Magnesium in PDB 7rim: Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 1

Enzymatic activity of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 1

All present enzymatic activity of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 1:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 1, PDB code: 7rim was solved by J.Oh, P.B.Dervan, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	82.43 / 2.90
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	167.22, 221.93, 193.71, 90, 99.63, 90
*R / R_free (%)*	21.5 / 25.1

Other elements in 7rim:

The structure of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 1 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 Hairpin Polyamide Py-Im 1, Scaffold 1 (pdb code 7rim). 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 Hairpin Polyamide Py-Im 1, Scaffold 1, PDB code: 7rim:

Magnesium binding site 1 out of 1 in 7rim

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Magnesium Binding Sites List in 7rim

Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 1

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 Hairpin Polyamide Py-Im 1, Scaffold 1 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1803 b:79.6 occ:1.00	O3'	R:G9	2.0	131.2	1.0
	OD2	A:ASP483	2.3	84.2	1.0
	OD2	A:ASP485	2.6	108.7	1.0
	OD1	A:ASP483	2.9	89.0	1.0
	CG	A:ASP483	2.9	83.6	1.0
	C3'	R:G9	3.0	99.9	1.0
	C4'	R:G9	3.1	87.3	1.0
	CB	A:ASP481	3.3	72.0	1.0
	CG	A:ASP485	3.4	103.5	1.0
	O2'	R:G9	3.4	133.2	1.0
	C5'	R:G9	3.7	84.0	1.0
	OD1	A:ASP485	3.8	109.3	1.0
	C2'	R:G9	3.8	102.5	1.0
	CG	A:ASP481	4.3	97.2	1.0
	CA	A:ASP481	4.4	65.1	1.0
	CB	A:ASP483	4.4	77.5	1.0
	O4'	R:G9	4.4	74.9	1.0
	CB	A:ASP485	4.5	84.3	1.0
	N	A:ASP481	4.6	62.5	1.0
	C	A:ASP481	4.6	66.1	1.0
	O	A:ASP481	4.7	65.3	1.0
	N	A:ASP485	4.7	62.8	1.0
	OD2	A:ASP481	4.7	108.4	1.0
	C1'	R:G9	4.8	79.9	1.0
	N	A:ASP483	4.8	67.9	1.0
	CA	A:ASP485	4.9	65.7	1.0

Reference:

J.Oh, T.Jia, J.Xu, J.Chong, P.B.Dervan, D.Wang. Rna Polymerase II Trapped on A Molecular Treadmill: Structural Basis of Persistent Transcriptional Arrest By A Minor Groove Dna Binder. Proc.Natl.Acad.Sci.Usa V. 119 2022.
ISSN: ESSN 1091-6490
PubMed: 35022237
DOI: 10.1073/PNAS.2114065119

Page generated: Thu Oct 3 07:52:30 2024

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