Nickel in PDB 7vq6: Structure of A Specialized Glyoxalase From Gossypium Hirsutum

All present enzymatic activity of Structure of A Specialized Glyoxalase From Gossypium Hirsutum:
4.4.1.5;

The structure of Structure of A Specialized Glyoxalase From Gossypium Hirsutum, PDB code: 7vq6 was solved by H.Li, Y.M.Hu, L.H.Dai, C.C.Chen, J.W.Huang, W.D.Liu, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.48 / 1.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.255, 49.507, 58.413, 90, 99.38, 90
R / Rfree (%)	15.7 / 18.6

The binding sites of Nickel atom in the Structure of A Specialized Glyoxalase From Gossypium Hirsutum (pdb code 7vq6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of A Specialized Glyoxalase From Gossypium Hirsutum, PDB code: 7vq6:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of A Specialized Glyoxalase From Gossypium Hirsutum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of A Specialized Glyoxalase From Gossypium Hirsutum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:30.0 occ:1.00 OE1 B:GLU167 2.0 8.9 1.0 OE1 A:GLN31 2.0 8.8 1.0 OE1 A:GLU97 2.1 10.1 1.0 NE2 B:HIS125 2.2 8.4 1.0 O B:HOH424 2.3 13.8 1.0 O A:HOH333 2.3 10.1 1.0 CD A:GLN31 3.1 7.4 1.0 CD A:GLU97 3.1 10.1 1.0 CD B:GLU167 3.1 10.8 1.0 CE1 B:HIS125 3.2 8.3 1.0 CD2 B:HIS125 3.2 7.2 1.0 OE2 A:GLU97 3.5 14.4 1.0 NE2 A:GLN31 3.5 8.9 1.0 OE2 B:GLU167 3.7 13.9 1.0 ND1 B:HIS125 4.3 7.4 1.0 CG B:HIS125 4.3 7.2 1.0 CG B:GLU167 4.4 9.6 1.0 CG A:GLN31 4.4 7.4 1.0 CG A:GLU97 4.4 7.7 1.0 CB B:GLU167 4.4 8.2 1.0 CE2 B:PHE169 4.6 11.7 1.0 CB A:MET33 4.7 6.2 1.0 CG A:MET33 4.8 6.9 1.0 CB A:GLU97 4.8 6.8 1.0 O A:HOH443 4.8 21.9 1.0

Nickel binding site 2 out of 2 in the Structure of A Specialized Glyoxalase From Gossypium Hirsutum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of A Specialized Glyoxalase From Gossypium Hirsutum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:30.0 occ:1.00 OE1 A:GLU167 1.8 8.6 1.0 OE1 B:GLN31 2.1 8.1 1.0 O B:HOH348 2.1 10.8 1.0 NE2 A:HIS125 2.2 8.3 1.0 OE2 B:GLU97 2.2 9.5 1.0 O B:HOH437 2.4 13.7 1.0 CD A:GLU167 3.0 10.0 1.0 CD B:GLN31 3.1 7.9 1.0 CD2 A:HIS125 3.2 7.4 1.0 CD B:GLU97 3.2 11.1 1.0 CE1 A:HIS125 3.2 8.0 1.0 NE2 B:GLN31 3.4 8.8 1.0 OE1 B:GLU97 3.5 18.2 1.0 OE2 A:GLU167 3.6 14.8 1.0 CG A:GLU167 4.2 8.8 1.0 CB A:GLU167 4.3 7.9 1.0 CG A:HIS125 4.3 7.4 1.0 ND1 A:HIS125 4.3 6.9 1.0 CG B:GLN31 4.4 7.6 1.0 CG B:GLU97 4.5 9.1 1.0 O A:HOH330 4.6 30.0 1.0 CE2 A:PHE169 4.6 30.0 1.0 CB B:MET33 4.8 8.3 1.0 CG B:MET33 4.8 8.8 1.0 O B:HOH447 4.8 24.5 1.0 CB B:GLU97 4.9 7.7 1.0 CE1 A:PHE157 5.0 11.9 1.0

Y.Hu, H.Li, J.Min, Y.Yu, W.Liu, J.W.Huang, L.Zhang, Y.Yang, L.Dai, C.C.Chen, R.T.Guo. Crystal Structure and Biochemical Analysis of the Specialized Deoxynivalenol-Detoxifying Glyoxalase Spg From Gossypium Hirsutum. Int.J.Biol.Macromol. V. 200 388 2022.
ISSN: ISSN 0141-8130
PubMed: 35051496
DOI: 10.1016/J.IJBIOMAC.2022.01.055