Chlorine 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
Sodium	(Na)	2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 3rji

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Chlorine Binding Sites List in 3rji

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl406 b:40.5 occ:1.00	O	T:HOH118	3.1	28.7	1.0
	N	A:HIS34	3.2	28.6	1.0
	CB	A:HIS34	3.2	30.8	1.0
	C	A:ALA32	3.5	28.8	1.0
	CB	A:ALA32	3.5	28.6	1.0
	N	A:LYS35	3.5	28.3	1.0
	CA	A:ALA32	3.6	29.3	1.0
	CA	A:HIS34	3.6	30.1	1.0
	O	A:ALA32	3.7	31.4	1.0
	CG	A:HIS34	3.9	33.9	1.0
	CD2	A:HIS34	3.9	33.9	1.0
	N	A:ILE33	3.9	27.9	1.0
	C	A:HIS34	4.0	29.1	1.0
	CG	A:LYS35	4.1	29.2	1.0
	C	A:ILE33	4.3	30.2	1.0
	CB	A:LYS35	4.6	28.1	1.0
	O6	D:DG1	4.6	34.3	1.0
	CA	A:LYS35	4.6	27.0	1.0
	CA	A:ILE33	4.7	29.2	1.0
	O	A:HOH686	4.9	29.3	1.0
	CG2	A:ILE33	4.9	30.4	1.0
	O	A:HOH515	4.9	32.9	1.0

Chlorine binding site 2 out of 2 in 3rji

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Chlorine Binding Sites List in 3rji

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl407 b:42.5 occ:1.00	OG1	A:THR297	3.3	26.8	1.0
	ND2	A:ASN294	3.4	28.1	1.0
	CB	A:TYR296	3.8	30.0	1.0
	NH1	A:ARG299	4.0	43.1	1.0
	OD1	A:ASN294	4.0	27.8	1.0
	CZ	A:ARG299	4.0	42.6	1.0
	CG	A:ASN294	4.1	26.5	1.0
	CD2	A:TYR296	4.1	27.5	1.0
	NH2	A:ARG299	4.4	41.2	1.0
	NE	A:ARG299	4.4	40.9	1.0
	CG	A:TYR296	4.4	28.0	1.0
	O	A:HOH566	4.6	45.0	1.0
	CB	A:THR297	4.6	29.0	1.0
	N	A:THR297	4.7	27.8	1.0
	O	T:HOH133	4.7	37.7	1.0
	CD	A:ARG299	4.8	38.5	1.0
	O	A:HOH585	4.9	33.9	1.0
	CA	A:TYR296	5.0	29.0	1.0
	OE1	A:GLN264	5.0	36.0	1.0
	C	A:TYR296	5.0	28.4	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: Sun Jul 21 03:43:29 2024

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