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Magnesium in PDB 3m4o: Rna Polymerase II Elongation Complex B

Enzymatic activity of Rna Polymerase II Elongation Complex B

All present enzymatic activity of Rna Polymerase II Elongation Complex B:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex B, PDB code: 3m4o was solved by D.Wang, G.Zhu, X.Huang, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.57
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.114, 222.131, 191.782, 90.00, 100.99, 90.00
R / Rfree (%) 24.1 / 29.2

Other elements in 3m4o:

The structure of Rna Polymerase II Elongation Complex B also contains other interesting chemical elements:

Platinum (Pt) 1 atom
Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex B (pdb code 3m4o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Rna Polymerase II Elongation Complex B, PDB code: 3m4o:

Magnesium binding site 1 out of 1 in 3m4o

Go back to Magnesium Binding Sites List in 3m4o
Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Polymerase II Elongation Complex B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:9.1
occ:1.00
OD2 A:ASP483 2.0 48.8 1.0
OD1 A:ASP481 2.0 51.7 1.0
OD1 A:ASP485 2.0 59.1 1.0
O3' R:A10 2.1 0.6 1.0
OD1 A:ASP483 2.5 52.2 1.0
CG A:ASP483 2.6 52.6 1.0
CG A:ASP481 2.8 53.9 1.0
CG A:ASP485 2.9 56.9 1.0
OD2 A:ASP481 2.9 54.4 1.0
O2' R:A10 3.0 0.1 1.0
OD2 A:ASP485 3.1 57.1 1.0
C3' R:A10 3.2 0.8 1.0
C4' R:A10 3.5 0.5 1.0
C2' R:A10 3.7 0.0 1.0
CB A:ASP483 4.1 53.3 1.0
CB A:ASP481 4.3 55.0 1.0
CB A:ASP485 4.4 55.8 1.0
C5' R:A10 4.4 0.0 1.0
N A:ASP485 4.6 55.2 1.0
NH2 A:ARG446 4.6 64.0 1.0
O4' R:A10 4.6 0.6 1.0
N A:ASP483 4.7 54.5 1.0
N A:ASP481 4.7 56.9 1.0
N A:GLY484 4.7 53.1 1.0
CA A:ASP483 4.8 53.5 1.0
C1' R:A10 4.8 0.6 1.0
C A:ASP483 4.8 53.5 1.0
O A:ASP481 4.8 54.5 1.0
CA A:ASP485 4.8 55.3 1.0
C A:ASP481 4.9 55.2 1.0
CA A:ASP481 4.9 55.6 1.0

Reference:

D.Wang, G.Zhu, X.Huang, S.J.Lippard. X-Ray Structure and Mechanism of Rna Polymerase II Stalled at An Antineoplastic Monofunctional Platinum-Dna Adduct. Proc.Natl.Acad.Sci.Usa V. 107 9584 2010.
ISSN: ISSN 0027-8424
PubMed: 20448203
DOI: 10.1073/PNAS.1002565107
Page generated: Mon Dec 14 08:25:36 2020

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