Magnesium in PDB 7ve6: N-Terminal Domain of Vrar

The structure of N-Terminal Domain of Vrar, PDB code: 7ve6 was solved by J.V.Kumar, C.Chen, C.H.Hsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.93 / 2.77
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.713, 122.713, 67.522, 90, 90, 120
R / Rfree (%)	17.8 / 21.7

The structure of N-Terminal Domain of Vrar also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the N-Terminal Domain of Vrar (pdb code 7ve6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the N-Terminal Domain of Vrar, PDB code: 7ve6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the N-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of N-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:34.1 occ:1.00 O A:LEU57 1.8 36.0 1.0 F3 A:BEF301 1.9 32.0 1.0 OD1 A:ASP10 1.9 39.5 1.0 OD2 A:ASP55 2.4 32.5 1.0 CG A:ASP10 2.8 35.3 1.0 OD2 A:ASP10 3.0 36.8 1.0 C A:LEU57 3.0 36.6 1.0 HB3 A:LEU57 3.2 55.9 1.0 BE A:BEF301 3.4 30.2 1.0 CG A:ASP55 3.5 36.3 1.0 HG2 A:MET58 3.6 39.8 1.0 HA A:MET58 3.7 48.7 1.0 HG A:LEU57 3.7 54.4 1.0 OD1 A:ASP55 3.8 30.7 1.0 CB A:LEU57 3.8 46.6 1.0 CA A:LEU57 3.8 33.9 1.0 H A:ASP10 3.9 40.4 1.0 H A:LEU57 4.0 39.9 1.0 N A:MET58 4.0 43.4 1.0 N A:LEU57 4.2 33.2 1.0 F1 A:BEF301 4.2 41.9 1.0 CB A:ASP10 4.2 30.9 1.0 CG A:LEU57 4.3 45.3 1.0 OD1 A:ASP9 4.3 39.6 1.0 CA A:MET58 4.3 40.6 1.0 HD23 A:LEU57 4.4 57.7 1.0 HB3 A:ASP10 4.4 37.0 1.0 HE2 A:PHE85 4.4 55.8 1.0 HE2 A:HIS11 4.4 34.7 1.0 NE2 A:HIS11 4.5 28.9 1.0 F2 A:BEF301 4.5 26.7 1.0 CG A:MET58 4.5 33.1 1.0 CD2 A:HIS11 4.6 31.7 1.0 HG3 A:MET58 4.7 39.8 1.0 HB2 A:LEU57 4.7 55.9 1.0 N A:ASP10 4.7 33.6 1.0 HA A:LEU57 4.7 40.8 1.0 HD2 A:HIS11 4.8 38.1 1.0 HZ1 A:LYS105 4.8 34.2 1.0 HB2 A:ASP10 4.8 37.0 1.0 H A:MET58 4.8 52.1 1.0 CB A:ASP55 4.8 27.0 1.0 HZ2 A:LYS105 4.9 34.2 1.0 CE1 A:HIS11 4.9 28.1 1.0 HZ3 A:LYS105 4.9 34.2 1.0 CB A:MET58 4.9 32.1 1.0 CD2 A:LEU57 4.9 48.0 1.0 HB3 A:ASP55 4.9 32.5 1.0 CA A:ASP10 5.0 29.6 1.0

Magnesium binding site 2 out of 2 in the N-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of N-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:30.8 occ:1.00 F3 B:BEF301 1.8 32.4 1.0 OD1 B:ASP10 2.0 39.5 1.0 OD2 B:ASP55 2.2 26.3 1.0 O B:LEU57 2.7 20.7 1.0 BE B:BEF301 2.9 29.4 1.0 CG B:ASP10 3.1 26.6 1.0 OD1 B:ASP9 3.1 33.0 1.0 CG B:ASP55 3.1 26.3 1.0 H B:ASP10 3.4 35.8 1.0 OD2 B:ASP10 3.5 27.0 1.0 OD1 B:ASP55 3.5 29.6 1.0 HZ1 B:LYS105 3.6 33.4 1.0 F2 B:BEF301 3.7 21.2 1.0 HB3 B:LEU57 3.8 36.3 1.0 HZ3 B:LYS105 3.8 33.4 1.0 O B:HOH414 3.8 24.5 1.0 NE2 B:HIS11 3.9 26.4 1.0 CE1 B:HIS11 3.9 30.5 1.0 C B:LEU57 3.9 28.5 1.0 HE2 B:HIS11 4.0 31.7 1.0 NZ B:LYS105 4.0 27.8 1.0 HZ2 B:LYS105 4.1 33.4 1.0 HG3 B:MET58 4.1 27.0 1.0 CD2 B:HIS11 4.2 23.7 1.0 CG B:ASP9 4.2 30.9 1.0 HE1 B:HIS11 4.2 36.6 1.0 ND1 B:HIS11 4.2 21.0 1.0 F1 B:BEF301 4.2 27.8 1.0 N B:ASP10 4.2 29.8 1.0 H B:HIS11 4.3 27.6 1.0 CG B:HIS11 4.3 19.6 1.0 CB B:ASP10 4.4 24.2 1.0 CB B:ASP55 4.4 24.5 1.0 HG2 B:MET58 4.5 27.0 1.0 H B:LEU57 4.5 33.8 1.0 HB3 B:ASP55 4.5 29.4 1.0 HD2 B:HIS11 4.5 28.5 1.0 OD2 B:ASP9 4.6 35.5 1.0 CB B:LEU57 4.6 30.2 1.0 HB2 B:ASP55 4.7 29.4 1.0 CA B:LEU57 4.7 26.9 1.0 HA B:MET58 4.7 30.7 1.0 CA B:ASP10 4.7 23.0 1.0 N B:HIS11 4.8 23.0 1.0 CG B:MET58 4.8 22.4 1.0 HA B:ASP9 4.8 33.3 1.0 N B:LEU57 4.8 28.1 1.0 HB3 B:ASP10 4.8 29.1 1.0 HG B:LEU57 4.9 35.4 1.0 N B:MET58 5.0 28.7 1.0

J.V.Kumar, T.S.Tseng, Y.C.Lou, S.Y.Wei, T.H.Wu, H.C.Tang, Y.C.Chiu, C.H.Hsu, C.Chen. Structural Insights Into Dna Binding Domain of Vancomycin-Resistance-Associated Response Regulator in Complex with Its Promoter Dna From Staphylococcus Aureus. Protein Sci. V. 31 E4286 2022.
ISSN: ESSN 1469-896X
PubMed: 35481641
DOI: 10.1002/PRO.4286