Magnesium in PDB 6upy: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E

Enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E

All present enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E, PDB code: 6upy was solved by J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.22 / 3.40
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	168.536, 223.125, 193.062, 90.00, 100.92, 90.00
*R / R_free (%)*	22.7 / 28.2

Other elements in 6upy:

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E 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 5-Guanidinohydantoin Lesion in State 2E (pdb code 6upy). 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 5-Guanidinohydantoin Lesion in State 2E, PDB code: 6upy:

Magnesium binding site 1 out of 1 in 6upy

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Magnesium Binding Sites List in 6upy

Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 2E

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 5-Guanidinohydantoin Lesion in State 2E within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1803 b:39.6 occ:1.00	OD2	A:ASP485	2.1	91.0	1.0
	O3'	R:G9	2.1	96.3	1.0
	OD1	A:ASP485	2.2	94.2	1.0
	OD2	A:ASP483	2.3	82.5	1.0
	CG	A:ASP485	2.4	86.4	1.0
	O2'	R:G9	3.2	85.0	1.0
	CG	A:ASP483	3.2	90.5	1.0
	C3'	R:G9	3.3	81.4	1.0
	CB	A:ASP481	3.4	79.9	1.0
	OD1	A:ASP483	3.5	91.4	1.0
	O	A:ASP481	3.7	0.7	1.0
	C2'	R:G9	3.8	83.3	1.0
	NH2	A:ARG446	3.9	61.8	1.0
	C4'	R:G9	3.9	80.3	1.0
	CB	A:ASP485	3.9	84.4	1.0
	O2B	B:APC1301	4.0	0.3	1.0
	N	A:ASP481	4.0	88.9	1.0
	CA	A:ASP481	4.1	74.3	1.0
	C	A:ASP481	4.2	82.7	1.0
	CG	A:ASP481	4.4	0.6	1.0
	CB	A:ASP483	4.6	0.2	1.0
	C5'	R:G9	4.7	78.4	1.0
	N	A:ASP485	4.7	75.3	1.0
	CA	A:ASP485	4.8	81.8	1.0
	OD1	A:ASP481	4.8	0.9	1.0
	N	A:ASP483	4.9	94.7	1.0

Reference:

J.Oh, A.M.Fleming, J.Xu, J.Chong, C.J.Burrows, D.Wang. Rna Polymerase II Stalls on Oxidative Dna Damage Via A Torsion-Latch Mechanism Involving Lone Pair-Pi and Ch-Pi Interactions. Proc.Natl.Acad.Sci.Usa V. 117 9338 2020.
ISSN: ESSN 1091-6490
PubMed: 32284409
DOI: 10.1073/PNAS.1919904117

Page generated: Wed Aug 13 18:40:42 2025

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