Magnesium in PDB 7z8e: Crystal Structure of the Substrate-Binding Protein Yeja From S. Meliloti in Complex with Peptide Fragment

The structure of Crystal Structure of the Substrate-Binding Protein Yeja From S. Meliloti in Complex with Peptide Fragment, PDB code: 7z8e was solved by S.Morera, V.Vigouroux, D.Y.Travin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.35 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.9, 73.77, 140.83, 90, 90, 90
R / Rfree (%)	16.9 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of the Substrate-Binding Protein Yeja From S. Meliloti in Complex with Peptide Fragment (pdb code 7z8e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Substrate-Binding Protein Yeja From S. Meliloti in Complex with Peptide Fragment, PDB code: 7z8e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Substrate-Binding Protein Yeja From S. Meliloti in Complex with Peptide Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Substrate-Binding Protein Yeja From S. Meliloti in Complex with Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:38.6 occ:0.80 O A:HOH811 1.9 25.2 1.0 O A:HOH1035 2.0 44.5 1.0 OD2 A:ASP579 2.1 24.4 1.0 O A:HOH1180 2.3 39.2 1.0 O A:HOH938 2.6 30.8 1.0 CG A:ASP579 3.2 27.0 1.0 OD1 A:ASP579 3.7 24.7 1.0 O A:HOH1014 3.7 23.6 1.0 O A:SER64 4.1 20.0 1.0 CB A:SER64 4.3 20.8 0.5 NH2 A:ARG234 4.3 25.0 1.0 O A:HOH816 4.4 57.9 1.0 CB A:SER64 4.4 23.5 0.5 OH A:TYR235 4.4 26.0 1.0 CB A:ASP579 4.5 16.4 1.0 CE1 A:TYR235 4.6 19.6 1.0 O A:HOH722 4.7 30.1 1.0 O A:HOH827 4.7 40.7 1.0 C A:SER64 4.8 22.3 1.0 CA A:SER64 4.9 19.5 0.5 CA A:SER64 4.9 18.9 0.5 OG A:SER64 5.0 33.5 0.5

Magnesium binding site 2 out of 2 in the Crystal Structure of the Substrate-Binding Protein Yeja From S. Meliloti in Complex with Peptide Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Substrate-Binding Protein Yeja From S. Meliloti in Complex with Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:20.1 occ:0.50 O A:HOH708 1.9 36.5 1.0 O A:HOH1090 2.0 32.5 1.0 O A:HOH1165 2.0 41.5 1.0 O A:HOH800 2.1 38.2 1.0 O A:HOH1045 2.1 38.2 1.0 O A:SER43 3.9 24.6 1.0 OE1 A:GLU57 4.1 37.6 1.0 OE2 A:GLU42 4.2 28.9 1.0 O A:VAL58 4.2 25.8 1.0 O A:THR45 4.3 19.1 1.0 CG A:GLU42 4.8 31.3 1.0 O A:HOH969 4.8 31.5 1.0 CD A:GLU42 4.9 45.2 1.0

D.Y.Travin, R.Jouan, A.Vigouroux, S.Inaba-Inoue, J.Lachat, F.Haq, T.Timchenko, D.Sutormin, S.Dubiley, K.Beis, S.Morera, K.Severinov, P.Mergaert. Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition By Gram-Negative Bacteria Mbio 2023.
ISSN: ESSN 2150-7511
DOI: 10.1128/MBIO.00217-23