Nickel in PDB 7w9y: Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel

The structure of Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel, PDB code: 7w9y was solved by H.Y.Cho, M.S.Nam, H.J.Hong, W.S.Song, S.I.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 1.93
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.036, 69.641, 87.609, 96.29, 91.03, 90.37
R / Rfree (%)	17 / 20.8

The binding sites of Nickel atom in the Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel (pdb code 7w9y). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel, PDB code: 7w9y:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:21.5 occ:1.00 NE2 A:HIS198 2.1 19.5 1.0 OD1 A:ASP194 2.2 16.9 1.0 NE2 A:HIS281 2.2 17.2 1.0 NE2 A:HIS267 2.2 16.8 1.0 CD2 A:HIS281 3.0 16.9 1.0 CD2 A:HIS198 3.0 18.5 1.0 CE1 A:HIS198 3.0 20.7 1.0 CD2 A:HIS267 3.1 19.3 1.0 CG A:ASP194 3.1 20.2 1.0 OD2 A:ASP194 3.3 22.4 1.0 CE1 A:HIS267 3.3 20.3 1.0 CE1 A:HIS281 3.4 18.4 1.0 CD1 A:LEU285 3.9 16.2 1.0 O A:HOH642 4.1 20.6 1.0 ND1 A:HIS198 4.1 14.7 1.0 CG A:HIS198 4.2 16.9 1.0 CG A:HIS281 4.3 14.9 1.0 CG A:HIS267 4.3 15.9 1.0 ND1 A:HIS267 4.4 16.1 1.0 ND1 A:HIS281 4.4 17.2 1.0 CB A:ASP194 4.5 12.6 1.0 N1N A:NAP501 4.5 18.4 1.0 O A:ASP194 4.7 14.1 1.0 CA A:ASP194 4.9 17.1 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:35.1 occ:1.00 NE2 B:HIS198 2.0 40.4 1.0 NE2 B:HIS281 2.2 38.5 1.0 OD1 B:ASP194 2.2 38.2 1.0 NE2 B:HIS267 2.5 27.6 1.0 CD2 B:HIS198 2.9 39.3 1.0 CD2 B:HIS281 2.9 33.8 1.0 CE1 B:HIS198 3.0 36.5 1.0 CG B:ASP194 3.1 34.1 1.0 CD2 B:HIS267 3.1 31.2 1.0 OD2 B:ASP194 3.2 37.4 1.0 CE1 B:HIS281 3.3 37.7 1.0 CE1 B:HIS267 3.6 28.4 1.0 ND1 B:HIS198 4.0 37.6 1.0 CG B:HIS198 4.0 36.8 1.0 O B:HOH634 4.1 31.8 1.0 CD1 B:LEU285 4.1 28.1 1.0 CG B:HIS281 4.2 40.0 1.0 ND1 B:HIS281 4.3 35.6 1.0 CG B:HIS267 4.4 33.1 1.0 CB B:ASP194 4.5 21.0 1.0 O B:ASP194 4.6 20.9 1.0 ND1 B:HIS267 4.6 29.3 1.0 N1N B:NAP501 4.7 33.9 1.0 CA B:ASP194 4.9 21.5 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni502 b:22.9 occ:1.00 NE2 C:HIS267 2.2 14.5 1.0 OD1 C:ASP194 2.2 21.8 1.0 NE2 C:HIS281 2.2 18.1 1.0 NE2 C:HIS198 2.2 15.7 1.0 CD2 C:HIS267 3.0 14.8 1.0 CD2 C:HIS281 3.0 18.6 1.0 CG C:ASP194 3.1 20.3 1.0 CD2 C:HIS198 3.1 22.0 1.0 CE1 C:HIS198 3.2 22.6 1.0 CE1 C:HIS267 3.3 18.1 1.0 OD2 C:ASP194 3.3 20.0 1.0 CE1 C:HIS281 3.3 19.6 1.0 CD1 C:LEU285 3.9 14.5 1.0 O C:HOH648 4.1 18.9 1.0 CG C:HIS267 4.2 15.8 1.0 CG C:HIS198 4.2 18.3 1.0 ND1 C:HIS198 4.2 19.4 1.0 CG C:HIS281 4.3 16.5 1.0 ND1 C:HIS267 4.3 16.3 1.0 ND1 C:HIS281 4.3 20.0 1.0 CB C:ASP194 4.5 14.0 1.0 O C:ASP194 4.7 16.3 1.0 N1N C:NAP501 4.7 21.9 1.0 CA C:ASP194 4.9 16.2 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Bacillus Subtilis Yugj in Complex with Nadp and Nickel within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni502 b:27.4 occ:1.00 OD1 D:ASP194 2.2 26.7 1.0 NE2 D:HIS198 2.2 24.4 1.0 NE2 D:HIS281 2.2 25.7 1.0 NE2 D:HIS267 2.3 22.6 1.0 CD2 D:HIS281 3.0 25.0 1.0 CD2 D:HIS267 3.1 24.2 1.0 CG D:ASP194 3.1 22.8 1.0 CD2 D:HIS198 3.1 24.9 1.0 CE1 D:HIS198 3.1 25.9 1.0 CE1 D:HIS281 3.3 26.9 1.0 OD2 D:ASP194 3.3 26.9 1.0 CE1 D:HIS267 3.5 23.1 1.0 CD1 D:LEU285 3.9 19.0 1.0 O D:HOH667 4.1 29.4 1.0 ND1 D:HIS198 4.2 23.5 1.0 CG D:HIS198 4.2 18.1 1.0 CG D:HIS281 4.2 26.9 1.0 CG D:HIS267 4.3 24.2 1.0 ND1 D:HIS281 4.3 25.3 1.0 ND1 D:HIS267 4.5 20.8 1.0 CB D:ASP194 4.5 15.1 1.0 N1N D:NAP501 4.5 23.4 1.0 O D:ASP194 4.7 13.3 1.0 CA D:ASP194 4.8 19.4 1.0

H.Y.Cho, M.S.Nam, H.J.Hong, W.S.Song, S.I.Yoon. Structural and Biochemical Analysis of the Furan Aldehyde Reductase Yugj From Bacillus Subtilis. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 35163804
DOI: 10.3390/IJMS23031882