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Magnesium in PDB 4a3m: Rna Polymerase II Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp

Enzymatic activity of Rna Polymerase II Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp

All present enzymatic activity of Rna Polymerase II Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp, PDB code: 4a3m was solved by A.C.M.Cheung, S.Sainsbury, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.65 / 3.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.270, 392.990, 282.160, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19

Other elements in 4a3m:

The structure of Rna Polymerase II Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp 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 Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp (pdb code 4a3m). 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 Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp, PDB code: 4a3m:

Magnesium binding site 1 out of 1 in 4a3m

Go back to Magnesium Binding Sites List in 4a3m
Magnesium binding site 1 out of 1 in the Rna Polymerase II Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 4NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2458

b:0.2
occ:1.00
 O3' P:A10 2.0 0.8 1.0
OD1 A:ASP481 2.2 0.3 1.0
OD1 A:ASP483 2.2 0.7 1.0
OD2 A:ASP485 2.2 0.3 1.0
CG A:ASP481 3.1 0.8 1.0
C3' P:A10 3.3 1.0 1.0
CG A:ASP483 3.3 0.3 1.0
CG A:ASP485 3.4 0.3 1.0
CB A:ASP481 3.5 0.1 1.0
O2' P:A10 3.6 0.5 1.0
O4' A:APC2455 3.8 0.4 1.0
N A:ASP481 3.9 0.6 1.0
C4' A:APC2455 3.9 0.0 1.0
OD2 A:ASP483 3.9 0.2 1.0
OD1 A:ASP485 3.9 0.1 1.0
C2' P:A10 3.9 0.3 1.0
C4' P:A10 4.0 0.1 1.0
OD2 A:ASP481 4.1 0.7 1.0
CA A:ASP481 4.1 0.9 1.0
O5' A:APC2455 4.2 0.9 1.0
O A:ASP483 4.3 0.7 1.0
C A:ASP481 4.4 0.8 1.0
NH2 A:ARG446 4.4 1.0 1.0
CB A:ASP485 4.5 0.2 1.0
N A:ASP483 4.5 0.9 1.0
CB A:ASP483 4.6 0.8 1.0
C5' A:APC2455 4.6 0.2 1.0
O A:ASP481 4.7 0.0 1.0
C5' P:A10 4.7 0.7 1.0
CA A:ASP483 4.8 0.5 1.0
C A:ASP483 4.8 0.9 1.0
N A:PHE482 4.9 0.9 1.0

Reference:

A.C.Cheung, S.Sainsbury, P.Cramer. Structural Basis of Initial Rna Polymerase II Transcription. Embo J. V. 30 4755 2011.
ISSN: ESSN 1460-2075
PubMed: 22056778
DOI: 10.1038/EMBOJ.2011.396
Page generated: Mon Aug 11 05:32:28 2025

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