Fluorine in PDB 6ctv: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp 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 CF2, Beta, Gamma Dctp Analogue, PDB code: 6ctv 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)*	23.62 / 2.02
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.666, 79.251, 55.337, 90.00, 107.75, 90.00
*R / R_free (%)*	18 / 22

Other elements in 6ctv:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom
Sodium	(Na)	3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue (pdb code 6ctv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue, PDB code: 6ctv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6ctv

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Fluorine Binding Sites List in 6ctv

Fluorine binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F406 b:21.2 occ:1.00	F3B	A:FFJ406	0.0	21.2	1.0
	C3B	A:FFJ406	1.4	23.2	1.0
	F4B	A:FFJ406	2.3	24.2	1.0
	PB	A:FFJ406	2.6	20.7	1.0
	PG	A:FFJ406	2.6	26.3	1.0
	O3A	A:FFJ406	2.7	24.4	1.0
	O1G	A:FFJ406	2.8	25.5	1.0
	O	A:HOH807	3.2	40.6	1.0
	O2G	A:FFJ406	3.3	23.2	1.0
	O	A:HOH657	3.3	22.1	1.0
	O	A:HOH735	3.4	29.2	1.0
	O2B	A:FFJ406	3.4	19.0	1.0
	O	A:HOH760	3.5	31.0	1.0
	O	A:HOH799	3.6	43.5	1.0
	O1B	A:FFJ406	3.9	20.0	1.0
	O3G	A:FFJ406	3.9	24.7	1.0
	PA	A:FFJ406	3.9	20.4	1.0
	O2A	A:FFJ406	4.0	21.3	1.0
	O	A:HOH742	4.2	34.4	1.0
	O	A:HOH628	4.2	36.4	1.0
	O1A	A:FFJ406	4.4	16.8	1.0
	O	A:HOH748	4.7	39.6	1.0
	MG	A:MG402	4.7	19.1	1.0
	NH2	A:ARG183	4.9	20.4	1.0

Fluorine binding site 2 out of 2 in 6ctv

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Fluorine Binding Sites List in 6ctv

Fluorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F406 b:24.2 occ:1.00	F4B	A:FFJ406	0.0	24.2	1.0
	C3B	A:FFJ406	1.4	23.2	1.0
	F3B	A:FFJ406	2.3	21.2	1.0
	PB	A:FFJ406	2.6	20.7	1.0
	PG	A:FFJ406	2.7	26.3	1.0
	O2B	A:FFJ406	2.9	19.0	1.0
	O3G	A:FFJ406	2.9	24.7	1.0
	NH2	A:ARG183	3.1	20.4	1.0
	O	A:HOH628	3.1	36.4	1.0
	O	A:HOH760	3.2	31.0	1.0
	O1G	A:FFJ406	3.3	25.5	1.0
	CB	A:SER180	3.4	23.5	1.0
	O	A:HOH799	3.4	43.5	1.0
	O1B	A:FFJ406	3.5	20.0	1.0
	OG	A:SER180	3.8	27.5	1.0
	O3A	A:FFJ406	3.8	24.4	1.0
	O2G	A:FFJ406	3.9	23.2	1.0
	O	A:HOH657	4.0	22.1	1.0
	CZ	A:ARG183	4.1	19.5	1.0
	NH1	A:ARG183	4.2	15.6	1.0
	N	A:SER180	4.2	20.8	1.0
	CA	A:SER180	4.3	18.9	1.0
	O	A:HOH682	4.5	31.8	1.0
	O	A:HOH515	4.5	33.7	1.0
	MG	A:MG402	4.9	19.1	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: Thu Aug 1 18:41:11 2024

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