Magnesium in PDB 5vez: Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog

Enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog, PDB code: 5vez was solved by B.D.Freudenthal, M.A.Schaich, A.M.Whitaker, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	31.84 / 2.04
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.469, 79.712, 55.523, 90.00, 107.50, 90.00
*R / R_free (%)*	18.7 / 23.2

Other elements in 5vez:

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog (pdb code 5vez). 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 Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog, PDB code: 5vez:

Magnesium binding site 1 out of 1 in 5vez

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Magnesium Binding Sites List in 5vez

Magnesium binding site 1 out of 1 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg401 b:21.9 occ:1.00	O1A	A:XC5404	2.0	20.6	1.0
	OD1	A:ASP190	2.0	25.3	1.0
	OD2	A:ASP192	2.0	19.2	1.0
	O3G	A:XC5404	2.0	23.2	1.0
	O2B	A:XC5404	2.1	18.9	1.0
	O	A:HOH593	2.2	24.1	1.0
	CG	A:ASP192	3.1	21.3	1.0
	CG	A:ASP190	3.1	18.8	1.0
	PB	A:XC5404	3.2	25.3	1.0
	PA	A:XC5404	3.3	26.6	1.0
	PG	A:XC5404	3.4	21.0	1.0
	OD1	A:ASP192	3.5	25.1	1.0
	OD2	A:ASP190	3.5	29.5	1.0
	O	A:HOH501	3.5	19.5	1.0
	C3A	A:XC5404	3.5	18.2	1.0
	O3B	A:XC5404	3.6	31.9	1.0
	O	A:HOH599	3.7	36.0	1.0
	C5'	A:XC5404	4.0	23.0	1.0
	O5'	A:XC5404	4.1	27.1	1.0
	O	A:ASP190	4.1	24.9	1.0
	O2G	A:XC5404	4.2	22.3	1.0
	O2A	A:XC5404	4.3	20.0	1.0
	C	A:ASP190	4.4	31.2	1.0
	CB	A:ASP192	4.4	22.5	1.0
	O	A:HOH574	4.4	25.9	1.0
	N	A:ASP190	4.4	21.2	1.0
	CB	A:ASP190	4.4	22.8	1.0
	O1G	A:XC5404	4.5	31.3	1.0
	CA	A:GLY179	4.5	22.1	1.0
	O1B	A:XC5404	4.5	22.2	1.0
	N	A:SER180	4.5	26.1	1.0
	OG	A:SER180	4.6	31.1	1.0
	CA	A:ASP190	4.6	23.8	1.0
	N	A:ASP192	4.8	23.3	1.0
	N	A:MET191	4.9	19.9	1.0

Reference:

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293

Page generated: Mon Sep 30 06:09:50 2024

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