Magnesium in PDB 7ve5: C-Terminal Domain of Vrar

The structure of C-Terminal Domain of Vrar, PDB code: 7ve5 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)	22.31 / 2.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	60.349, 60.349, 171.521, 90, 90, 120
R / Rfree (%)	19.5 / 25.5

The binding sites of Magnesium atom in the C-Terminal Domain of Vrar (pdb code 7ve5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the C-Terminal Domain of Vrar, PDB code: 7ve5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the C-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 C-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:21.8 occ:1.00 OD2 A:ASP194 2.0 18.6 1.0 O A:HOH415 2.0 22.4 1.0 O C:HOH205 2.1 18.0 1.0 O A:HOH420 2.1 23.6 1.0 O C:HOH218 2.2 17.9 1.0 O A:HOH424 2.2 21.2 1.0 CG A:ASP194 3.1 18.0 1.0 CB A:ASP194 3.6 15.3 1.0 OP1 C:DA8 3.7 20.0 1.0 OD1 A:ASP194 4.2 22.4 1.0 O A:HOH406 4.2 25.9 1.0 O A:HOH408 4.4 21.4 1.0 O D:HOH226 4.4 20.9 1.0 O C:HOH239 4.4 24.2 1.0 O3' C:DA7 4.5 18.2 1.0 CB B:SER164 4.5 17.9 1.0 CA B:SER164 4.7 19.4 1.0 OE1 A:GLN193 4.7 27.8 1.0 P C:DA8 4.8 17.4 1.0 NE2 A:GLN197 4.9 19.8 1.0 N B:SER164 4.9 17.1 1.0 O B:GLY162 5.0 25.9 1.0

Magnesium binding site 2 out of 6 in the C-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 C-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:20.5 occ:1.00 O D:HOH222 1.9 19.9 1.0 O B:HOH412 2.0 19.8 1.0 O B:HOH420 2.0 19.3 1.0 OD2 B:ASP194 2.1 19.6 1.0 O D:HOH201 2.3 19.0 1.0 O B:HOH425 2.4 19.1 1.0 CG B:ASP194 3.2 18.9 1.0 CB B:ASP194 3.6 15.7 1.0 O B:HOH413 3.7 23.8 1.0 OP1 D:DA15 3.9 18.1 1.0 O B:HOH401 4.2 25.1 1.0 OD1 B:ASP194 4.3 19.3 1.0 O C:HOH224 4.3 14.3 1.0 O3' D:DT14 4.5 18.7 1.0 CB A:SER164 4.6 18.3 1.0 O B:HOH415 4.6 24.8 1.0 OE1 B:GLN193 4.7 26.4 1.0 NE2 B:GLN197 4.8 19.3 1.0 CA A:SER164 4.8 19.3 1.0 P D:DA15 4.9 19.4 1.0 CA B:ASP194 5.0 14.6 1.0 O A:GLY162 5.0 21.4 1.0

Magnesium binding site 3 out of 6 in the C-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of C-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:20.6 occ:1.00 OP2 C:DC4 2.0 16.7 1.0 O C:HOH225 2.1 17.8 1.0 O C:HOH223 2.2 17.6 1.0 P C:DC4 3.5 19.4 1.0 O C:HOH229 4.2 27.3 1.0 C3' C:DA3 4.2 16.9 1.0 O C:HOH227 4.2 22.0 1.0 O3' C:DA3 4.2 16.7 1.0 O5' C:DC4 4.3 17.0 1.0 OP1 C:DC4 4.4 18.3 1.0 O C:HOH219 4.5 18.9 1.0 C5 C:DC4 4.7 13.5 1.0 O C:HOH209 4.8 22.5 1.0 C6 C:DC4 4.8 16.2 1.0

Magnesium binding site 4 out of 6 in the C-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of C-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:26.2 occ:1.00 O C:HOH215 2.1 25.3 1.0 O D:HOH218 2.1 16.6 1.0 O C:HOH238 2.2 30.3 1.0 O C:HOH237 4.0 27.8 1.0 N3 C:DA11 4.3 21.1 1.0 C5' C:DT12 4.5 34.0 1.0 N3 D:DA10 4.6 14.3 1.0 O4' D:DC11 4.7 19.8 1.0 O4' C:DT12 4.8 30.7 1.0 C2' D:DA10 4.9 16.4 1.0 C2 C:DA11 4.9 25.2 1.0 C4' C:DT12 4.9 31.9 1.0

Magnesium binding site 5 out of 6 in the C-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of C-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:25.1 occ:1.00 OP2 D:DC11 2.1 18.9 1.0 O D:HOH229 2.2 19.5 1.0 O D:HOH225 2.2 18.4 1.0 P D:DC11 3.5 19.2 1.0 C3' D:DA10 4.2 17.4 1.0 O3' D:DA10 4.2 16.4 1.0 O5' D:DC11 4.4 22.6 1.0 O D:HOH227 4.4 23.6 1.0 O D:HOH230 4.5 20.3 1.0 O D:HOH215 4.5 21.0 1.0 OP1 D:DC11 4.5 17.2 1.0 C5' D:DA10 4.6 17.4 1.0 C5 D:DC11 4.8 14.2 1.0 O D:HOH202 4.9 24.0 1.0 C6 D:DC11 5.0 18.1 1.0 C4' D:DA10 5.0 18.2 1.0

Magnesium binding site 6 out of 6 in the C-Terminal Domain of Vrar


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of C-Terminal Domain of Vrar within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg102 b:28.9 occ:1.00 O D:HOH213 1.9 23.2 1.0 O C:HOH204 2.3 15.1 1.0 O2 D:DC18 3.9 20.8 1.0 C5' D:DT19 4.3 33.5 1.0 O4' D:DT19 4.4 32.2 1.0 C4' D:DT19 4.5 33.8 1.0 N3 C:DA3 4.6 12.1 1.0 N2 C:DG2 4.7 25.6 1.0 O4' C:DC4 4.8 16.7 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