Zinc in PDB 9jrr: Crystal Structure of Yjgk From Salmonella Typhimurium

The structure of Crystal Structure of Yjgk From Salmonella Typhimurium, PDB code: 9jrr was solved by M.D.Seo, S.Y.Choi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.37 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.082, 86.896, 91.174, 90, 90, 90
R / Rfree (%)	15.7 / 20.2

The binding sites of Zinc atom in the Crystal Structure of Yjgk From Salmonella Typhimurium (pdb code 9jrr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Yjgk From Salmonella Typhimurium, PDB code: 9jrr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Yjgk From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Yjgk From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:16.7 occ:0.74 OE2 A:GLU62 2.1 16.3 1.0 OD2 A:ASP69 2.2 26.5 1.0 NE2 A:HIS64 2.2 11.6 1.0 NE2 A:HIS128 2.3 14.4 1.0 CE1 A:HIS64 3.1 13.7 1.0 CD A:GLU62 3.2 17.0 1.0 CG A:ASP69 3.2 18.5 1.0 CE1 A:HIS128 3.2 14.0 1.0 CD2 A:HIS64 3.3 11.4 1.0 CD2 A:HIS128 3.3 14.3 1.0 OD1 A:ASP69 3.7 17.8 1.0 NE2 A:GLN71 3.7 18.1 1.0 CG A:GLU62 3.9 11.1 1.0 O A:HOH485 4.0 28.4 1.0 NZ A:LYS146 4.0 15.2 1.0 OE1 A:GLU62 4.1 16.6 1.0 ND1 A:HIS64 4.3 12.2 1.0 CB A:ASP69 4.3 13.7 1.0 CG A:HIS64 4.4 9.1 1.0 ND1 A:HIS128 4.4 10.6 1.0 CG A:HIS128 4.4 12.7 1.0 O A:HOH307 4.5 22.7 1.0 O A:HOH545 4.8 35.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Yjgk From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Yjgk From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:16.9 occ:1.00 OD2 B:ASP69 2.0 18.2 1.0 O B:HOH377 2.1 13.7 1.0 NE2 B:HIS64 2.2 11.3 1.0 NE2 B:HIS128 2.2 14.1 1.0 CD2 B:HIS64 3.1 11.3 1.0 OE2 B:GLU62 3.1 22.7 1.0 CG B:ASP69 3.1 16.0 1.0 CE1 B:HIS128 3.2 13.7 1.0 CE1 B:HIS64 3.2 12.5 1.0 CD2 B:HIS128 3.2 14.1 1.0 OD1 B:ASP69 3.6 14.2 1.0 NE2 B:GLN71 3.7 14.6 1.0 NZ B:LYS146 3.8 11.7 1.0 CD B:GLU62 3.9 19.0 1.0 O B:HOH302 4.2 28.5 1.0 CG B:GLU62 4.2 15.1 1.0 CG B:HIS64 4.2 8.8 1.0 ND1 B:HIS128 4.3 9.2 1.0 ND1 B:HIS64 4.3 9.5 1.0 CB B:ASP69 4.3 9.5 1.0 CG B:HIS128 4.3 11.2 1.0 O B:HOH503 4.4 29.6 1.0 CE B:LYS146 4.8 16.6 1.0 OE1 B:GLU62 4.9 21.6 1.0

S.Y.Choi, E.Kim, H.Yoon, H.N.Kim, J.H.Kim, S.H.Seok, M.D.Seo. Crystal Structure and Functional Characterization of Yjgk From Salmonella Typhimurium. Proteins 2025.
ISSN: ESSN 1097-0134
PubMed: 40525813
DOI: 10.1002/PROT.26854