Magnesium in PDB 5w4u: Pol II Elongation Complex with An N6-Methyladenine-Containing Template

Enzymatic activity of Pol II Elongation Complex with An N6-Methyladenine-Containing Template

All present enzymatic activity of Pol II Elongation Complex with An N6-Methyladenine-Containing Template:
2.7.7.6;

Protein crystallography data

The structure of Pol II Elongation Complex with An N6-Methyladenine-Containing Template, PDB code: 5w4u was solved by W.Wang, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	81.02 / 3.60
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	167.210, 221.990, 192.700, 90.00, 100.58, 90.00
*R / R_free (%)*	22.7 / 25.9

Other elements in 5w4u:

The structure of Pol II Elongation Complex with An N6-Methyladenine-Containing Template also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template (pdb code 5w4u). 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 Pol II Elongation Complex with An N6-Methyladenine-Containing Template, PDB code: 5w4u:

Magnesium binding site 1 out of 1 in 5w4u

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Magnesium Binding Sites List in 5w4u

Magnesium binding site 1 out of 1 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1803 b:37.9 occ:1.00	O3'	R:G9	2.0	52.1	1.0
	OD1	A:ASP483	2.2	54.5	1.0
	OD1	A:ASP481	2.2	80.2	1.0
	OD2	A:ASP483	2.6	57.9	1.0
	OD1	A:ASP485	2.7	58.7	1.0
	CG	A:ASP483	2.8	56.2	1.0
	C3'	R:G9	2.9	50.0	1.0
	C4'	R:G9	3.0	47.9	1.0
	CG	A:ASP481	3.2	80.3	1.0
	OD2	A:ASP485	3.3	57.3	1.0
	CG	A:ASP485	3.4	57.1	1.0
	OD2	A:ASP481	3.4	82.5	1.0
	C5'	R:G9	3.5	46.0	1.0
	O2'	R:G9	3.6	53.0	1.0
	C2'	R:G9	3.9	51.2	1.0
	CB	A:ASP483	4.3	55.9	1.0
	O4'	R:G9	4.3	46.9	1.0
	O5'	R:G9	4.4	44.2	1.0
	CB	A:ASP481	4.5	77.2	1.0
	N	A:ASP481	4.6	73.4	1.0
	N	A:ASP483	4.7	51.8	1.0
	C1'	R:G9	4.7	48.8	1.0
	CB	A:ASP485	4.8	54.7	1.0
	NH2	A:ARG446	4.8	36.5	1.0
	CA	A:ASP483	4.9	53.3	1.0

Reference:

W.Wang, L.Xu, L.Hu, J.Chong, C.He, D.Wang. Epigenetic Dna Modification N6-Methyladenine Causes Site-Specific Rna Polymerase II Transcriptional Pausing. J.Am.Chem.Soc. V. 139 14436 2017.
ISSN: ESSN 1520-5126
PubMed: 28933854
DOI: 10.1021/JACS.7B06381

Page generated: Mon Sep 30 06:28:29 2024

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