Magnesium in PDB 4a3j: Rna Polymerase II Initial Transcribing Complex with A 2NT Dna-Rna Hybrid and Soaked with Gmpcpp

Enzymatic activity of Rna Polymerase II Initial Transcribing Complex with A 2NT Dna-Rna Hybrid and Soaked with Gmpcpp

All present enzymatic activity of Rna Polymerase II Initial Transcribing Complex with A 2NT Dna-Rna Hybrid and Soaked with Gmpcpp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initial Transcribing Complex with A 2NT Dna-Rna Hybrid and Soaked with Gmpcpp, PDB code: 4a3j 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)*	50.00 / 3.70
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	223.290, 392.790, 282.660, 90.00, 90.00, 90.00
*R / R_free (%)*	15.67 / 19.39

Other elements in 4a3j:

The structure of Rna Polymerase II Initial Transcribing Complex with A 2NT Dna-Rna Hybrid and Soaked with Gmpcpp 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 2NT Dna-Rna Hybrid and Soaked with Gmpcpp (pdb code 4a3j). 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 2NT Dna-Rna Hybrid and Soaked with Gmpcpp, PDB code: 4a3j:

Magnesium binding site 1 out of 1 in 4a3j

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Magnesium Binding Sites List in 4a3j

Magnesium binding site 1 out of 1 in the Rna Polymerase II Initial Transcribing Complex with A 2NT Dna-Rna Hybrid and Soaked with Gmpcpp

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 2NT Dna-Rna Hybrid and Soaked with Gmpcpp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg2458 b:0.3 occ:1.00	OD1	A:ASP481	2.0	0.9	1.0
	O3'	P:A10	2.1	0.4	1.0
	OD1	A:ASP485	2.2	0.3	1.0
	OD1	A:ASP483	2.3	1.0	1.0
	OD2	A:ASP481	2.3	0.3	1.0
	O2'	P:A10	2.4	0.5	1.0
	CG	A:ASP481	2.5	0.1	1.0
	C3'	P:A10	3.0	0.4	1.0
	CG	A:ASP483	3.1	0.5	1.0
	C2'	P:A10	3.2	0.5	1.0
	CG	A:ASP485	3.2	0.2	1.0
	C4'	P:A10	3.5	0.5	1.0
	OD2	A:ASP485	3.6	0.9	1.0
	OD2	A:ASP483	3.8	0.7	1.0
	CB	A:ASP481	4.0	0.4	1.0
	CB	A:ASP483	4.2	0.4	1.0
	C1'	P:A10	4.3	0.6	1.0
	N	A:ASP483	4.4	0.4	1.0
	O5'	T:G2P1024	4.4	0.1	1.0
	O4'	P:A10	4.4	0.4	1.0
	CA	A:ASP483	4.5	1.0	1.0
	CB	A:ASP485	4.5	97.6	1.0
	C5'	P:A10	4.5	0.6	1.0
	C	A:ASP483	4.6	0.1	1.0
	C4'	T:G2P1024	4.7	0.2	1.0
	O1A	T:G2P1024	4.7	0.2	1.0
	O	A:ASP481	4.8	0.7	1.0
	N	A:ASP485	4.8	95.5	1.0
	C	A:ASP481	4.8	0.7	1.0
	CA	A:ASP481	4.9	0.5	1.0
	O4'	T:G2P1024	5.0	0.1	1.0
	O	A:ASP483	5.0	0.5	1.0
	N	A:ASP481	5.0	0.7	1.0
	N	A:GLY484	5.0	97.2	1.0

Reference:

A.C.M.Cheung, S.Sainsbury, P.Cramer. Structural Basis of Initial Rna Polymerase II Transcription. Embo J. V. 30 4755 2011.
ISSN: ISSN 0261-4189
PubMed: 22056778
DOI: 10.1038/EMBOJ.2011.396

Page generated: Mon Aug 11 05:32:18 2025

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