Magnesium in PDB 5sy4: Atomic Resolution Structure of Reduced E. Coli Yajl

The structure of Atomic Resolution Structure of Reduced E. Coli Yajl, PDB code: 5sy4 was solved by M.A.Wilson, J.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.52 / 0.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.875, 78.313, 99.434, 90.00, 90.00, 90.00
R / Rfree (%)	11.4 / 12.7

The binding sites of Magnesium atom in the Atomic Resolution Structure of Reduced E. Coli Yajl (pdb code 5sy4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Atomic Resolution Structure of Reduced E. Coli Yajl, PDB code: 5sy4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Atomic Resolution Structure of Reduced E. Coli Yajl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atomic Resolution Structure of Reduced E. Coli Yajl within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:22.9 occ:1.00 O A:HOH468 2.0 41.3 1.0 O A:HOH308 2.0 21.8 1.0 O A:HOH500 2.0 34.5 1.0 O A:HOH414 2.0 39.4 1.0 O A:HOH481 2.2 27.5 1.0 O A:HOH492 2.2 33.8 1.0 OE2 A:GLU137 4.0 19.4 0.6 O A:HOH326 4.3 27.8 1.0 O A:HOH317 4.3 20.3 1.0 O A:HOH372 4.3 32.2 1.0 O A:PRO120 4.3 12.3 0.5 OE1 A:GLN138 4.3 9.9 0.6 O A:PRO120 4.4 14.6 0.5 OE2 A:GLU137 4.4 17.8 0.4 CG A:PRO135 4.5 9.9 0.6 CG A:PRO135 4.5 13.1 0.4 OD1 A:ASP117 4.5 20.6 1.0 CB A:PRO135 4.7 9.8 0.6 O A:HOH323 4.7 17.7 1.0 CB A:PRO135 4.9 13.7 0.4 OE1 A:GLN138 5.0 16.5 0.4

Magnesium binding site 2 out of 2 in the Atomic Resolution Structure of Reduced E. Coli Yajl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atomic Resolution Structure of Reduced E. Coli Yajl within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:13.8 occ:1.00 O B:HOH332 2.0 15.8 1.0 O B:HOH373 2.0 13.6 1.0 O B:HOH372 2.1 16.3 1.0 O B:HOH487 2.1 18.6 1.0 O B:HOH516 2.1 18.7 1.0 O B:HOH490 2.1 15.9 1.0 OE2 B:GLU137 4.1 15.9 1.0 O B:HOH345 4.2 13.1 1.0 OD1 B:ASP117 4.3 13.2 1.0 O B:PRO120 4.3 10.7 1.0 CG B:PRO135 4.6 12.1 1.0 OE1 B:GLN138 4.6 10.4 1.0 CA B:PRO120 4.9 10.4 1.0 CB B:PRO135 4.9 11.4 1.0 O B:HOH347 5.0 16.4 1.0

J.Lin, E.Pozharski, M.A.Wilson. Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons. Biochemistry V. 56 391 2017.
ISSN: ISSN 1520-4995
PubMed: 27989121
DOI: 10.1021/ACS.BIOCHEM.6B00906