Magnesium in PDB 4ieg: Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (P1 Crystal Form)

The structure of Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (P1 Crystal Form), PDB code: 4ieg was solved by Z.Ren, M.C.Franklin, R.Ghose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	87.874, 94.470, 96.481, 75.16, 63.11, 83.79
R / Rfree (%)	21.7 / 27.8

The binding sites of Magnesium atom in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (P1 Crystal Form) (pdb code 4ieg). 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 and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (P1 Crystal Form), PDB code: 4ieg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (P1 Crystal Form)


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 (P1 Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:16.2 occ:1.00 OE1 A:GLU503 1.9 29.6 1.0 OD1 A:ASP470 1.9 26.7 1.0 O A:HOH1126 1.9 20.1 1.0 O A:HOH1121 2.1 15.7 1.0 O A:HOH1431 2.1 8.9 1.0 O A:VAL507 2.2 23.8 1.0 CD A:GLU503 2.8 31.4 1.0 CG A:ASP470 3.0 24.6 1.0 OE2 A:GLU503 3.1 30.9 1.0 C A:VAL507 3.3 23.3 1.0 OD2 A:ASP470 3.6 24.8 1.0 O A:GLY348 3.6 28.4 1.0 CB A:ASP470 4.2 24.9 1.0 CG A:GLU503 4.2 31.5 1.0 CA A:PHE508 4.2 23.3 1.0 N A:PHE508 4.2 23.4 1.0 CA A:VAL507 4.2 23.8 1.0 CA A:ASP470 4.3 25.6 1.0 CB A:VAL507 4.4 23.2 1.0 N A:VAL507 4.4 24.8 1.0 O A:HOH1196 4.5 26.4 1.0 CB A:GLU503 4.6 32.0 1.0 O A:HOH1313 4.7 25.4 1.0 N A:GLU471 4.7 26.0 1.0 C A:GLY348 4.8 28.6 1.0 O A:GLU471 4.9 26.3 1.0 CB A:PHE508 4.9 24.0 1.0 C A:ASP470 4.9 25.8 1.0 CG1 A:VAL507 5.0 22.4 1.0

Magnesium binding site 2 out of 4 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (P1 Crystal Form)


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 (P1 Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:18.9 occ:1.00 OE1 B:GLU503 1.9 27.4 1.0 O B:HOH1520 1.9 23.2 1.0 OD1 B:ASP470 1.9 24.6 1.0 O B:HOH1519 2.1 17.6 1.0 O B:HOH1518 2.1 19.3 1.0 O B:VAL507 2.2 19.4 1.0 CD B:GLU503 3.0 27.8 1.0 CG B:ASP470 3.1 22.6 1.0 C B:VAL507 3.3 18.3 1.0 O B:GLY348 3.5 21.4 1.0 OE2 B:GLU503 3.5 29.8 1.0 OD2 B:ASP470 3.7 24.6 1.0 CA B:PHE508 4.1 17.9 1.0 N B:PHE508 4.2 18.0 1.0 CB B:ASP470 4.2 21.5 1.0 CA B:VAL507 4.2 18.3 1.0 CA B:ASP470 4.2 21.5 1.0 CG B:GLU503 4.3 27.3 1.0 CB B:VAL507 4.3 17.8 1.0 CB B:GLU503 4.4 25.8 1.0 N B:VAL507 4.4 18.5 1.0 N B:GLU471 4.5 19.6 1.0 C B:GLY348 4.6 21.6 1.0 O B:GLU471 4.6 19.2 1.0 CG1 B:VAL507 4.7 17.6 1.0 O B:HOH1363 4.8 21.2 1.0 C B:ASP470 4.8 20.7 1.0 CB B:PHE508 4.9 18.0 1.0 CD2 B:PHE347 5.0 19.1 1.0 CD1 B:PHE508 5.0 18.6 1.0

Magnesium binding site 3 out of 4 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (P1 Crystal Form)


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 (P1 Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:16.4 occ:1.00 O C:HOH1534 1.9 15.5 1.0 OD1 C:ASP470 1.9 23.0 1.0 OE1 C:GLU503 1.9 26.7 1.0 O C:HOH1536 2.1 18.4 1.0 O C:VAL507 2.2 23.0 1.0 O C:HOH1535 2.2 19.7 1.0 CG C:ASP470 2.9 22.7 1.0 CD C:GLU503 3.0 27.2 1.0 C C:VAL507 3.3 22.7 1.0 OE2 C:GLU503 3.5 24.3 1.0 OD2 C:ASP470 3.6 22.4 1.0 O C:GLY348 3.7 25.5 1.0 CB C:ASP470 4.0 23.2 1.0 CA C:PHE508 4.1 21.8 1.0 CA C:ASP470 4.2 23.9 1.0 N C:PHE508 4.2 22.4 1.0 CA C:VAL507 4.3 23.1 1.0 CG C:GLU503 4.3 27.8 1.0 CB C:VAL507 4.4 22.7 1.0 N C:VAL507 4.4 23.9 1.0 N C:GLU471 4.5 24.3 1.0 CB C:GLU503 4.5 28.4 1.0 O C:GLU471 4.6 24.7 1.0 C C:ASP470 4.7 24.1 1.0 C C:GLY348 4.8 25.4 1.0 CB C:PHE508 4.9 22.2 1.0 CD2 C:PHE347 4.9 22.5 1.0 CG1 C:VAL507 4.9 22.1 1.0 O C:HOH1248 5.0 19.2 1.0

Magnesium binding site 4 out of 4 in the Structure and Interactions of the Rna-Dependent Rna Polymerase From Bacteriophage PHI12 (P1 Crystal Form)


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 (P1 Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:18.3 occ:1.00 OD1 D:ASP470 1.9 24.5 1.0 OE1 D:GLU503 1.9 28.9 1.0 O D:HOH1479 2.0 20.8 1.0 O D:HOH1478 2.0 23.6 1.0 O D:HOH1480 2.1 15.9 1.0 O D:VAL507 2.2 20.6 1.0 CD D:GLU503 2.9 29.7 1.0 CG D:ASP470 3.0 23.4 1.0 OE2 D:GLU503 3.3 31.8 1.0 C D:VAL507 3.3 19.5 1.0 O D:GLY348 3.4 24.3 1.0 OD2 D:ASP470 3.6 24.2 1.0 CA D:PHE508 4.1 18.6 1.0 N D:PHE508 4.1 18.9 1.0 CB D:ASP470 4.2 22.4 1.0 CG D:GLU503 4.2 28.9 1.0 CA D:ASP470 4.2 22.7 1.0 CA D:VAL507 4.3 19.7 1.0 CB D:VAL507 4.4 19.7 1.0 CB D:GLU503 4.4 28.3 1.0 N D:GLU471 4.5 21.6 1.0 C D:GLY348 4.6 24.5 1.0 N D:VAL507 4.6 19.9 1.0 O D:HOH1191 4.6 17.0 1.0 O D:GLU471 4.7 19.8 1.0 C D:ASP470 4.8 22.4 1.0 CB D:PHE508 4.9 18.8 1.0 N D:GLY348 5.0 23.2 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