Chlorine in PDB 6cti: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, 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 CCL2, Beta, Gamma Dttp Analogue, PDB code: 6cti 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)*	26.49 / 2.00
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.618, 79.117, 55.407, 90.00, 107.00, 90.00
*R / R_free (%)*	17.7 / 22.7

Other elements in 6cti:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp 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 CCL2, Beta, Gamma Dttp Analogue (pdb code 6cti). 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 Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp Analogue, PDB code: 6cti:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6cti

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Chlorine Binding Sites List in 6cti

Chlorine binding site 1 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, 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 CCL2, Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl403 b:36.4 occ:1.00	N	A:HIS34	3.3	30.5	1.0
	C	A:ALA32	3.4	31.0	1.0
	CB	A:ALA32	3.5	28.4	1.0
	CB	A:HIS34	3.5	26.5	1.0
	CA	A:ALA32	3.5	36.2	1.0
	N	A:LYS35	3.6	25.8	1.0
	N	A:ILE33	3.6	29.5	1.0
	O	A:ALA32	3.7	29.9	1.0
	CA	A:HIS34	3.8	31.0	1.0
	CD2	A:HIS34	3.8	34.4	1.0
	CG	A:HIS34	4.0	32.3	1.0
	CG	A:LYS35	4.1	31.7	1.0
	C	A:HIS34	4.2	28.5	1.0
	C	A:ILE33	4.3	28.2	1.0
	O	A:HOH608	4.4	32.1	1.0
	CA	A:ILE33	4.6	32.7	1.0
	CB	A:LYS35	4.6	28.7	1.0
	CA	A:LYS35	4.7	28.5	1.0
	O	D:HOH207	4.8	41.4	1.0
	N	A:ALA32	4.9	31.1	1.0

Chlorine binding site 2 out of 4 in 6cti

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Chlorine Binding Sites List in 6cti

Chlorine binding site 2 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, 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 CCL2, Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl404 b:31.2 occ:0.79	CL1	A:VT8404	0.0	31.2	0.8
	C3B	A:VT8404	1.8	28.7	1.0
	CL2	A:VT8404	2.8	41.4	1.0
	PG	A:VT8404	2.9	34.0	1.0
	PB	A:VT8404	3.0	22.1	1.0
	O3G	A:VT8404	3.1	31.3	1.0
	O2B	A:VT8404	3.1	23.4	1.0
	NH2	A:ARG183	3.3	27.1	1.0
	O	A:HOH737	3.5	38.1	1.0
	O2G	A:VT8404	3.5	38.8	1.0
	O	A:HOH505	3.6	43.1	1.0
	CB	A:SER180	3.7	25.2	1.0
	O1B	A:VT8404	3.9	20.0	1.0
	OG	A:SER180	4.0	27.2	1.0
	O	A:HOH544	4.1	36.8	1.0
	O1G	A:VT8404	4.1	26.8	1.0
	O3A	A:VT8404	4.2	24.7	1.0
	O	A:HOH659	4.2	21.8	1.0
	CZ	A:ARG183	4.4	27.4	1.0
	O	A:HOH682	4.4	37.8	1.0
	NH1	A:ARG183	4.6	21.5	1.0
	CA	A:SER180	4.7	22.1	1.0
	N	A:SER180	4.7	23.2	1.0

Chlorine binding site 3 out of 4 in 6cti

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Chlorine Binding Sites List in 6cti

Chlorine binding site 3 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, 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 CCL2, Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl404 b:41.4 occ:1.00	CL2	A:VT8404	0.0	41.4	1.0
	C3B	A:VT8404	1.7	28.7	1.0
	CL1	A:VT8404	2.8	31.2	0.8
	PG	A:VT8404	2.8	34.0	1.0
	PB	A:VT8404	3.0	22.1	1.0
	O3A	A:VT8404	3.0	24.7	1.0
	O2G	A:VT8404	3.0	38.8	1.0
	O	A:HOH719	3.3	37.6	1.0
	O1G	A:VT8404	3.4	26.8	1.0
	O	A:HOH507	3.7	42.2	1.0
	O	A:HOH659	3.7	21.8	1.0
	O2A	A:VT8404	3.7	23.2	1.0
	O2B	A:VT8404	3.8	23.4	1.0
	PA	A:VT8404	3.9	27.4	1.0
	O3G	A:VT8404	4.1	31.3	1.0
	O	A:HOH737	4.1	38.1	1.0
	O	A:HOH672	4.2	37.7	1.0
	O1B	A:VT8404	4.2	20.0	1.0
	O	A:HOH505	4.4	43.1	1.0
	O1A	A:VT8404	4.5	24.7	1.0
	MG	A:MG401	4.9	20.6	1.0

Chlorine binding site 4 out of 4 in 6cti

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Chlorine Binding Sites List in 6cti

Chlorine binding site 4 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp Analogue

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CCL2, Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl405 b:39.9 occ:1.00	O	A:HOH703	3.0	45.5	1.0
	O	A:HOH732	3.0	42.1	1.0
	OG1	A:THR297	3.2	28.2	1.0
	ND2	A:ASN294	3.3	25.6	1.0
	CB	A:TYR296	3.9	29.1	1.0
	CG2	A:THR297	3.9	25.3	1.0
	OD1	A:ASN294	4.0	26.3	1.0
	CG	A:ASN294	4.1	28.6	1.0
	CD2	A:TYR296	4.1	28.8	1.0
	CB	A:THR297	4.1	30.3	1.0
	NE	A:ARG299	4.2	43.0	1.0
	CZ	A:ARG299	4.2	46.0	1.0
	NH2	A:ARG299	4.2	44.4	1.0
	CG	A:TYR296	4.4	27.2	1.0
	N	A:THR297	4.7	25.0	1.0
	O	T:HOH106	4.7	39.9	1.0
	NH1	A:ARG299	4.8	51.5	1.0
	O	A:HOH648	4.8	28.1	1.0
	CD	A:ARG299	4.8	33.4	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 12:33:11 2025

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