Fluorine in PDB 4do9: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4do9 was solved by V.K.Batra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.28 / 2.05
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.693, 79.914, 55.607, 90.00, 107.66, 90.00
*R / R_free (%)*	18.8 / 24.3

Other elements in 4do9:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	5 atoms
Sodium	(Na)	3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer (pdb code 4do9). 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 of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4do9:

Fluorine binding site 1 out of 1 in 4do9

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Fluorine Binding Sites List in 4do9

Fluorine binding site 1 out of 1 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F410 b:18.7 occ:1.00	F3B	A:GFH410	0.0	18.7	1.0
	C3B	A:GFH410	1.4	15.9	1.0
	PG	A:GFH410	2.6	21.2	1.0
	PB	A:GFH410	2.7	15.6	1.0
	O1B	A:GFH410	2.8	14.8	1.0
	O3G	A:GFH410	2.9	20.9	1.0
	NH2	A:ARG183	3.1	14.5	1.0
	O	A:HOH611	3.1	24.1	1.0
	O2G	A:GFH410	3.1	23.8	1.0
	O	A:HOH568	3.2	22.1	1.0
	CB	A:SER180	3.5	16.3	1.0
	O2B	A:GFH410	3.6	14.9	1.0
	O3A	A:GFH410	3.8	15.9	1.0
	O1G	A:GFH410	3.8	17.1	1.0
	O	A:HOH507	3.9	16.4	1.0
	OG	A:SER180	4.0	17.8	1.0
	CZ	A:ARG183	4.1	15.9	1.0
	NH1	A:ARG183	4.2	14.1	1.0
	N	A:SER180	4.3	17.3	1.0
	O	A:HOH600	4.4	22.5	1.0
	CA	A:SER180	4.4	13.5	1.0
	O	A:HOH578	4.6	30.2	1.0
	MG	A:MG401	4.9	15.8	1.0
	O	A:HOH662	4.9	31.4	1.0

Reference:

Y.Wu, V.M.Zakharova, B.A.Kashemirov, M.F.Goodman, V.K.Batra, S.H.Wilson, C.E.Mckenna. Beta,Gamma-Chf- and Beta,Gamma-Chcl-Dgtp Diastereomers: Synthesis, Discrete (31)P uc(Nmr) Signatures, and Absolute Configurations of New Stereochemical Probes For Dna Polymerases J.Am.Chem.Soc. V. 134 8734 2012.
ISSN: ISSN 0002-7863
PubMed: 22397499
DOI: 10.1021/JA300218X

Page generated: Thu Aug 1 01:03:29 2024

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