Fluorine in PDB 4da4: Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna

All present enzymatic activity of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna:
2.1.1.37;

The structure of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna, PDB code: 4da4 was solved by J.Song, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.47 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.680, 152.042, 96.053, 90.00, 94.54, 90.00
R / Rfree (%)	19.6 / 24.6

The structure of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Fluorine atom in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna (pdb code 4da4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna, PDB code: 4da4:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:F18 b:34.6 occ:1.00 F D:C4918 0.0 34.6 1.0 C5 D:C4918 1.5 31.4 1.0 CM5 D:C4918 2.3 29.4 1.0 C4 D:C4918 2.4 28.8 1.0 N A:CYS1229 2.5 32.0 1.0 C6 D:C4918 2.5 30.0 1.0 N4 D:C4918 2.6 27.7 1.0 SG A:CYS1229 2.9 38.4 1.0 O A:PRO1227 2.9 28.5 1.0 CB A:CYS1229 3.0 32.8 1.0 C A:PRO1228 3.2 33.0 1.0 CA A:PRO1228 3.2 31.9 1.0 CA A:CYS1229 3.3 33.1 1.0 C A:PRO1227 3.7 27.6 1.0 N3 D:C4918 3.7 26.0 1.0 N1 D:C4918 3.8 26.1 1.0 NE2 A:GLN1230 3.8 41.1 1.0 N A:PRO1228 3.9 29.2 1.0 C2 D:C4918 4.2 27.2 1.0 O A:PRO1228 4.2 34.4 1.0 O A:HOH1906 4.4 32.8 1.0 C A:CYS1229 4.5 36.0 1.0 CB A:PRO1228 4.6 35.9 1.0 ND2 A:ASN1270 4.6 27.7 1.0 N A:GLN1230 4.7 36.6 1.0 O A:GLY1226 4.7 33.1 1.0 OD1 A:ASN1580 4.8 20.7 1.0 C5' A:SAH1701 4.9 35.1 0.7 SD A:SAH1701 5.0 40.1 0.7 C A:GLY1226 5.0 26.9 1.0

Fluorine binding site 2 out of 2 in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:F18 b:33.2 occ:1.00 F F:C4918 0.0 33.2 1.0 C5 F:C4918 1.5 30.3 1.0 C4 F:C4918 2.3 29.7 1.0 CM5 F:C4918 2.3 29.4 1.0 N4 F:C4918 2.5 29.4 1.0 C6 F:C4918 2.6 28.8 1.0 N B:CYS1229 2.7 32.5 1.0 SG B:CYS1229 2.8 33.5 1.0 O B:PRO1227 2.9 27.7 1.0 CB B:CYS1229 3.2 36.0 1.0 C B:PRO1228 3.3 33.5 1.0 CA B:PRO1228 3.3 34.4 1.0 CA B:CYS1229 3.5 35.8 1.0 N3 F:C4918 3.7 28.2 1.0 C B:PRO1227 3.7 30.4 1.0 N1 F:C4918 3.8 25.7 1.0 N B:PRO1228 3.9 34.6 1.0 NE2 B:GLN1230 4.2 45.6 1.0 C2 F:C4918 4.2 27.4 1.0 O B:HOH1913 4.3 29.6 1.0 O B:PRO1228 4.3 38.7 1.0 O B:GLY1226 4.6 31.1 1.0 C B:CYS1229 4.7 39.2 1.0 CB B:PRO1228 4.7 37.9 1.0 SD B:SAH1701 4.8 38.5 0.7 C5' B:SAH1701 4.8 35.5 0.7 O B:HOH2009 4.9 28.9 1.0 C B:GLY1226 4.9 26.4 1.0 N B:GLN1230 5.0 41.1 1.0 CA B:PRO1227 5.0 29.9 1.0

J.Song, M.Teplova, S.Ishibe-Murakami, D.J.Patel. Structure-Based Mechanistic Insights Into DNMT1-Mediated Maintenance Dna Methylation. Science V. 335 709 2012.
ISSN: ISSN 0036-8075
PubMed: 22323818
DOI: 10.1126/SCIENCE.1214453