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

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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

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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: Thu Aug 15 10:30:42 2024

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