Nickel in PDB 5yqw: Structure and Function of A Novel Periplasmic Chitooligosaccharide- Binding Protein From Marine Vibrio Bacteria

The structure of Structure and Function of A Novel Periplasmic Chitooligosaccharide- Binding Protein From Marine Vibrio Bacteria, PDB code: 5yqw was solved by W.Suginta, N.Sritho, A.Ranok, Y.Kitaoku, D.M.Bulmer, B.Van Den Berg, T.Fukamizo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.84 / 1.36
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	54.730, 54.730, 306.442, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 22.6

The binding sites of Nickel atom in the Structure and Function of A Novel Periplasmic Chitooligosaccharide- Binding Protein From Marine Vibrio Bacteria (pdb code 5yqw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Structure and Function of A Novel Periplasmic Chitooligosaccharide- Binding Protein From Marine Vibrio Bacteria, PDB code: 5yqw:

Nickel binding site 1 out of 1 in the Structure and Function of A Novel Periplasmic Chitooligosaccharide- Binding Protein From Marine Vibrio Bacteria


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure and Function of A Novel Periplasmic Chitooligosaccharide- Binding Protein From Marine Vibrio Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni603 b:15.9 occ:1.00 OG A:SER298 3.3 11.9 1.0 NE2 A:GLN471 3.3 14.1 1.0 N A:SER298 3.6 10.5 1.0 N A:ALA297 3.7 10.8 1.0 CB A:SER298 3.7 11.8 1.0 O A:HOH966 3.8 18.6 1.0 CA A:HIS313 3.9 15.0 1.0 CG A:GLN471 3.9 14.5 1.0 CD2 A:PHE296 3.9 14.4 1.0 CB A:PHE296 3.9 11.3 1.0 CA A:PHE296 3.9 11.6 1.0 C A:PHE296 4.0 10.9 1.0 CB A:ALA475 4.1 12.6 1.0 CD A:GLN471 4.1 14.0 1.0 CG2 A:THR312 4.1 16.4 1.0 N A:HIS313 4.2 15.3 1.0 CA A:SER298 4.2 10.3 1.0 CB A:HIS313 4.3 15.1 1.0 CA A:ALA297 4.4 10.7 1.0 CG A:PHE296 4.4 13.2 1.0 C A:ALA297 4.5 11.1 1.0 CD2 A:HIS313 4.5 14.9 1.0 C A:THR312 4.5 17.1 1.0 O A:THR312 4.5 15.3 1.0 CB A:ALA297 4.6 11.8 1.0 CG A:HIS313 4.7 15.3 1.0 O A:PHE296 4.9 12.8 1.0 O A:GLN471 5.0 11.9 1.0 C A:HIS313 5.0 15.8 1.0

W.Suginta, N.Sritho, A.Ranok, D.M.Bulmer, Y.Kitaoku, B.Van Den Berg, T.Fukamizo. Structure and Function of A Novel Periplasmic Chitooligosaccharide-Binding Protein From Marinevibriobacteria. J. Biol. Chem. V. 293 5150 2018.
ISSN: ESSN 1083-351X
PubMed: 29444825
DOI: 10.1074/JBC.RA117.001012