Chlorine 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:

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 (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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3rjf

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Chlorine Binding Sites List in 3rjf

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl344 b:40.0 occ:1.00	ND2	A:ASN294	3.1	28.4	1.0
	OG1	A:THR297	3.3	32.4	1.0
	O	A:HOH496	3.4	46.3	1.0
	O	A:HOH495	3.5	44.2	1.0
	NH2	A:ARG299	3.8	48.2	1.0
	NE	A:ARG299	3.8	44.0	1.0
	CZ	A:ARG299	3.9	46.6	1.0
	CB	A:TYR296	3.9	28.9	1.0
	OD1	A:ASN294	4.0	27.6	1.0
	CG	A:ASN294	4.0	28.4	1.0
	CD2	A:TYR296	4.2	26.9	1.0
	O	T:HOH210	4.2	44.7	1.0
	CG	A:TYR296	4.5	28.0	1.0
	NH1	A:ARG299	4.5	45.0	1.0
	CD	A:ARG299	4.6	40.8	1.0
	CB	A:THR297	4.6	34.1	1.0
	N	A:THR297	4.7	30.2	1.0
	O	A:HOH443	4.8	25.6	1.0
	CG2	A:THR297	5.0	34.3	1.0

Chlorine binding site 2 out of 4 in 3rjf

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Chlorine Binding Sites List in 3rjf

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl345 b:51.3 occ:1.00	N	A:LEU82	3.2	35.7	1.0
	NH2	A:ARG89	3.3	50.7	1.0
	NH1	A:ARG89	3.4	48.5	1.0
	O	A:HOH547	3.7	48.7	1.0
	CA	A:LYS81	3.8	40.0	1.0
	CZ	A:ARG89	3.8	50.2	1.0
	CB	A:LYS81	3.9	42.4	1.0
	O	A:LEU82	3.9	38.0	1.0
	C	A:LYS81	4.0	38.3	1.0
	CD1	A:LEU85	4.0	35.0	1.0
	CB	A:LEU82	4.0	37.3	1.0
	CA	A:LEU82	4.1	36.6	1.0
	CB	A:LEU85	4.1	37.2	1.0
	C	A:LEU82	4.5	37.1	1.0
	CG	A:LEU85	4.7	36.4	1.0
	CE1	A:PHE76	4.9	34.2	1.0

Chlorine binding site 3 out of 4 in 3rjf

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Chlorine Binding Sites List in 3rjf

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl346 b:47.6 occ:1.00	CB	A:HIS34	3.2	34.9	1.0
	O	A:HOH536	3.3	40.1	1.0
	CB	A:ALA32	3.3	25.5	1.0
	N	A:HIS34	3.4	32.8	1.0
	N	A:LYS35	3.5	32.7	1.0
	CA	A:ALA32	3.6	29.8	1.0
	C	A:ALA32	3.6	30.2	1.0
	CD2	A:HIS34	3.7	39.1	1.0
	CA	A:HIS34	3.7	34.0	1.0
	CG	A:HIS34	3.7	38.3	1.0
	O	A:ALA32	3.8	31.7	1.0
	CG	A:LYS35	4.0	34.2	1.0
	C	A:HIS34	4.1	34.3	1.0
	N	A:ILE33	4.1	31.5	1.0
	C	A:ILE33	4.5	32.7	1.0
	CB	A:LYS35	4.5	33.0	1.0
	CA	A:LYS35	4.6	32.2	1.0
	O	A:HOH396	4.9	35.5	1.0
	CA	A:ILE33	4.9	34.0	1.0
	CD	A:LYS35	5.0	34.4	1.0
	NE2	A:HIS34	5.0	39.0	1.0
	CD1	A:ILE33	5.0	40.5	1.0

Chlorine binding site 4 out of 4 in 3rjf

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Chlorine Binding Sites List in 3rjf

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl347 b:48.2 occ:1.00	N	A:CYS267	3.1	27.1	1.0
	C	A:GLN264	3.5	32.5	1.0
	O	A:GLN264	3.5	34.2	1.0
	CA	A:GLN264	3.6	33.8	1.0
	N	A:TYR266	3.6	30.2	1.0
	CB	A:CYS267	3.6	25.3	1.0
	SG	A:CYS267	3.6	26.2	1.0
	CB	A:TYR266	3.7	31.9	1.0
	CG1	A:VAL313	3.8	30.1	1.0
	O	A:ASP263	3.9	37.0	1.0
	CA	A:TYR266	3.9	29.8	1.0
	CB	A:VAL313	3.9	32.0	1.0
	CA	A:CYS267	4.0	25.4	1.0
	C	A:TYR266	4.0	28.5	1.0
	N	A:TYR265	4.0	32.1	1.0
	C	A:TYR265	4.3	31.6	1.0
	O	A:TYR296	4.3	26.5	1.0
	CD2	A:TYR266	4.5	37.0	1.0
	CB	A:GLN264	4.5	34.4	1.0
	N	A:GLN264	4.5	34.3	1.0
	C	A:ASP263	4.6	34.7	1.0
	CG	A:TYR266	4.6	35.8	1.0
	O	A:VAL313	4.6	34.1	1.0
	CG2	A:VAL313	4.7	29.6	1.0
	CA	A:TYR265	4.7	31.7	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: Fri Jul 11 09:51:55 2025

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