Magnesium in PDB 3h3v: Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site

Enzymatic activity of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site

All present enzymatic activity of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site:
2.7.7.6;

Protein crystallography data

The structure of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site, PDB code: 3h3v was solved by S.Dengl, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 4.00
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	222.470, 391.620, 284.120, 90.00, 90.00, 90.00
*R / R_free (%)*	20.5 / 24.1

Other elements in 3h3v:

The structure of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site (pdb code 3h3v). 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 Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site, PDB code: 3h3v:

Magnesium binding site 1 out of 1 in 3h3v

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Magnesium Binding Sites List in 3h3v

Magnesium binding site 1 out of 1 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg1736 b:0.2 occ:1.00	O3'	P:A10	2.3	0.7	1.0
	OD1	B:ASP481	2.3	0.8	1.0
	OD2	B:ASP483	2.3	0.8	1.0
	OD2	B:ASP485	2.4	0.9	1.0
	OD2	B:ASP481	2.7	0.4	1.0
	CG	B:ASP481	2.8	0.3	1.0
	OD1	B:ASP485	2.9	0.3	1.0
	CG	B:ASP485	3.0	0.1	1.0
	CG	B:ASP483	3.2	0.4	1.0
	O2'	P:A10	3.4	0.8	1.0
	OD1	B:ASP483	3.5	0.2	1.0
	C3'	P:A10	3.6	0.7	1.0
	C2'	P:A10	4.0	0.4	1.0
	C4'	P:A10	4.2	0.7	1.0
	CB	B:ASP481	4.3	0.0	1.0
	NH2	B:ARG446	4.4	1.0	1.0
	CB	B:ASP485	4.5	0.3	1.0
	CB	B:ASP483	4.6	0.2	1.0
	N	B:ASP481	4.6	0.6	1.0
	N	B:ASP483	4.8	0.2	1.0
	O	B:ASP481	4.8	0.8	1.0
	C	B:ASP481	4.8	0.5	1.0
	CA	B:ASP481	4.8	0.4	1.0

Reference:

S.Dengl, P.Cramer. Torpedo Nuclease RAT1 Is Insufficient to Terminate Rna Polymerase II in Vitro J.Biol.Chem. V. 284 21270 2009.
ISSN: ISSN 0021-9258
PubMed: 19535338
DOI: 10.1074/JBC.M109.013847

Page generated: Wed Aug 14 15:03:22 2024

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