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Magnesium in PDB 3s2d: Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U

Enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U, PDB code: 3s2d was solved by X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.286, 220.768, 192.241, 90.00, 97.69, 90.00
R / Rfree (%) 18.3 / 23.1

Other elements in 3s2d:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Bromine (Br) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U (pdb code 3s2d). 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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U, PDB code: 3s2d:

Magnesium binding site 1 out of 1 in 3s2d

Go back to Magnesium Binding Sites List in 3s2d
Magnesium binding site 1 out of 1 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U


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 Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:21.1
occ:1.00
 O3' R:G10 1.9 76.4 1.0
OD1 A:ASP485 2.3 55.3 1.0
OD1 A:ASP481 2.4 63.4 1.0
OD2 A:ASP483 2.5 58.4 1.0
CG A:ASP483 3.1 51.8 1.0
OD1 A:ASP483 3.1 51.6 1.0
CG A:ASP485 3.1 54.8 1.0
OD2 A:ASP485 3.2 57.4 1.0
CG A:ASP481 3.2 62.3 1.0
C3' R:G10 3.2 76.5 1.0
OD2 A:ASP481 3.4 69.8 1.0
C4' R:G10 3.8 76.7 1.0
C5' R:G10 4.1 77.7 1.0
O2' R:G10 4.2 76.5 1.0
C2' R:G10 4.2 76.5 1.0
CB A:ASP483 4.5 44.3 1.0
NH2 A:ARG446 4.5 49.2 1.0
CB A:ASP485 4.6 46.1 1.0
CB A:ASP481 4.6 47.8 1.0
O A:ASP481 4.7 49.6 1.0
N A:ASP483 4.8 44.0 1.0
C A:ASP481 4.9 49.9 1.0
N A:ASP481 4.9 45.9 1.0

Reference:

X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg. Initiation Complex Structure and Promoter Proofreading. Science V. 333 633 2011.
ISSN: ISSN 0036-8075
PubMed: 21798951
DOI: 10.1126/SCIENCE.1206629
Page generated: Mon Aug 11 02:55:40 2025

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