ B:TYR266 3.7 36.5 1.0 C B:LEU136 3.7 35.7 1.0 CA B:LEU137 3.8 36.6 1.0 C B:ASP160 3.8 40.3 1.0 CD2 B:PHE162 4.1 38.5 1.0 N B:LEU137 4.2 36.1 1.0 CB B:ASP160 4.3 40.1 1.0 N B:ASN139 4.3 38.0 1.0 CE2 B:PHE162 4.4 38.3 1.0 CA B:ASP160 4.5 40.4 1.0 CB B:ASN139 4.6 38.5 1.0 N B:ARG138 4.6 35.9 1.0 CD2 B:TYR266 4.7 36.0 1.0 CA B:ASN139 4.7 36.5 1.0 N B:GLU161 4.7 39.1 1.0 CA B:GLU161 4.9 40.3 1.0 CA B:LEU136 5.0 34.0 1.0

Magnesium binding site 2 out of 3 in the Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:39.5 occ:1.00 O C:ASP160 2.5 39.9 1.0 OH C:TYR266 2.8 40.2 1.0 O C:LEU136 2.9 38.2 1.0 OD1 C:ASP160 3.0 41.2 1.0 CG C:ASP160 3.3 41.4 1.0 O C:LEU137 3.4 39.6 1.0 C C:ASP160 3.5 40.2 1.0 CE2 C:TYR266 3.6 40.6 1.0 OD2 C:ASP160 3.6 43.1 1.0 CZ C:TYR266 3.6 40.4 1.0 CD1 C:PHE162 3.7 39.3 1.0 C C:LEU137 3.8 38.1 1.0 CA C:LEU137 3.9 37.6 1.0 C C:LEU136 3.9 38.5 1.0 CE1 C:PHE162 3.9 39.6 1.0 CB C:ASP160 4.1 40.3 1.0 CA C:ASP160 4.3 40.0 1.0 N C:LEU137 4.4 36.8 1.0 N C:GLU161 4.4 39.6 1.0 N C:ASN139 4.5 38.6 1.0 CB C:ASN139 4.7 38.5 1.0 CA C:GLU161 4.7 39.2 1.0 N C:ARG138 4.7 38.8 1.0 CD2 C:TYR266 4.9 41.0 1.0 N C:PHE162 4.9 39.0 1.0 CA C:ASN139 4.9 38.0 1.0 CG C:PHE162 4.9 39.2 1.0 O C:HOH504 5.0 41.0 1.0 CE1 C:TYR266 5.0 41.2 1.0

Magnesium binding site 3 out of 3 in the Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Formate Dehydrogenase Wild-Type Enzyme From Candida Dubliniensis Complexed with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:38.3 occ:1.00 O D:ASP160 2.5 38.6 1.0 OH D:TYR266 2.7 39.4 1.0 O D:LEU136 2.8 37.5 1.0 OD1 D:ASP160 2.9 40.4 1.0 O D:LEU137 3.3 38.2 1.0 CG D:ASP160 3.4 41.2 1.0 CE2 D:TYR266 3.5 39.5 1.0 C D:ASP160 3.5 40.2 1.0 CZ D:TYR266 3.5 40.2 1.0 C D:LEU137 3.7 36.8 1.0 OD2 D:ASP160 3.7 41.9 1.0 CD1 D:PHE162 3.8 38.3 1.0 CA D:LEU137 3.8 36.7 1.0 C D:LEU136 3.9 37.3 1.0 CE1 D:PHE162 4.0 38.7 1.0 CB D:ASP160 4.2 40.7 1.0 N D:LEU137 4.3 35.4 1.0 CA D:ASP160 4.3 40.1 1.0 N D:GLU161 4.5 39.2 1.0 N D:ASN139 4.5 37.3 1.0 CA D:GLU161 4.7 37.8 1.0 CB D:ASN139 4.7 37.8 1.0 N D:ARG138 4.7 36.4 1.0 O D:HOH509 4.8 40.6 1.0 CD2 D:TYR266 4.8 40.2 1.0 N D:PHE162 4.9 37.5 1.0 CE1 D:TYR266 4.9 40.4 1.0 CA D:ASN139 4.9 37.1 1.0 CG D:PHE162 5.0 38.2 1.0

W.Ma, Q.Geng, C.Chen, Y.C.Zheng, H.L.Yu, J.H.Xu. Engineering A Formate Dehydrogenase For Nadph Regeneration. Chembiochem 00390 2023.
ISSN: ESSN 1439-7633
PubMed: 37455264
DOI: 10.1002/CBIC.202300390