Magnesium in PDB 4gzk: Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12

The structure of Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12, PDB code: 4gzk was solved by Z.Ren, M.Franklin, R.Ghose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.85 / 1.69
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	134.805, 72.320, 96.828, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 16.7

The binding sites of Magnesium atom in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (pdb code 4gzk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12, PDB code: 4gzk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:24.6 occ:1.00 O A:HOH1093 2.4 27.9 1.0 OE1 A:GLU269 2.6 29.3 1.0 OE2 A:GLU269 2.8 23.9 1.0 CD A:GLU269 2.9 23.8 1.0 O A:HOH1109 3.6 33.5 1.0 CG A:GLU269 4.1 19.7 1.0 O A:HOH1037 4.2 35.2 1.0

Magnesium binding site 2 out of 5 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:29.4 occ:1.00 O A:ASP626 2.2 28.4 1.0 O A:ILE629 2.3 25.2 1.0 O A:HOH1406 2.4 38.9 1.0 O A:HOH1611 2.5 39.0 1.0 O A:HOH1779 2.7 36.5 1.0 O A:HOH1697 2.7 48.0 1.0 C A:ILE629 3.3 24.0 1.0 O A:HOH1602 3.4 32.3 1.0 C A:ASP626 3.4 28.5 1.0 NE2 A:GLN634 3.8 23.9 1.0 OD1 A:ASP626 3.9 31.3 1.0 CA A:ARG630 3.9 24.9 1.0 N A:ARG630 4.0 24.2 1.0 N A:ILE629 4.0 23.8 1.0 C A:GLU627 4.2 29.5 1.0 CA A:GLU627 4.2 30.6 1.0 CG A:ASP626 4.2 31.0 1.0 N A:GLU627 4.2 29.5 1.0 O A:GLU627 4.3 29.8 1.0 CA A:ILE629 4.3 23.4 1.0 C A:ARG630 4.4 24.9 1.0 OD1 A:ASP631 4.5 34.2 1.0 CA A:ASP626 4.5 28.5 1.0 OD2 A:ASP626 4.5 35.0 1.0 N A:ASP631 4.5 25.3 1.0 O A:HOH1023 4.6 41.0 1.0 N A:GLU628 4.7 27.7 1.0 O A:HOH1560 4.8 55.2 1.0 O A:HOH1517 4.9 46.7 1.0 CB A:ASP626 5.0 29.0 1.0

Magnesium binding site 3 out of 5 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:40.5 occ:1.00 O A:HOH1789 2.1 40.5 1.0 O A:HOH1104 2.4 30.4 1.0 O A:HOH1215 2.4 41.6 1.0 O A:HOH1246 2.4 29.3 1.0 O A:HOH931 2.5 23.5 1.0 O A:HOH1939 2.7 43.3 1.0 O A:HOH1586 2.9 37.6 1.0 NZ A:LYS280 3.1 40.9 1.0 O A:HOH978 4.0 24.1 1.0 O A:HOH1131 4.0 30.4 1.0 N A:GLY255 4.2 21.1 1.0 CA A:GLY255 4.3 22.8 1.0 O A:HOH968 4.3 23.8 1.0 O A:HOH1147 4.3 29.1 1.0 O A:HOH1769 4.3 51.4 1.0 CE A:LYS280 4.4 40.9 1.0 O A:PHE291 4.5 13.8 1.0 CD A:LYS280 4.5 38.2 1.0 O A:HOH1340 4.5 33.4 1.0 O A:THR279 4.6 20.4 1.0 O A:ASP289 4.7 18.7 1.0 O A:HOH1943 4.7 50.8 1.0

Magnesium binding site 4 out of 5 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:23.9 occ:1.00 OE2 A:GLU503 2.0 26.6 1.0 OD1 A:ASP470 2.1 22.9 1.0 O A:GLY348 2.3 18.8 1.0 O A:HOH972 2.6 23.1 1.0 O A:HOH960 2.6 22.1 1.0 CD A:GLU503 3.1 24.3 1.0 CG A:ASP470 3.2 17.9 1.0 C A:GLY348 3.5 16.5 1.0 O A:HOH1126 3.5 29.6 1.0 CG A:GLU503 3.5 24.7 1.0 CA A:ASP470 3.7 13.8 1.0 O A:ASP469 3.9 19.6 1.0 CA A:ASP349 3.9 16.5 1.0 CB A:ASP470 4.0 14.1 1.0 O A:HOH1016 4.1 26.6 1.0 N A:ASP349 4.1 16.9 1.0 O A:HOH1000 4.2 27.4 1.0 OD2 A:ASP470 4.2 18.5 1.0 O A:VAL507 4.3 14.1 1.0 OE1 A:GLU503 4.3 26.1 1.0 N A:ASP470 4.5 14.3 1.0 C A:ASP469 4.5 16.5 1.0 N A:GLU471 4.6 12.8 1.0 CB A:ASP349 4.7 17.0 1.0 CA A:GLY348 4.7 16.3 1.0 C A:ASP470 4.7 13.3 1.0 O A:HOH1071 4.8 23.4 1.0 N A:VAL350 4.9 16.4 1.0 O A:HOH1433 4.9 39.3 1.0 N A:GLY348 5.0 15.5 1.0 C A:ASP349 5.0 16.7 1.0 CB A:GLU503 5.0 23.8 1.0

Magnesium binding site 5 out of 5 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:33.8 occ:1.00 OD2 A:ASP28 2.6 30.1 1.0 O A:HOH1310 3.6 48.4 1.0 CG A:ASP28 3.6 31.0 1.0 OD1 A:ASP28 3.9 35.2 1.0 O A:HOH1364 4.0 32.9 1.0 CB A:ASP28 4.9 29.3 1.0

Z.Ren, M.C Franklin, R.Ghose. Structure of the Rna-Directed Rna Polymerase From the Cystovirus 12. Proteins V. 81 1479 2013.
ISSN: ISSN 0887-3585
PubMed: 23568335
DOI: 10.1002/PROT.24297