Fluorine in PDB 1dct: Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna

All present enzymatic activity of Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna:
2.1.1.73;

The structure of Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna, PDB code: 1dct was solved by K.M.Reinisch, L.Chen, G.L.Verdine, W.N.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.570, 108.040, 155.790, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 32.6

The structure of Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Fluorine atom in the Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna (pdb code 1dct). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna, PDB code: 1dct:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:F10 b:22.5 occ:1.00 F F:C4910 0.0 22.5 1.0 C5 F:C4910 1.3 18.1 1.0 CM5 F:C4910 2.2 17.0 1.0 C6 F:C4910 2.2 18.5 1.0 C4 F:C4910 2.3 18.1 1.0 SG A:CYS71 2.4 20.7 1.0 N A:CYS71 2.4 18.9 1.0 CB A:CYS71 2.5 17.5 1.0 N4 F:C4910 2.7 16.3 1.0 CA A:CYS71 3.0 18.2 1.0 C A:PRO70 3.3 18.7 1.0 N3 F:C4910 3.3 18.7 1.0 N1 F:C4910 3.4 18.9 1.0 CA A:PRO70 3.6 15.7 1.0 O A:PRO69 3.6 16.2 1.0 HD22 A:ASN306 3.9 0.0 1.0 C2 F:C4910 3.9 20.3 1.0 HE21 A:GLN72 3.9 20.0 1.0 O A:GLY68 4.0 16.9 1.0 C A:CYS71 4.1 20.8 1.0 OE1 A:GLN72 4.2 36.0 1.0 C A:PRO69 4.3 14.3 1.0 N A:GLN72 4.3 20.6 1.0 NE2 A:GLN72 4.3 34.0 1.0 N A:PRO70 4.3 14.7 1.0 O A:PRO70 4.4 21.8 1.0 CD A:GLN72 4.4 32.3 1.0 C1' F:C4910 4.6 15.7 1.0 ND2 A:ASN306 4.7 34.1 1.0 HD21 A:ASN110 4.7 0.0 1.0 HE22 A:GLN72 4.8 20.0 1.0 HD21 A:ASN306 4.9 0.0 1.0 CB A:PRO70 4.9 15.5 1.0

Fluorine binding site 2 out of 2 in the Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dna (Cytosine-5) Methylase From Haeiii Covalently Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:F10 b:17.5 occ:1.00 F G:C4910 0.0 17.5 1.0 C5 G:C4910 1.3 16.6 1.0 CM5 G:C4910 2.2 17.9 1.0 C6 G:C4910 2.2 17.1 1.0 C4 G:C4910 2.3 17.5 1.0 N B:CYS71 2.5 18.2 1.0 SG B:CYS71 2.5 17.2 1.0 CB B:CYS71 2.5 15.2 1.0 N4 G:C4910 2.8 16.8 1.0 CA B:CYS71 3.0 17.5 1.0 O B:PRO69 3.2 14.1 1.0 C B:PRO70 3.3 17.2 1.0 N3 G:C4910 3.4 17.6 1.0 N1 G:C4910 3.5 17.3 1.0 CA B:PRO70 3.6 15.4 1.0 C2 G:C4910 3.9 18.9 1.0 C B:PRO69 4.0 12.1 1.0 HD22 B:ASN306 4.1 0.0 1.0 OE1 B:GLN72 4.1 30.5 1.0 HD21 B:ASN110 4.1 0.0 1.0 C B:CYS71 4.2 17.4 1.0 N B:PRO70 4.2 14.0 1.0 O B:GLY68 4.3 12.0 1.0 O B:PRO70 4.3 21.8 1.0 N B:GLN72 4.6 18.4 1.0 C1' G:C4910 4.6 14.7 1.0 ND2 B:ASN110 4.6 9.9 1.0 ND2 B:ASN306 4.9 24.8 1.0 CD B:GLN72 4.9 30.5 1.0 HE21 B:GLN72 4.9 20.0 1.0 C2' G:C4910 5.0 14.4 1.0

K.M.Reinisch, L.Chen, G.L.Verdine, W.N.Lipscomb. The Crystal Structure of Haeiii Methyltransferase Convalently Complexed to Dna: An Extrahelical Cytosine and Rearranged Base Pairing. Cell(Cambridge,Mass.) V. 82 143 1995.
ISSN: ISSN 0092-8674
PubMed: 7606780
DOI: 10.1016/0092-8674(95)90060-8