Magnesium in PDB 6zj2: Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-

The structure of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-, PDB code: 6zj2 was solved by J.Huesa, A.Marina, P.Casino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.99 / 3.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.356, 111.514, 146.262, 90, 90.36, 90
R / Rfree (%)	26.6 / 31.9

The structure of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- (pdb code 6zj2). 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 Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-, PDB code: 6zj2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:72.9 occ:1.00 O B:SER58 2.0 87.1 1.0 OD2 B:ASP56 2.4 69.7 1.0 F1 B:BFD301 2.8 57.9 1.0 BE B:BFD301 2.8 58.8 1.0 OD1 B:ASP11 2.8 96.0 1.0 C B:SER58 3.2 87.8 1.0 CG B:ASP56 3.4 72.5 1.0 CE1 B:HIS12 3.6 92.7 1.0 CG B:ASP11 3.7 95.5 1.0 CB B:SER58 3.7 88.3 1.0 OD1 B:ASP56 3.7 72.9 1.0 F3 B:BFD301 3.7 59.0 1.0 F2 B:BFD301 3.9 58.3 1.0 OD2 B:ASP11 3.9 95.8 1.0 CA B:SER58 3.9 86.5 1.0 NZ B:LYS109 4.1 55.3 1.0 ND1 B:HIS12 4.1 93.0 1.0 OD1 B:ASP10 4.2 97.2 1.0 N B:MET59 4.3 90.3 1.0 N B:SER58 4.5 83.2 1.0 NE2 B:HIS12 4.5 93.3 1.0 CA B:MET59 4.7 93.1 1.0 OG B:SER58 4.7 88.5 1.0 CB B:ASP56 4.8 73.7 1.0 CB B:ASP11 4.9 94.9 1.0

Magnesium binding site 2 out of 4 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:71.2 occ:1.00 F1 A:BFD301 2.1 83.9 1.0 O A:SER58 2.3 66.6 1.0 OD2 A:ASP56 2.6 53.1 1.0 OD1 A:ASP11 2.8 64.7 1.0 OD2 A:ASP11 2.9 66.9 1.0 CG A:ASP11 3.2 66.0 1.0 BE A:BFD301 3.3 82.9 1.0 C A:SER58 3.3 65.6 1.0 CB A:SER58 3.4 65.9 1.0 CE1 A:HIS12 3.5 70.5 1.0 CG A:ASP56 3.5 52.6 1.0 OD1 A:ASP56 3.7 50.9 1.0 CA A:SER58 3.8 65.1 1.0 F3 A:BFD301 4.1 81.4 1.0 N A:SER58 4.1 63.0 1.0 NE2 A:HIS12 4.2 69.8 1.0 ND1 A:HIS12 4.2 69.1 1.0 F2 A:BFD301 4.4 82.9 1.0 N A:MET59 4.5 64.8 1.0 OG A:SER58 4.6 67.3 1.0 CB A:ASP11 4.7 65.2 1.0 CB A:ASP56 4.8 53.0 1.0

Magnesium binding site 3 out of 4 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:77.9 occ:1.00 OD1 D:ASP56 2.1 94.5 1.0 CG D:ASP56 3.3 94.7 1.0 CB D:SER58 3.4 107.5 1.0 NZ D:LYS109 3.4 43.9 1.0 O D:SER58 3.6 105.4 1.0 CE1 D:HIS12 3.7 53.3 1.0 N D:MET88 3.8 68.0 1.0 OD2 D:ASP56 3.8 93.5 1.0 CB D:MET88 3.9 67.1 1.0 OG D:SER58 4.0 106.9 1.0 OG1 D:THR87 4.0 67.9 1.0 N D:SER58 4.0 105.5 1.0 CA D:SER58 4.1 107.7 1.0 C D:SER58 4.2 108.1 1.0 CE D:LYS109 4.3 43.6 1.0 OD1 D:ASP11 4.3 67.9 1.0 ND1 D:HIS12 4.4 53.2 1.0 CB D:ASP56 4.4 95.2 1.0 CD D:LYS109 4.4 43.2 1.0 CA D:THR87 4.5 68.5 1.0 CA D:MET88 4.5 67.6 1.0 C D:THR87 4.6 67.6 1.0 NE2 D:HIS12 4.7 54.3 1.0 CB D:THR87 4.8 69.4 1.0

Magnesium binding site 4 out of 4 in the Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3-


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Rcsb From Salmonella Enterica Serovar Typhimurium Bound to Promoter Rpra in the Presence of Phosphomimetic BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:43.3 occ:1.00 OD2 C:ASP56 2.6 61.3 1.0 OD1 C:ASP56 2.8 62.5 1.0 CG C:ASP56 3.0 62.1 1.0 O C:SER58 3.0 74.4 1.0 CB C:SER58 3.7 75.2 1.0 C C:SER58 3.9 75.5 1.0 N C:SER58 3.9 73.2 1.0 CA C:SER58 4.1 74.4 1.0 OG1 C:THR87 4.3 62.8 1.0 N C:MET88 4.5 62.5 1.0 CB C:ASP56 4.5 61.1 1.0 OD1 C:ASP11 4.6 61.7 1.0 CE1 C:HIS12 4.6 59.6 1.0 OG C:SER58 4.8 75.1 1.0 CB C:MET88 4.8 64.9 1.0 N C:LEU57 4.8 66.3 1.0 OD1 C:ASP10 4.9 52.7 1.0 C C:LEU57 5.0 70.6 1.0

J.Huesa, J.Giner-Lamia, M.G.Pucciarelli, F.Paredes-Martinez, F.Garcia-Del Portillo, A.Marina, P.Casino. Structure-Based Analyses of Salmonella Rcsb Variants Unravel New Features of the Rcs Regulon Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAB060