Chlorine in PDB 6cr8: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue, PDB code: 6cr8 was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.28 / 2.05
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.585, 78.601, 55.473, 90.00, 107.14, 90.00
*R / R_free (%)*	19.1 / 24.8

Other elements in 6cr8:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue (pdb code 6cr8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue, PDB code: 6cr8:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6cr8

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Chlorine Binding Sites List in 6cr8

Chlorine binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl401 b:46.8 occ:0.99	CL1	A:VA4401	0.0	46.8	1.0
	C3B	A:VA4401	1.8	31.5	1.0
	PG	A:VA4401	2.9	36.2	1.0
	PB	A:VA4401	3.0	28.1	1.0
	O3G	A:VA4401	3.1	30.0	1.0
	O2B	A:VA4401	3.1	24.0	1.0
	NH2	A:ARG183	3.3	20.7	1.0
	O2G	A:VA4401	3.6	38.0	1.0
	O	A:HOH529	3.8	26.6	1.0
	CB	A:SER180	3.8	24.9	1.0
	O1B	A:VA4401	3.9	22.1	1.0
	OG	A:SER180	4.1	26.8	1.0
	O3A	A:VA4401	4.2	27.2	1.0
	O1G	A:VA4401	4.2	27.6	1.0
	CZ	A:ARG183	4.4	20.4	1.0
	O	A:HOH671	4.6	36.1	1.0
	NH1	A:ARG183	4.7	22.0	1.0
	CA	A:SER180	4.8	24.7	1.0
	N	A:SER180	4.9	22.6	1.0
	O	A:HOH612	4.9	31.4	1.0

Chlorine binding site 2 out of 3 in 6cr8

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Chlorine Binding Sites List in 6cr8

Chlorine binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl406 b:39.7 occ:1.00	OG1	A:THR297	3.0	26.8	1.0
	O	A:HOH737	3.0	39.8	1.0
	O	A:HOH719	3.3	41.1	1.0
	ND2	A:ASN294	3.4	22.7	1.0
	CG2	A:THR297	3.7	26.9	1.0
	OD1	A:ASN294	3.9	26.5	1.0
	CB	A:THR297	3.9	26.5	1.0
	CB	A:TYR296	4.0	34.7	1.0
	NE	A:ARG299	4.0	43.0	1.0
	CG	A:ASN294	4.1	23.5	1.0
	CZ	A:ARG299	4.1	51.3	1.0
	CD2	A:TYR296	4.2	27.0	1.0
	NH2	A:ARG299	4.3	39.6	1.0
	CG	A:TYR296	4.5	24.0	1.0
	CD	A:ARG299	4.5	32.9	1.0
	N	A:THR297	4.5	24.0	1.0
	O	A:HOH575	4.6	26.1	1.0
	NH1	A:ARG299	4.6	55.1	1.0
	CA	A:THR297	4.9	26.4	1.0
	O	A:HOH722	4.9	47.3	1.0

Chlorine binding site 3 out of 3 in 6cr8

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Chlorine Binding Sites List in 6cr8

Chlorine binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl407 b:41.3 occ:1.00	N	A:HIS34	3.2	28.4	1.0
	CB	A:HIS34	3.3	25.9	1.0
	N	A:LYS35	3.5	27.6	1.0
	C	A:ALA32	3.5	25.7	1.0
	CD2	A:HIS34	3.6	35.3	1.0
	CB	A:ALA32	3.6	23.4	1.0
	CA	A:ALA32	3.7	31.0	1.0
	CA	A:HIS34	3.7	29.5	1.0
	CG	A:HIS34	3.8	36.0	1.0
	N	A:ILE33	3.8	28.0	1.0
	O	A:ALA32	3.8	29.4	1.0
	CG	A:LYS35	4.0	30.1	1.0
	C	A:HIS34	4.1	28.8	1.0
	O	A:HOH600	4.2	45.8	1.0
	C	A:ILE33	4.3	27.1	1.0
	CB	A:LYS35	4.5	24.5	1.0
	CA	A:LYS35	4.6	27.1	1.0
	CA	A:ILE33	4.7	29.5	1.0
	O6	D:DG1	4.8	26.4	1.0
	NE2	A:HIS34	4.9	48.0	1.0
	O	D:HOH107	5.0	44.3	1.0

Reference:

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418

Page generated: Sat Jul 12 12:31:35 2025

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