Chlorine in PDB 3rjh: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site, PDB code: 3rjh 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)*	21.35 / 2.20
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.530, 79.910, 55.460, 90.00, 108.04, 90.00
*R / R_free (%)*	20.4 / 25.9

Other elements in 3rjh:

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site 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 (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site (pdb code 3rjh). 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:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site, PDB code: 3rjh:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3rjh

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Chlorine Binding Sites List in 3rjh

Chlorine binding site 1 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

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:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl406 b:34.6 occ:1.00	O	A:HOH565	3.1	24.6	1.0
	NH2	A:ARG299	3.1	35.4	1.0
	ND2	A:ASN294	3.3	22.5	1.0
	OG1	A:THR297	3.4	26.9	1.0
	NE	A:ARG299	3.6	37.2	1.0
	CZ	A:ARG299	3.6	36.1	1.0
	CG2	A:THR297	3.9	19.4	1.0
	O	A:HOH591	4.0	39.6	1.0
	OD1	A:ASN294	4.0	26.2	1.0
	CB	A:TYR296	4.1	23.3	1.0
	CG	A:ASN294	4.1	25.7	1.0
	CD2	A:TYR296	4.2	20.1	1.0
	CB	A:THR297	4.3	24.9	1.0
	O	T:HOH127	4.4	48.4	1.0
	CG	A:TYR296	4.6	21.3	1.0
	N	A:THR297	4.7	22.3	1.0
	CD	A:ARG299	4.7	34.6	1.0
	NH1	A:ARG299	4.7	38.3	1.0
	O	A:HOH604	4.8	25.7	1.0
	O	A:HOH656	4.9	39.0	1.0

Chlorine binding site 2 out of 4 in 3rjh

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Chlorine Binding Sites List in 3rjh

Chlorine binding site 2 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

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:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl407 b:39.2 occ:1.00	O	A:HOH726	3.1	43.2	1.0
	N	A:CYS267	3.4	25.5	1.0
	N	A:TYR266	3.6	26.9	1.0
	CA	A:GLN264	3.6	26.6	1.0
	C	A:GLN264	3.7	26.2	1.0
	CB	A:TYR266	3.7	28.4	1.0
	CG1	A:VAL313	3.8	34.1	1.0
	O	A:GLN264	3.8	26.2	1.0
	CB	A:VAL313	3.8	34.4	1.0
	SG	A:CYS267	3.8	27.2	1.0
	CA	A:TYR266	3.9	28.1	1.0
	CB	A:CYS267	4.1	26.5	1.0
	O	A:ASP263	4.1	29.1	1.0
	C	A:TYR266	4.1	27.1	1.0
	N	A:TYR265	4.2	26.0	1.0
	CA	A:CYS267	4.3	24.8	1.0
	O	A:VAL313	4.3	33.4	1.0
	O	A:TYR296	4.4	21.3	1.0
	CD2	A:TYR266	4.4	35.3	1.0
	CB	A:GLN264	4.5	27.5	1.0
	C	A:TYR265	4.5	27.1	1.0
	CG	A:TYR266	4.6	32.9	1.0
	CG2	A:VAL313	4.6	34.2	1.0
	N	A:GLN264	4.7	27.0	1.0
	C	A:ASP263	4.8	27.4	1.0
	C	A:VAL313	4.8	35.3	1.0
	CA	A:VAL313	4.9	35.2	1.0
	CA	A:TYR265	4.9	27.1	1.0
	CG	A:GLN264	5.0	29.8	1.0

Chlorine binding site 3 out of 4 in 3rjh

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Chlorine Binding Sites List in 3rjh

Chlorine binding site 3 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

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:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl408 b:51.4 occ:1.00	N	A:HIS34	3.1	28.8	1.0
	CB	A:HIS34	3.3	31.5	1.0
	C	A:ALA32	3.3	29.7	1.0
	CA	A:ALA32	3.4	30.4	1.0
	CB	A:ALA32	3.5	28.2	1.0
	N	A:LYS35	3.6	27.4	1.0
	CA	A:HIS34	3.6	29.6	1.0
	O	A:ALA32	3.6	30.1	1.0
	N	A:ILE33	3.7	29.3	1.0
	CG	A:HIS34	3.9	35.1	1.0
	CD2	A:HIS34	4.0	34.2	1.0
	C	A:HIS34	4.1	28.9	1.0
	C	A:ILE33	4.1	29.8	1.0
	O	A:HOH564	4.2	39.7	1.0
	CA	A:ILE33	4.4	29.6	1.0
	CG	A:LYS35	4.4	30.2	1.0
	CG2	A:ILE33	4.7	29.8	1.0
	CA	A:LYS35	4.7	26.3	1.0
	CB	A:LYS35	4.7	27.2	1.0
	O	A:HOH653	4.9	36.8	1.0
	N	A:ALA32	4.9	30.8	1.0
	O6	D:DG1	4.9	26.6	1.0

Chlorine binding site 4 out of 4 in 3rjh

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Chlorine Binding Sites List in 3rjh

Chlorine binding site 4 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

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:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl409 b:45.4 occ:1.00	O	A:HOH717	2.9	32.9	1.0
	N	A:LEU82	3.1	41.5	1.0
	NH2	A:ARG89	3.2	55.7	1.0
	O	A:HOH716	3.3	34.7	1.0
	NH1	A:ARG89	3.4	54.6	1.0
	CA	A:LYS81	3.7	42.5	1.0
	CZ	A:ARG89	3.7	54.4	1.0
	CB	A:LYS81	3.7	44.0	1.0
	C	A:LYS81	3.9	41.7	1.0
	O	A:LEU82	3.9	43.7	1.0
	CB	A:LEU85	4.0	40.8	1.0
	CA	A:LEU82	4.0	43.5	1.0
	CD1	A:LEU85	4.0	37.9	1.0
	CB	A:LEU82	4.0	43.5	1.0
	C	A:LEU82	4.4	44.0	1.0
	CG	A:LEU85	4.6	39.3	1.0
	OE1	A:GLU86	4.9	58.1	1.0
	CG	A:LYS81	5.0	47.0	1.0
	NE	A:ARG89	5.0	53.2	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: Sat Dec 12 10:07:19 2020

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