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Magnesium in PDB 3s1r: Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp

Enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp, PDB code: 3s1r 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) 29.97 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.670, 221.320, 193.210, 90.00, 98.31, 90.00
R / Rfree (%) 17.7 / 22.6

Other elements in 3s1r:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp (pdb code 3s1r). 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 3'-Deoxy Rna Soaked with Gtp, PDB code: 3s1r:

Magnesium binding site 1 out of 1 in 3s1r

Go back to Magnesium Binding Sites List in 3s1r
Magnesium binding site 1 out of 1 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Gtp


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 3'-Deoxy Rna Soaked with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:60.9
occ:1.00
 OD1 A:ASP485 2.2 70.2 1.0
OD1 A:ASP481 2.5 97.7 1.0
C3' R:G10 2.6 0.8 1.0
OD2 A:ASP483 2.7 77.7 1.0
CG A:ASP485 3.1 70.6 1.0
OD1 A:ASP483 3.2 78.5 1.0
O1B R:GTP100 3.3 0.8 1.0
CG A:ASP483 3.3 74.9 1.0
OD2 A:ASP485 3.3 75.3 1.0
CG A:ASP481 3.6 94.8 1.0
NH2 A:ARG446 3.6 84.7 1.0
C2' R:G10 3.7 0.6 1.0
O2' R:G10 3.7 0.4 1.0
C4' R:G10 3.7 0.1 1.0
OD2 A:ASP481 4.0 0.3 1.0
CB A:ASP485 4.5 61.4 1.0
C5' R:G10 4.5 0.7 1.0
PB R:GTP100 4.5 0.8 1.0
O2B R:GTP100 4.6 0.9 1.0
CB A:ASP483 4.8 62.8 1.0
C1' R:G10 4.8 0.8 1.0
O4' R:G10 4.8 0.8 1.0
N A:ASP481 4.8 67.8 1.0
CB A:ASP481 4.9 70.2 1.0
O A:ASP481 4.9 68.0 1.0
N A:ASP485 4.9 60.2 1.0
CZ A:ARG446 4.9 0.2 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 02:55:22 2025

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