Fluorine in PDB 5db6: Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc

Enzymatic activity of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc

All present enzymatic activity of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc, PDB code: 5db6 was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.71 / 2.83
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	54.138, 78.828, 54.764, 90.00, 105.92, 90.00
*R / R_free (%)*	18.5 / 26.6

Other elements in 5db6:

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc (pdb code 5db6). 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 Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc, PDB code: 5db6:

Fluorine binding site 1 out of 1 in 5db6

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Fluorine Binding Sites List in 5db6

Fluorine binding site 1 out of 1 in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
P:F4 b:38.6 occ:1.00	F1'	P:FMG4	0.0	38.6	1.0
	C2'	P:FMG4	1.4	30.3	1.0
	C3'	P:FMG4	2.3	30.7	1.0
	C1'	P:FMG4	2.4	25.8	1.0
	O5'	P:FMG4	2.8	29.9	1.0
	C8	P:FMG4	2.9	30.1	1.0
	N9	P:FMG4	2.9	29.9	1.0
	O4'	P:FMG4	2.9	37.5	1.0
	C4'	P:FMG4	3.0	28.6	1.0
	O3'	P:FMG4	3.5	28.4	1.0
	C5'	P:FMG4	3.5	28.6	1.0
	OP2	P:FMG4	4.1	30.2	1.0
	P	P:FMG4	4.1	38.1	1.0
	N7	P:FMG4	4.2	25.7	1.0
	C4	P:FMG4	4.2	25.8	1.0
	OP2	P:DA5	4.2	27.3	1.0
	C2'	P:DT3	4.4	33.0	1.0
	P	P:DA5	4.5	33.0	1.0
	N7	P:DA5	4.7	19.9	1.0
	C5	P:FMG4	4.8	19.6	1.0
	C8	P:DA5	4.9	21.1	1.0
	O3'	P:DT3	5.0	37.5	1.0

Reference:

Y.Kou, M.C.Koag, S.Lee. N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex Dna. J.Am.Chem.Soc. V. 137 14067 2015.
ISSN: ESSN 1520-5126
PubMed: 26517568
DOI: 10.1021/JACS.5B10172

Page generated: Tue Jul 15 02:58:53 2025

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