Magnesium in PDB 7kef: Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing State

Enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing State

All present enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing State:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing State, PDB code: 7kef 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)*	48.70 / 3.89
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	167.713, 221.711, 193.255, 90, 101.78, 90
*R / R_free (%)*	26.8 / 32.6

Other elements in 7kef:

The structure of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing 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 Unnatural Base DTPT3, Rnam in Swing State (pdb code 7kef). 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 Unnatural Base DTPT3, Rnam in Swing State, PDB code: 7kef:

Magnesium binding site 1 out of 1 in 7kef

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Magnesium Binding Sites List in 7kef

Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing 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 Unnatural Base DTPT3, Rnam in Swing State within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg2001 b:88.9 occ:1.00	OP2	R:WC411	1.9	106.9	1.0
	OD2	A:ASP483	2.0	97.7	1.0
	OD1	A:ASP483	2.0	99.1	1.0
	OP1	R:WC411	2.2	107.2	1.0
	CG	A:ASP483	2.3	94.9	1.0
	P	R:WC411	2.4	110.3	1.0
	OD2	A:ASP485	3.0	82.1	1.0
	CB	A:ASP481	3.3	89.4	1.0
	O5'	R:WC411	3.3	119.1	1.0
	O06	R:WC411	3.5	123.2	1.0
	O3'	R:A10	3.6	106.6	1.0
	C08	R:WC411	3.7	114.5	1.0
	CB	A:ASP483	3.8	81.7	1.0
	C07	R:WC411	3.8	118.3	1.0
	N	A:ASP481	3.9	89.2	1.0
	CG	A:ASP481	3.9	99.3	1.0
	CG	A:ASP485	4.0	86.0	1.0
	CA	A:ASP481	4.0	86.0	1.0
	OD2	A:ASP481	4.2	90.4	1.0
	O	A:ASP481	4.4	88.8	1.0
	C	A:ASP481	4.4	86.2	1.0
	OD1	A:ASP485	4.4	82.9	1.0
	O	A:ASP483	4.5	77.0	1.0
	N	A:ASP483	4.5	82.8	1.0
	OD1	A:ASP481	4.6	110.8	1.0
	CA	A:ASP483	4.6	73.5	1.0
	C4'	R:A10	4.7	95.0	1.0
	C3'	R:A10	4.7	95.4	1.0
	O02	R:WC411	4.7	101.1	1.0
	C	A:ASP483	4.8	64.5	1.0
	C05	R:WC411	4.9	119.0	1.0

Reference:

J.Oh, W.Wang, D.Wang. Transcriptional Processing of Unnatural Base Pair By Eukaryotic Rna Polymerase II Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-021-00817-3

Page generated: Wed Oct 2 22:15:10 2024

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