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

Go back to

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

Go back to

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

Go back to

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

Go back to

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: Sun Jul 21 03:43:09 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1

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