Magnesium in PDB 3rjf: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)

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

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp), PDB code: 3rjf 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)*	21.17 / 2.30
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.550, 79.810, 55.690, 90.00, 107.88, 90.00
*R / R_free (%)*	19.3 / 25.6

Other elements in 3rjf:

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

Chlorine	(Cl)	4 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 (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) (pdb code 3rjf). 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 (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp), PDB code: 3rjf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3rjf

Go back to

Magnesium Binding Sites List in 3rjf

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

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 (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg339 b:17.1 occ:1.00	OD1	A:ASP190	1.9	15.1	1.0
	O2B	A:F2A338	1.9	13.2	1.0
	O3G	A:F2A338	2.0	21.4	1.0
	O	A:HOH472	2.1	25.6	1.0
	O1A	A:F2A338	2.2	17.8	1.0
	OD2	A:ASP192	2.2	25.4	1.0
	PB	A:F2A338	2.9	18.7	1.0
	CG	A:ASP190	3.0	20.4	1.0
	PG	A:F2A338	3.1	24.9	1.0
	CG	A:ASP192	3.3	27.0	1.0
	PA	A:F2A338	3.3	21.4	1.0
	O3B	A:F2A338	3.3	25.6	1.0
	C3A	A:F2A338	3.3	20.6	1.0
	OD2	A:ASP190	3.5	16.8	1.0
	O2G	A:F2A338	3.5	22.2	1.0
	MG	A:MG340	3.6	18.3	1.0
	OD1	A:ASP192	3.7	27.2	1.0
	O	A:ASP190	3.9	20.9	1.0
	C5'	A:F2A338	4.0	21.4	1.0
	O	A:HOH378	4.0	22.6	1.0
	O5'	A:F2A338	4.1	21.7	1.0
	OG	A:SER180	4.2	20.4	1.0
	O1G	A:F2A338	4.3	24.2	1.0
	CB	A:ASP190	4.3	18.3	1.0
	C	A:ASP190	4.3	21.6	1.0
	N	A:ASP190	4.3	19.9	1.0
	O1B	A:F2A338	4.3	21.4	1.0
	N	A:SER180	4.4	20.8	1.0
	O	A:HOH350	4.4	14.2	1.0
	CA	A:GLY179	4.5	19.6	1.0
	O2A	A:F2A338	4.5	22.4	1.0
	CA	A:ASP190	4.6	20.8	1.0
	CB	A:ASP192	4.6	25.5	1.0
	O	A:HOH470	4.7	20.2	1.0
	N	A:ASP192	5.0	23.6	1.0

Magnesium binding site 2 out of 2 in 3rjf

Go back to

Magnesium Binding Sites List in 3rjf

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

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 (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg340 b:18.3 occ:1.00	O3'	P:DA10	2.0	25.1	1.0
	OD1	A:ASP192	2.0	27.2	1.0
	OD2	A:ASP190	2.0	16.8	1.0
	O1A	A:F2A338	2.1	17.8	1.0
	OD2	A:ASP256	2.2	30.6	1.0
	O	A:HOH470	2.2	20.2	1.0
	CG	A:ASP192	3.0	27.0	1.0
	PA	A:F2A338	3.0	21.4	1.0
	CG	A:ASP190	3.1	20.4	1.0
	C3'	P:DA10	3.3	27.6	1.0
	OD2	A:ASP192	3.3	25.4	1.0
	CG	A:ASP256	3.3	31.5	1.0
	O5'	A:F2A338	3.4	21.7	1.0
	OD1	A:ASP190	3.4	15.1	1.0
	O2A	A:F2A338	3.5	22.4	1.0
	MG	A:MG339	3.6	17.1	1.0
	C5'	A:F2A338	3.9	21.4	1.0
	CB	A:ASP256	3.9	29.5	1.0
	C4'	P:DA10	4.0	25.2	1.0
	C5'	P:DA10	4.2	26.9	1.0
	O	A:HOH378	4.3	22.6	1.0
	OD1	A:ASP256	4.3	35.5	1.0
	CB	A:ASP192	4.3	25.5	1.0
	CB	A:ASP190	4.4	18.3	1.0
	C2'	P:DA10	4.4	26.0	1.0
	OP1	P:DA10	4.5	29.8	1.0
	O5'	P:DA10	4.6	27.6	1.0
	C3A	A:F2A338	4.6	20.6	1.0
	O3G	A:F2A338	4.7	21.4	1.0
	O2B	A:F2A338	4.7	13.2	1.0
	O	A:MET191	4.8	24.6	1.0
	O	P:HOH216	4.9	41.9	1.0
	CA	A:ASP192	4.9	23.9	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 10:30:22 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW

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