Chlorine in PDB 6ctj: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CHCH3, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CHCH3, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CHCH3, Beta, Gamma Dttp 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 CHCH3, Beta, Gamma Dttp Analogue, PDB code: 6ctj 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)*	23.12 / 2.10
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	48.469, 76.947, 55.014, 90.00, 103.88, 90.00
*R / R_free (%)*	19.1 / 25.7

Other elements in 6ctj:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CHCH3, Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	2 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 CHCH3, Beta, Gamma Dttp Analogue (pdb code 6ctj). 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 CHCH3, Beta, Gamma Dttp Analogue, PDB code: 6ctj:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6ctj

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Chlorine Binding Sites List in 6ctj

Chlorine binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CHCH3, Beta, Gamma Dttp 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 CHCH3, Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl403 b:46.3 occ:1.00	OG1	A:THR297	3.1	36.5	1.0
	ND2	A:ASN294	3.1	30.3	1.0
	OD1	A:ASN294	3.8	32.6	1.0
	CG	A:ASN294	3.9	32.9	1.0
	CZ	A:ARG299	4.1	52.7	1.0
	CG2	A:THR297	4.1	32.9	1.0
	NE	A:ARG299	4.1	47.4	1.0
	CB	A:TYR296	4.1	34.2	1.0
	CB	A:THR297	4.2	37.3	1.0
	NH2	A:ARG299	4.2	51.7	1.0
	NH1	A:ARG299	4.4	48.9	1.0
	CD2	A:TYR296	4.4	32.8	1.0
	O	A:HOH544	4.5	37.3	1.0
	CD	A:ARG299	4.6	48.4	1.0
	N	A:THR297	4.7	36.7	1.0
	CG	A:TYR296	4.7	32.8	1.0

Chlorine binding site 2 out of 3 in 6ctj

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Chlorine Binding Sites List in 6ctj

Chlorine binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CHCH3, Beta, Gamma Dttp 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 CHCH3, Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl404 b:50.5 occ:1.00	NH2	A:ARG89	3.1	39.2	1.0
	N	A:LEU82	3.2	33.4	1.0
	NH1	A:ARG89	3.6	49.0	1.0
	CA	A:LYS81	3.6	36.8	1.0
	CZ	A:ARG89	3.7	45.5	1.0
	CB	A:LEU85	3.8	32.1	1.0
	CD1	A:LEU85	3.9	34.8	1.0
	C	A:LYS81	3.9	33.7	1.0
	CB	A:LYS81	4.0	36.7	1.0
	O	A:LEU82	4.1	30.8	1.0
	CG	A:LYS81	4.2	39.8	1.0
	CA	A:LEU82	4.2	36.0	1.0
	CB	A:LEU82	4.3	40.7	1.0
	CG	A:LEU85	4.5	33.4	1.0
	C	A:LEU82	4.6	36.6	1.0
	O	A:GLY80	4.6	30.9	1.0
	N	A:LYS81	4.8	36.5	1.0
	CG	A:GLU86	4.9	40.1	1.0
	NE	A:ARG89	5.0	46.2	1.0

Chlorine binding site 3 out of 3 in 6ctj

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Chlorine Binding Sites List in 6ctj

Chlorine binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CHCH3, Beta, Gamma Dttp 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 CHCH3, Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl405 b:42.2 occ:1.00	O	D:HOH105	2.4	47.1	1.0
	N	A:HIS34	3.3	31.0	1.0
	CB	A:ALA32	3.5	32.8	1.0
	C	A:ALA32	3.5	28.5	1.0
	CB	A:HIS34	3.5	36.0	1.0
	N	A:LYS35	3.5	27.8	1.0
	CA	A:ALA32	3.6	31.7	1.0
	O	A:ALA32	3.7	29.1	1.0
	CD2	A:HIS34	3.8	35.3	1.0
	CA	A:HIS34	3.8	33.6	1.0
	N	A:ILE33	3.8	30.3	1.0
	CG	A:LYS35	3.9	28.7	1.0
	CG	A:HIS34	4.0	37.0	1.0
	C	A:HIS34	4.1	28.5	1.0
	CB	A:LYS35	4.4	28.0	1.0
	C	A:ILE33	4.4	35.4	1.0
	CA	A:LYS35	4.5	31.1	1.0
	O6	D:DG1	4.6	28.2	1.0
	CD	A:LYS35	4.7	34.6	1.0
	CA	A:ILE33	4.7	30.5	1.0
	C6	D:DG1	4.9	34.9	1.0
	CE	A:LYS35	4.9	35.5	1.0
	O	A:HOH517	5.0	39.0	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 12:33:14 2025

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