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

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

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 1 Soaked with Ctp, PDB code: 7rip 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)*	49.23 / 3.30
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	168.158, 223.041, 193.464, 90, 100.67, 90
*R / R_free (%)*	21.9 / 26.1

Other elements in 7rip:

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

Magnesium binding site 1 out of 1 in 7rip

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Magnesium Binding Sites List in 7rip

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

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 Soaked with Ctp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
R:Mg2001 b:106.9 occ:1.00	O3'	R:G9	2.1	106.2	1.0
	OD1	A:ASP483	2.2	103.0	1.0
	OP1	R:C10	2.2	111.4	1.0
	OD2	A:ASP483	2.6	84.9	1.0
	P	R:C10	2.7	107.1	1.0
	CG	A:ASP483	2.7	87.0	1.0
	C3'	R:G9	3.3	89.8	1.0
	OD1	A:ASP485	3.6	85.9	1.0
	O5'	R:C10	3.7	116.7	1.0
	C4'	R:G9	3.8	88.7	1.0
	C5'	R:C10	3.8	114.1	1.0
	OP2	R:C10	3.9	95.5	1.0
	O2'	R:G9	3.9	98.7	1.0
	CB	A:ASP481	4.0	81.3	1.0
	OD2	A:ASP485	4.1	83.8	1.0
	CG	A:ASP485	4.2	83.1	1.0
	C2'	R:G9	4.2	89.4	1.0
	NZ	B:LYS987	4.2	97.2	1.0
	CB	A:ASP483	4.2	74.2	1.0
	C5'	R:G9	4.3	88.0	1.0
	CG	A:ASP481	4.6	95.8	1.0
	OD2	A:ASP481	4.6	108.7	1.0
	C4'	R:C10	4.8	103.9	1.0
	O4'	R:C10	4.9	92.5	1.0
	O31	B:PPV1301	4.9	175.6	1.0
	O5'	R:G9	5.0	98.6	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 07:52:41 2024

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