Magnesium 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:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas, PDB code: 3zeu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1340 b:15.8 occ:1.00 OD1 B:ASP11 2.0 13.8 1.0 O B:HOH2015 2.0 16.8 1.0 O B:HOH2017 2.1 15.4 1.0 O B:HOH2020 2.1 21.1 1.0 OE1 B:GLU12 2.1 16.9 1.0 O B:HOH2016 2.1 22.4 1.0 CG B:ASP11 3.1 18.8 1.0 CD B:GLU12 3.1 18.4 1.0 OE2 B:GLU12 3.4 21.9 1.0 OD2 B:ASP11 3.4 18.7 1.0 O2B B:ADP1343 3.8 26.4 0.2 O B:HOH2003 3.8 27.4 1.0 O2B B:AGS1342 4.0 25.9 0.8 O B:HOH2019 4.2 22.6 1.0 O2A B:ADP1343 4.3 16.7 0.2 O B:HOH2022 4.3 41.1 1.0 O2A B:AGS1342 4.3 11.3 0.8 N B:ASP11 4.4 11.7 1.0 CB B:ASP11 4.4 13.1 1.0 OD2 B:ASP300 4.4 16.6 1.0 CG B:GLU12 4.5 15.5 1.0 C B:ASP11 4.6 12.2 1.0 N B:GLU12 4.6 11.9 1.0 CA B:ASP11 4.7 10.2 1.0 O B:HOH2262 4.7 30.5 1.0 SG B:CYS10 4.7 18.8 1.0 CB B:CYS10 4.8 12.5 1.0 CG B:ASP300 4.8 15.5 1.0 CB B:GLU12 4.8 10.7 1.0 CB B:ASP300 4.9 11.2 1.0

Magnesium binding site 2 out of 4 in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg1380 b:35.0 occ:1.00 O B:HOH2140 2.1 45.8 1.0 O B:HOH2139 2.1 34.5 1.0 O B:HOH2142 2.1 29.7 1.0 O B:HOH2141 2.2 28.3 1.0 O B:HOH2265 2.4 42.4 1.0 OE1 D:GLU214 4.2 46.3 1.0 O B:ILE158 4.2 17.8 1.0 O B:HOH2144 4.2 24.6 1.0 O B:SER157 4.3 18.0 1.0 CA B:ILE158 4.4 18.9 1.0 C B:ILE158 4.5 19.8 1.0 OE2 B:GLU156 4.5 42.8 1.0 OE2 D:GLU214 4.5 47.8 1.0 O D:HOH2148 4.6 39.6 1.0 CD D:GLU214 4.8 50.5 1.0

Magnesium binding site 3 out of 4 in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1340 b:15.0 occ:1.00 OD1 E:ASP11 2.0 13.9 1.0 OE1 E:GLU12 2.0 15.0 1.0 O E:HOH2014 2.0 14.6 1.0 O E:HOH2015 2.1 20.9 1.0 O E:HOH2016 2.1 16.7 1.0 O E:HOH2019 2.1 18.8 1.0 CD E:GLU12 3.0 18.1 1.0 CG E:ASP11 3.1 17.7 1.0 OE2 E:GLU12 3.3 21.2 1.0 OD2 E:ASP11 3.5 18.3 1.0 O E:HOH2001 3.9 26.9 1.0 O2B E:ADP1342 4.0 22.3 0.3 O2B E:AGS1341 4.0 23.5 0.7 O E:HOH2018 4.3 22.3 1.0 O2A E:ADP1342 4.3 15.7 0.3 O E:HOH2021 4.3 34.9 1.0 O2A E:AGS1341 4.3 10.1 0.7 N E:ASP11 4.4 10.1 1.0 CG E:GLU12 4.4 16.1 1.0 CB E:ASP11 4.4 11.3 1.0 OD2 E:ASP300 4.5 15.9 1.0 C E:ASP11 4.5 10.5 1.0 N E:GLU12 4.6 11.0 1.0 CA E:ASP11 4.6 8.5 1.0 O E:HOH2246 4.6 31.9 1.0 SG E:CYS10 4.7 19.6 1.0 CB E:CYS10 4.8 11.9 1.0 CB E:GLU12 4.8 10.7 1.0 CB E:ASP300 4.9 11.2 1.0 CG E:ASP300 4.9 11.6 1.0 O E:ASP11 5.0 12.2 1.0 O3A E:AGS1341 5.0 25.4 0.7 PB E:AGS1341 5.0 21.0 0.7

Magnesium binding site 4 out of 4 in the Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Salmonella Typhimurium Ygjd-Yeaz Heterodimer Bound to Atpgammas within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1380 b:36.3 occ:1.00 O E:HOH2137 2.0 33.2 1.0 O E:HOH2249 2.0 43.0 1.0 O E:HOH2138 2.2 27.9 1.0 O E:HOH2139 4.2 23.0 1.0 O E:ILE158 4.3 16.9 1.0 O E:SER157 4.4 18.4 1.0 CA E:ILE158 4.4 16.0 1.0 C E:ILE158 4.6 18.4 1.0 OE2 E:GLU156 4.6 37.6 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