Sodium 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
Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3rji

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Sodium Binding Sites List in 3rji

Sodium 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 Sodium with other atoms in the Na 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:Na404 b:22.6 occ:1.00	O	A:THR101	2.3	22.6	1.0
	O	A:HOH551	2.4	42.4	1.0
	O	A:HOH605	2.5	23.1	1.0
	O	A:VAL103	2.5	19.3	1.0
	OP1	P:DG9	2.6	26.3	1.0
	O	A:ILE106	2.6	19.1	1.0
	C	A:THR101	3.3	20.8	1.0
	C	A:VAL103	3.4	18.8	1.0
	P	P:DG9	3.5	29.2	1.0
	OP2	P:DG9	3.5	27.9	1.0
	C	A:ILE106	3.6	19.7	1.0
	O	A:HOH719	3.7	45.7	1.0
	N	A:ILE106	3.8	19.8	1.0
	CA	A:THR101	3.9	21.9	1.0
	CA	A:SER104	4.0	18.7	1.0
	N	A:GLY105	4.0	18.8	1.0
	N	A:VAL103	4.1	19.3	1.0
	N	A:SER104	4.1	17.5	1.0
	CA	A:ILE106	4.2	18.9	1.0
	O3'	P:DC8	4.3	26.3	1.0
	C	A:SER104	4.3	18.3	1.0
	N	A:ARG102	4.3	18.9	1.0
	C	A:ARG102	4.3	19.9	1.0
	O	P:HOH115	4.4	30.2	1.0
	CA	A:VAL103	4.4	18.5	1.0
	N	A:GLY107	4.5	18.6	1.0
	CB	A:THR101	4.5	22.9	1.0
	CB	A:ILE106	4.6	19.4	1.0
	CA	A:ARG102	4.6	19.1	1.0
	C	A:GLY105	4.7	19.9	1.0
	CA	A:GLY107	4.8	20.2	1.0
	O5'	P:DG9	4.8	28.3	1.0
	O	A:LEU100	4.8	16.4	1.0
	O	A:ARG102	4.9	18.6	1.0
	CA	A:GLY105	5.0	19.2	1.0

Sodium binding site 2 out of 2 in 3rji

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Sodium Binding Sites List in 3rji

Sodium 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 Sodium with other atoms in the Na 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:Na405 b:39.0 occ:1.00	OP1	D:DC3	2.5	41.5	1.0
	O	A:HOH586	2.5	34.9	1.0
	O	A:LYS60	2.6	41.6	1.0
	O	A:VAL65	2.6	35.7	1.0
	O	A:LEU62	2.6	38.6	1.0
	O	D:HOH101	2.8	35.4	1.0
	P	D:DC3	3.5	43.0	1.0
	C	A:LEU62	3.5	39.4	1.0
	OP2	D:DC3	3.5	40.3	1.0
	C	A:VAL65	3.6	35.5	1.0
	CA	A:PRO63	3.7	39.0	1.0
	C	A:LYS60	3.7	41.3	1.0
	N	A:VAL65	3.8	35.1	1.0
	N	A:PRO63	3.9	39.5	1.0
	N	A:GLY64	3.9	37.7	1.0
	O	A:LYS61	4.0	43.4	1.0
	CA	A:VAL65	4.2	35.0	1.0
	C	A:PRO63	4.2	39.0	1.0
	C	A:LYS61	4.2	42.4	1.0
	CA	A:LYS60	4.5	40.4	1.0
	CG	A:LYS60	4.5	39.6	1.0
	CB	A:VAL65	4.5	35.8	1.0
	O3'	D:DT2	4.5	42.3	1.0
	N	A:LEU62	4.5	40.7	1.0
	CA	A:LEU62	4.7	39.2	1.0
	N	A:GLY66	4.7	34.9	1.0
	O5'	D:DC3	4.7	43.9	1.0
	N	A:LYS61	4.7	42.0	1.0
	C	A:GLY64	4.8	36.9	1.0
	CA	A:LYS61	4.9	43.4	1.0
	CB	A:PRO63	4.9	40.2	1.0
	CA	A:GLY66	5.0	34.1	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: Mon Oct 7 12:48:51 2024

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