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

Go back to

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

Go back to

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

Go back to

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

Go back to

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: Sun Jul 21 03:43:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy