Atomistry » Magnesium » PDB 4gyi-4h99 » 4gzk
Atomistry »
  Magnesium »
    PDB 4gyi-4h99 »
      4gzk »

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

Protein crystallography data

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

Magnesium Binding Sites:

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 4gzk

Go back to Magnesium Binding Sites List in 4gzk
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 4gzk

Go back to Magnesium Binding Sites List in 4gzk
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 4gzk

Go back to Magnesium Binding Sites List in 4gzk
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 4gzk

Go back to Magnesium Binding Sites List in 4gzk
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 4gzk

Go back to Magnesium Binding Sites List in 4gzk
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

Reference:

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
Page generated: Mon Dec 14 16:59:44 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy