Zinc in PDB 3zeu: Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas

The structure of Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas, PDB code: 3zeu was solved by C.E.Nichols, H.K.Lamb, P.Thompson, K.El Omari, M.Lockyer, I.Charles, A.R.Hawkins, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.09 / 1.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.214, 68.084, 87.624, 107.66, 92.63, 116.45
R / Rfree (%)	15.9 / 18.6

The structure of Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas (pdb code 3zeu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas, PDB code: 3zeu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1339 b:17.9 occ:1.00 O1B B:AGS1342 2.0 29.1 0.8 O1B B:ADP1343 2.0 25.2 0.2 OD1 B:ASP300 2.0 18.5 1.0 NE2 B:HIS111 2.1 12.5 1.0 NE2 B:HIS115 2.1 13.2 1.0 S1G B:AGS1342 2.8 25.8 0.8 CE1 B:HIS111 3.0 15.0 1.0 CG B:ASP300 3.0 15.5 1.0 CD2 B:HIS115 3.0 13.8 1.0 CD2 B:HIS111 3.1 13.4 1.0 CE1 B:HIS115 3.1 11.9 1.0 PB B:AGS1342 3.3 21.5 0.8 O1A B:AGS1342 3.3 16.9 0.8 OD2 B:ASP300 3.4 16.6 1.0 PB B:ADP1343 3.4 21.7 0.2 O1A B:ADP1343 3.4 16.3 0.2 O2A B:ADP1343 3.6 16.7 0.2 O3A B:AGS1342 3.8 26.4 0.8 PA B:AGS1342 3.8 13.9 0.8 PA B:ADP1343 3.8 16.1 0.2 O B:HOH2009 3.8 19.5 1.0 PG B:AGS1342 3.9 22.3 0.8 O3A B:ADP1343 3.9 20.8 0.2 O3B B:AGS1342 3.9 18.6 0.8 ND1 B:HIS111 4.1 15.0 1.0 ND1 B:HIS115 4.2 10.5 1.0 CG B:HIS111 4.2 12.3 1.0 CG B:HIS115 4.2 8.9 1.0 O2A B:AGS1342 4.2 11.3 0.8 O2G B:AGS1342 4.2 26.2 0.8 O3B B:ADP1343 4.3 19.7 0.2 CB B:ASP300 4.3 11.2 1.0 O2B B:ADP1343 4.3 26.4 0.2 O2B B:AGS1342 4.4 25.9 0.8 CA B:ASP300 4.5 9.4 1.0 CE B:MET304 4.6 13.7 1.0 N B:ASP300 4.6 10.0 1.0 CB B:SER136 5.0 14.1 1.0

Zinc binding site 2 out of 2 in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1339 b:16.9 occ:1.00 OD1 E:ASP300 1.9 15.2 1.0 O1B E:AGS1341 2.0 26.6 0.7 NE2 E:HIS115 2.0 12.4 1.0 NE2 E:HIS111 2.1 15.5 1.0 O1B E:ADP1342 2.1 25.5 0.3 S1G E:AGS1341 2.7 25.1 0.7 CG E:ASP300 2.9 11.6 1.0 CD2 E:HIS115 3.0 12.5 1.0 CE1 E:HIS115 3.0 12.3 1.0 CE1 E:HIS111 3.1 13.1 1.0 CD2 E:HIS111 3.1 11.4 1.0 O1A E:AGS1341 3.2 18.6 0.7 PB E:AGS1341 3.3 21.0 0.7 OD2 E:ASP300 3.3 15.9 1.0 O1A E:ADP1342 3.4 16.9 0.3 PB E:ADP1342 3.5 19.0 0.3 O2A E:ADP1342 3.6 15.7 0.3 PG E:AGS1341 3.8 18.8 0.7 PA E:AGS1341 3.8 13.4 0.7 O3A E:AGS1341 3.8 25.4 0.7 PA E:ADP1342 3.9 15.6 0.3 O3A E:ADP1342 3.9 20.6 0.3 O E:HOH2006 3.9 17.0 1.0 O3B E:AGS1341 3.9 17.1 0.7 O2G E:AGS1341 4.1 22.2 0.7 O3B E:ADP1342 4.1 19.6 0.3 ND1 E:HIS115 4.1 9.5 1.0 CG E:HIS115 4.1 11.2 1.0 ND1 E:HIS111 4.2 14.1 1.0 CG E:HIS111 4.2 11.2 1.0 O2A E:AGS1341 4.3 10.1 0.7 CB E:ASP300 4.3 11.2 1.0 O2B E:AGS1341 4.4 23.5 0.7 CA E:ASP300 4.6 12.2 1.0 O2B E:ADP1342 4.6 22.3 0.3 CE E:MET304 4.6 14.2 1.0 N E:ASP300 4.6 11.3 1.0 CB E:SER136 4.9 17.4 1.0

C.E.Nichols, H.K.Lamb, P.Thompson, K.E.Omari, M.Lockyer, I.Charles, A.R.Hawkins, D.K.Stammers. Crystal Structure of the Dimer of Two Essential Salmonella Typhimurium Proteins, Ygjd & Yeaz and Calorimetric Evidence For the Formation of A Ternary Ygjd-Yeaz-Yjee Complex. Protein Sci. V. 22 628 2013.
ISSN: ISSN 0961-8368
PubMed: 23471679
DOI: 10.1002/PRO.2247