Magnesium in PDB 3rji: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp)

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp)

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp):
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp), PDB code: 3rji was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	23.38 / 2.30
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.760, 80.180, 55.790, 90.00, 107.96, 90.00
*R / R_free (%)*	20.7 / 26.6

Other elements in 3rji:

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp) also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp) (pdb code 3rji). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp), PDB code: 3rji:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3rji

Go back to

Magnesium Binding Sites List in 3rji

Magnesium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg402 b:15.7 occ:1.00	OD1	A:ASP190	2.0	17.7	1.0
	OD2	A:ASP192	2.0	15.7	1.0
	O2B	A:6CF401	2.0	14.6	1.0
	O1A	A:6CF401	2.0	10.4	1.0
	O3G	A:6CF401	2.1	14.6	1.0
	O	A:HOH502	2.1	11.6	1.0
	CG	A:ASP192	3.0	15.3	1.0
	CG	A:ASP190	3.1	15.3	1.0
	P2	A:6CF401	3.1	15.8	1.0
	P3	A:6CF401	3.2	18.9	1.0
	P1	A:6CF401	3.3	13.8	1.0
	OD1	A:ASP192	3.3	17.6	1.0
	MG	A:MG403	3.4	19.9	1.0
	OD2	A:ASP190	3.5	20.5	1.0
	O3B	A:6CF401	3.5	14.0	1.0
	O2G	A:6CF401	3.5	17.9	1.0
	C3A	A:6CF401	3.6	17.2	1.0
	O	A:HOH592	3.8	21.1	1.0
	C5'	A:6CF401	3.9	17.5	1.0
	F2A	A:6CF401	3.9	15.7	1.0
	O	A:ASP190	4.0	16.1	1.0
	O5'	A:6CF401	4.0	14.6	1.0
	C	A:ASP190	4.3	16.2	1.0
	CB	A:ASP192	4.3	19.1	1.0
	N	A:ASP190	4.3	15.1	1.0
	CB	A:ASP190	4.3	17.0	1.0
	O	A:HOH512	4.4	15.3	1.0
	O1G	A:6CF401	4.4	19.6	1.0
	O1B	A:6CF401	4.5	17.0	1.0
	O2A	A:6CF401	4.5	15.7	1.0
	O	P:HOH101	4.5	26.6	1.0
	CA	A:ASP190	4.6	14.8	1.0
	CA	A:GLY179	4.6	17.1	1.0
	N	A:SER180	4.8	19.2	1.0
	N	A:ASP192	4.8	19.8	1.0
	F1A	A:6CF401	4.8	15.8	1.0
	N	A:MET191	4.9	15.7	1.0

Magnesium binding site 2 out of 2 in 3rji

Go back to

Magnesium Binding Sites List in 3rji

Magnesium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg403 b:19.9 occ:1.00	OD1	A:ASP192	1.9	17.6	1.0
	OD2	A:ASP190	2.2	20.5	1.0
	OD2	A:ASP256	2.3	24.4	1.0
	O	P:HOH101	2.3	26.6	1.0
	O1A	A:6CF401	2.3	10.4	1.0
	O3'	P:DA10	2.4	14.6	1.0
	CG	A:ASP192	2.9	15.3	1.0
	CG	A:ASP190	3.1	15.3	1.0
	OD1	A:ASP190	3.3	17.7	1.0
	P1	A:6CF401	3.3	13.8	1.0
	OD2	A:ASP192	3.4	15.7	1.0
	CG	A:ASP256	3.4	24.3	1.0
	MG	A:MG402	3.4	15.7	1.0
	C3'	P:DA10	3.6	18.5	1.0
	O2A	A:6CF401	3.7	15.7	1.0
	O5'	A:6CF401	3.7	14.6	1.0
	CB	A:ASP256	4.0	20.8	1.0
	C5'	P:DA10	4.2	18.2	1.0
	C5'	A:6CF401	4.2	17.5	1.0
	C4'	P:DA10	4.2	20.2	1.0
	O	A:HOH592	4.2	21.1	1.0
	CB	A:ASP192	4.2	19.1	1.0
	OD1	A:ASP256	4.5	26.3	1.0
	CB	A:ASP190	4.5	17.0	1.0
	OP1	P:DA10	4.5	21.0	1.0
	O	P:HOH114	4.6	36.7	1.0
	O3G	A:6CF401	4.7	14.6	1.0
	O5'	P:DA10	4.7	19.9	1.0
	NH2	A:ARG254	4.8	22.4	1.0
	O	A:MET191	4.8	19.3	1.0
	CA	A:ASP192	4.8	19.1	1.0
	O2B	A:6CF401	4.8	14.6	1.0
	C2'	P:DA10	4.9	17.7	1.0
	C3A	A:6CF401	4.9	17.2	1.0

Reference:

V.K.Batra, D.D.Shock, W.A.Beard, C.E.Mckenna, S.H.Wilson. Binary Complex Crystal Structure of Dna Polymerase Beta Reveals Multiple Conformations of the Templating 8-Oxoguanine Lesion Proc.Natl.Acad.Sci.Usa V. 109 113 2012.
ISSN: ISSN 0027-8424
PubMed: 22178760
DOI: 10.1073/PNAS.1112235108

Page generated: Mon Dec 14 08:45:02 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy