Sodium in PDB 5vs3: Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S

Enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S

All present enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S, PDB code: 5vs3 was solved by A.J.Reed, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	52.76 / 1.70
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.400, 79.600, 55.200, 90.00, 107.10, 90.00
*R / R_free (%)*	20.6 / 24.9

Other elements in 5vs3:

The structure of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S (pdb code 5vs3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S, PDB code: 5vs3:

Sodium binding site 1 out of 1 in 5vs3

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Sodium Binding Sites List in 5vs3

Sodium binding site 1 out of 1 in the Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta 8-Oxog:Da Extension with Dttp After 90 S within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na404 b:22.6 occ:1.00	O	A:HOH730	2.9	41.6	1.0
	O	A:HOH746	3.0	38.2	1.0
	OG1	A:THR297	3.2	19.9	1.0
	O	A:HOH691	3.2	29.9	1.0
	ND2	A:ASN294	3.3	17.3	1.0
	CB	A:TYR296	4.0	19.3	1.0
	OD1	A:ASN294	4.0	16.5	1.0
	CZ	A:ARG299	4.0	30.4	1.0
	CG2	A:THR297	4.0	19.6	1.0
	CG	A:ASN294	4.1	16.2	1.0
	CD2	A:TYR296	4.1	18.8	1.0
	NE	A:ARG299	4.1	27.2	1.0
	CB	A:THR297	4.2	19.8	1.0
	O	T:HOH229	4.2	37.6	1.0
	NH1	A:ARG299	4.3	32.0	1.0
	NH2	A:ARG299	4.3	32.2	1.0
	CG	A:TYR296	4.4	18.9	1.0
	CD	A:ARG299	4.6	26.1	1.0
	N	A:THR297	4.8	18.6	1.0
	O	A:HOH639	4.8	18.9	1.0

Reference:

A.J.Reed, Z.Suo. Time-Dependent Extension From An 8-Oxoguanine Lesion By Human Dna Polymerase Beta. J. Am. Chem. Soc. V. 139 9684 2017.
ISSN: ESSN 1520-5126
PubMed: 28682600
DOI: 10.1021/JACS.7B05048

Page generated: Mon Aug 18 02:52:58 2025

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