Magnesium in PDB 9n5d: Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added

Enzymatic activity of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added

All present enzymatic activity of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added, PDB code: 9n5d 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)*	49.31 / 3.35
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	165.899, 222.27, 193.145, 90, 100.27, 90
*R / R_free (%)*	26.5 / 30

Other elements in 9n5d:

The structure of Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added 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 8-Oxog at +1 Site, Cmp Added (pdb code 9n5d). 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 8-Oxog at +1 Site, Cmp Added, PDB code: 9n5d:

Magnesium binding site 1 out of 1 in 9n5d

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Magnesium Binding Sites List in 9n5d

Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with 8-Oxog at +1 Site, Cmp Added

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 8-Oxog at +1 Site, Cmp Added within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1803 b:88.2 occ:1.00	OD2	A:ASP483	2.4	78.9	1.0
	OD1	A:ASP483	2.7	84.3	1.0
	OD2	A:ASP485	2.8	74.1	1.0
	CG	A:ASP483	2.9	76.3	1.0
	CB	A:ASP481	3.0	79.9	1.0
	OP1	R:C10	3.0	91.0	1.0
	O3'	R:G9	3.1	112.9	1.0
	OD1	A:ASP485	3.1	81.6	1.0
	CG	A:ASP485	3.3	70.5	1.0
	C5'	R:C10	3.4	127.6	1.0
	P	R:C10	3.6	131.2	1.0
	O5'	R:C10	3.9	122.6	1.0
	CG	A:ASP481	4.0	88.2	1.0
	O2'	R:G9	4.1	82.1	1.0
	NH2	A:ARG446	4.1	87.4	1.0
	OD2	A:ASP481	4.1	101.8	1.0
	CA	A:ASP481	4.1	77.9	1.0
	C3'	R:G9	4.2	97.5	1.0
	N	A:ASP481	4.3	72.3	1.0
	CB	A:ASP483	4.3	67.6	1.0
	C4'	R:G9	4.4	83.0	1.0
	C4'	R:C10	4.4	118.1	1.0
	C	A:ASP481	4.6	72.0	1.0
	O4'	R:C10	4.7	128.8	1.0
	O	A:ASP481	4.7	75.2	1.0
	C2'	R:G9	4.7	82.0	1.0
	CB	A:ASP485	4.8	61.6	1.0
	OD1	A:ASP481	4.9	84.2	1.0
	N	A:ASP483	4.9	76.8	1.0
	OP2	R:C10	5.0	124.2	1.0

Reference:

J.Oh, K.A.Konovalov, P.Hou, J.Chong, X.Huang, D.Wang. Transcription-Coupled Template Reconfiguration of 8-Oxoguanine For Error-Prone Transcription Revealed By Time-Resolved X-Ray Crystallography and Molecular Dynamics. J.Am.Chem.Soc. V. 147 16396 2025.
ISSN: ESSN 1520-5126
PubMed: 40305462
DOI: 10.1021/JACS.5C02687

Page generated: Sat Aug 23 06:06:24 2025

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