Magnesium in PDB 8ukq: Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State

Enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State

All present enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State, PDB code: 8ukq was solved by P.Hou, J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.44 / 3.50
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	161.54, 223.485, 191.472, 90, 98.38, 90
*R / R_free (%)*	26.8 / 30.2

Other elements in 8ukq:

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State (pdb code 8ukq). 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 Elongation Complex with Fapy-Dg Lesion in Apo State, PDB code: 8ukq:

Magnesium binding site 1 out of 1 in 8ukq

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Magnesium Binding Sites List in 8ukq

Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion in Apo State

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 Elongation Complex with Fapy-Dg Lesion in Apo State within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1803 b:129.8 occ:1.00	OD1	A:ASP483	2.2	134.2	1.0
	OD1	A:ASP485	2.3	132.1	1.0
	C3'	R:G9	3.1	115.1	1.0
	C4'	R:G9	3.2	120.7	1.0
	CG	A:ASP483	3.2	110.9	1.0
	CG	A:ASP485	3.2	128.8	1.0
	C5'	R:G9	3.5	107.4	1.0
	OD2	A:ASP485	3.5	119.5	1.0
	OD2	A:ASP483	3.6	81.5	1.0
	O	A:ASP483	3.7	123.9	1.0
	O2'	R:G9	3.9	130.9	1.0
	O	A:ASP481	4.1	117.8	1.0
	O5'	R:G9	4.1	110.7	1.0
	C2'	R:G9	4.1	124.5	1.0
	CB	A:ASP483	4.4	103.5	1.0
	CB	A:ASP485	4.5	99.1	1.0
	O4'	R:G9	4.6	132.9	1.0
	C	A:ASP483	4.6	83.7	1.0
	NH2	A:ARG446	4.8	113.5	1.0
	CA	A:ASP485	4.9	76.1	1.0
	CA	A:ASP483	4.9	80.5	1.0
	N	A:ASP483	4.9	100.0	1.0
	N	A:ASP485	4.9	76.0	1.0

Reference:

S.Gao, P.Hou, J.Oh, D.Wang, M.M.Greenberg. Molecular Mechanism of Rna Polymerase II Transcriptional Mutagenesis By the Epimerizable Dna Lesion, Fapy·Dg. J.Am.Chem.Soc. V. 146 6274 2024.
ISSN: ESSN 1520-5126
PubMed: 38393762
DOI: 10.1021/JACS.3C14476

Page generated: Fri Aug 15 16:58:40 2025

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