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

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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

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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

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