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

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, 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 Cfcl, Beta, Gamma Dctp Analogue, PDB code: 6ctu 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)*	23.72 / 1.90
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.810, 79.636, 55.483, 90.00, 107.78, 90.00
*R / R_free (%)*	17.1 / 20.6

Other elements in 6ctu:

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

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms
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 Cfcl, Beta, Gamma Dctp Analogue (pdb code 6ctu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue, PDB code: 6ctu:

Fluorine binding site 1 out of 1 in 6ctu

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Fluorine Binding Sites List in 6ctu

Fluorine binding site 1 out of 1 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, 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 Cfcl, Beta, Gamma Dctp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F404 b:20.9 occ:1.00	F4B	A:VC6404	0.0	20.9	1.0
	C3B	A:VC6404	1.4	21.6	1.0
	CL1	A:VC6404	2.5	23.8	1.0
	PG	A:VC6404	2.7	24.4	1.0
	PB	A:VC6404	2.7	16.2	1.0
	O2B	A:VC6404	2.9	14.6	1.0
	O3G	A:VC6404	3.1	21.9	1.0
	NH2	A:ARG183	3.1	18.1	1.0
	O	A:HOH581	3.3	32.0	1.0
	O1G	A:VC6404	3.3	30.6	1.0
	O	A:HOH834	3.4	24.9	1.0
	CB	A:SER180	3.5	16.7	1.0
	O1B	A:VC6404	3.7	14.0	1.0
	OG	A:SER180	3.9	22.0	1.0
	O3A	A:VC6404	3.9	15.9	1.0
	O2G	A:VC6404	3.9	16.9	1.0
	O	A:HOH661	4.0	30.0	1.0
	O	A:HOH681	4.1	16.2	1.0
	CZ	A:ARG183	4.1	16.9	1.0
	NH1	A:ARG183	4.3	14.1	1.0
	N	A:SER180	4.4	17.7	1.0
	CA	A:SER180	4.4	14.0	1.0
	O	A:HOH749	4.5	28.6	1.0
	O	A:HOH722	4.9	32.5	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 18:41:05 2024

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