Magnesium in PDB 6upz: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3

Enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3

All present enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3, PDB code: 6upz 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)*	49.04 / 3.10
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	167.664, 222.901, 193.486, 90.00, 100.85, 90.00
*R / R_free (%)*	22.4 / 26.9

Other elements in 6upz:

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3 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 3 (pdb code 6upz). 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 3, PDB code: 6upz:

Magnesium binding site 1 out of 1 in 6upz

Go back to

Magnesium Binding Sites List in 6upz

Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 3

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 3 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1803 b:47.6 occ:1.00	OD1	A:ASP483	2.1	59.5	1.0
	OP1	R:A10	2.2	0.8	1.0
	OD1	A:ASP485	2.2	75.6	1.0
	OD2	A:ASP485	2.6	66.1	1.0
	CB	A:ASP481	2.6	60.4	1.0
	CG	A:ASP485	2.6	68.1	1.0
	P	R:A10	2.9	0.3	1.0
	CG	A:ASP483	3.0	52.1	1.0
	O3'	R:G9	3.1	0.8	1.0
	OD2	A:ASP483	3.2	58.5	1.0
	OP2	R:A10	3.3	0.7	1.0
	CG	A:ASP481	3.5	89.0	1.0
	CA	A:ASP481	3.5	51.6	1.0
	OD2	A:ASP481	3.5	98.9	1.0
	N	A:ASP481	3.6	58.1	1.0
	C	A:ASP481	3.9	39.4	1.0
	CB	A:ASP485	4.1	48.8	1.0
	N	A:ASP483	4.2	55.3	1.0
	O	A:ASP481	4.3	34.5	1.0
	O5'	R:A10	4.4	0.9	1.0
	CB	A:ASP483	4.4	53.8	1.0
	C3'	R:G9	4.4	0.2	1.0
	N	A:PHE482	4.5	43.1	1.0
	N	A:ASP485	4.5	50.9	1.0
	OD1	A:ASP481	4.6	94.5	1.0
	CA	A:ASP483	4.7	55.8	1.0
	CA	A:ASP485	4.8	44.6	1.0
	C4'	R:G9	4.8	0.2	1.0
	C5'	R:A10	4.9	0.2	1.0
	C	A:ALA480	4.9	53.4	1.0
	C	A:ASP483	4.9	43.4	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: Tue Oct 1 21:14:13 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy