Chlorine in PDB 6ctm: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), 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 Chcl(R-Isomer), Beta, Gamma Dttp Analogue, PDB code: 6ctm 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)*	23.69 / 2.10
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	48.404, 76.853, 54.961, 90.00, 103.76, 90.00
*R / R_free (%)*	18.6 / 25.8

Other elements in 6ctm:

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

Chlorine binding site 1 out of 3 in 6ctm

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Chlorine Binding Sites List in 6ctm

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-Isomer), 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 Chcl(R-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl402 b:27.0 occ:0.92	CL1	A:FDJ402	0.0	27.0	0.9
	C3B	A:FDJ402	1.8	24.6	1.0
	PB	A:FDJ402	3.0	22.2	1.0
	O2B	A:FDJ402	3.0	22.1	1.0
	PG	A:FDJ402	3.0	23.9	1.0
	O3G	A:FDJ402	3.2	25.3	1.0
	O	A:HOH678	3.5	35.2	1.0
	O2G	A:FDJ402	3.5	24.7	1.0
	NH2	A:ARG183	3.5	31.6	1.0
	CB	A:SER180	3.9	24.4	1.0
	O1B	A:FDJ402	3.9	23.2	1.0
	O	A:HOH623	3.9	25.2	1.0
	O3A	A:FDJ402	4.0	20.4	1.0
	O1G	A:FDJ402	4.3	24.6	1.0
	NH2	A:ARG149	4.3	31.7	1.0
	OG	A:SER180	4.4	24.2	1.0
	O	A:HOH644	4.5	31.0	1.0
	CZ	A:ARG183	4.6	27.0	1.0
	NH1	A:ARG183	4.8	23.3	1.0
	CA	A:SER180	4.9	27.6	1.0
	N	A:SER180	5.0	30.1	1.0

Chlorine binding site 2 out of 3 in 6ctm

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Chlorine Binding Sites List in 6ctm

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-Isomer), 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 Chcl(R-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl404 b:43.4 occ:1.00	NH2	A:ARG89	2.6	44.2	1.0
	N	A:LEU82	3.5	23.0	1.0
	CZ	A:ARG89	3.6	43.8	1.0
	CB	A:LEU85	3.7	28.3	1.0
	NH1	A:ARG89	3.8	41.4	1.0
	CA	A:LYS81	3.8	30.6	1.0
	CD1	A:LEU85	3.9	27.3	1.0
	O	A:HOH518	4.0	40.0	1.0
	O	A:HOH672	4.0	38.6	1.0
	O	A:LEU82	4.1	30.4	1.0
	CG	A:LYS81	4.1	33.6	1.0
	CB	A:LYS81	4.1	26.1	1.0
	C	A:LYS81	4.2	24.9	1.0
	CG	A:LEU85	4.4	32.8	1.0
	CA	A:LEU82	4.5	28.6	1.0
	O	A:GLY80	4.7	26.6	1.0
	CB	A:LEU82	4.7	27.3	1.0
	C	A:LEU82	4.7	33.9	1.0
	N	A:GLU86	4.7	29.9	1.0
	NE	A:ARG89	4.8	47.6	1.0
	CA	A:LEU85	4.9	29.8	1.0
	C	A:LEU85	4.9	29.2	1.0

Chlorine binding site 3 out of 3 in 6ctm

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Chlorine Binding Sites List in 6ctm

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-Isomer), 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 Chcl(R-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl405 b:34.6 occ:1.00	OG1	A:THR297	3.2	36.1	1.0
	ND2	A:ASN294	3.3	25.3	1.0
	NH1	A:ARG299	3.8	50.0	1.0
	OD1	A:ASN294	3.8	29.7	1.0
	CG2	A:THR297	3.8	32.1	1.0
	CG	A:ASN294	4.0	31.3	1.0
	CB	A:TYR296	4.0	31.2	1.0
	CB	A:THR297	4.1	31.9	1.0
	CD2	A:TYR296	4.5	29.8	1.0
	O	A:HOH577	4.5	34.9	1.0
	O	T:HOH134	4.5	42.6	1.0
	CD	A:ARG299	4.6	40.5	1.0
	N	A:THR297	4.6	29.0	1.0
	O	T:HOH140	4.6	47.7	1.0
	CG	A:TYR296	4.7	30.7	1.0
	CZ	A:ARG299	4.8	51.6	1.0
	CA	A:THR297	5.0	26.8	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 12:33:45 2025

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