Chlorine in PDB 3lk9: Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P:
2.7.7.7;

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P, PDB code: 3lk9 was solved by M.Zibinsky, G.K.Surya Prakash, T.G.Upton, B.A.Kashemirov, C.E.Mckenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.28 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.960, 79.800, 55.050, 90.00, 108.46, 90.00
R / Rfree (%)	19.8 / 28.1

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P (pdb code 3lk9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P, PDB code: 3lk9:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl343 b:40.1 occ:1.00 O A:HOH388 3.0 29.6 1.0 NH2 A:ARG299 3.0 47.5 1.0 ND2 A:ASN294 3.4 36.7 1.0 NE A:ARG299 3.6 46.8 1.0 OG1 A:THR297 3.7 33.8 1.0 CZ A:ARG299 3.7 48.7 1.0 CB A:TYR296 3.8 34.6 1.0 CD2 A:TYR296 3.9 29.2 1.0 OD1 A:ASN294 4.1 34.5 1.0 CG A:ASN294 4.2 34.9 1.0 CG A:TYR296 4.3 31.6 1.0 O A:HOH448 4.4 54.2 1.0 O T:HOH155 4.7 42.5 1.0 CG2 A:THR297 4.8 35.0 1.0 CB A:THR297 4.8 35.4 1.0 N A:THR297 4.9 37.0 1.0 CD A:ARG299 4.9 44.7 1.0 CE2 A:TYR296 5.0 28.7 1.0 NH1 A:ARG299 5.0 48.9 1.0

Chlorine binding site 2 out of 3 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl344 b:49.3 occ:1.00 CB A:ALA32 3.3 39.3 1.0 CA A:ALA32 3.3 40.3 1.0 N A:HIS34 3.4 39.1 1.0 C A:ALA32 3.4 39.5 1.0 CB A:HIS34 3.6 37.1 1.0 N A:LYS35 3.6 36.3 1.0 O A:ALA32 3.7 40.2 1.0 N A:ILE33 3.8 39.5 1.0 CA A:HIS34 3.9 37.8 1.0 CG A:LYS35 4.1 38.4 1.0 O A:HOH382 4.2 37.3 1.0 C A:HIS34 4.2 37.8 1.0 CD2 A:HIS34 4.3 39.4 1.0 CG A:HIS34 4.3 39.5 1.0 C A:ILE33 4.4 40.0 1.0 CB A:LYS35 4.5 36.6 1.0 CA A:ILE33 4.6 41.0 1.0 CA A:LYS35 4.7 33.9 1.0 O A:HOH447 4.8 32.9 1.0 N A:ALA32 4.8 39.5 1.0 CD A:LYS35 4.9 42.6 1.0

Chlorine binding site 3 out of 3 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl345 b:58.9 occ:1.00 N A:CYS267 3.3 45.5 1.0 C A:GLN264 3.5 43.4 1.0 CA A:GLN264 3.5 41.1 1.0 O A:GLN264 3.5 44.9 1.0 SG A:CYS267 3.5 40.2 1.0 N A:TYR266 3.7 46.9 1.0 CB A:TYR266 3.8 47.9 1.0 CB A:CYS267 3.8 43.6 1.0 O A:ASP263 4.0 39.2 1.0 CA A:TYR266 4.1 46.9 1.0 O A:TYR296 4.1 35.5 1.0 CB A:VAL313 4.1 50.7 1.0 CG1 A:VAL313 4.1 50.3 1.0 C A:TYR266 4.1 46.3 1.0 CA A:CYS267 4.1 43.7 1.0 N A:TYR265 4.2 44.9 1.0 O A:VAL313 4.3 52.1 1.0 CB A:GLN264 4.3 40.5 1.0 CD2 A:TYR266 4.5 49.6 1.0 N A:GLN264 4.6 40.3 1.0 C A:TYR265 4.6 46.8 1.0 CG A:TYR266 4.6 49.0 1.0 C A:ASP263 4.7 39.1 1.0 CG A:GLN264 4.9 39.6 1.0 C A:VAL313 4.9 52.8 1.0 CA A:TYR265 5.0 45.3 1.0

G.K.Surya Prakash, M.Zibinsky, T.G.Upton, B.A.Kashemirov, C.E.Mckenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, D.D.Shock, S.H.Wilson, G.A.Olah. Synthesis and Biological Evaluation of Fluorinated Deoxynucleotide Analogs Based on Bis-(Difluoromethylene)Triphosphoric Acid. Proc.Natl.Acad.Sci.Usa V. 107 15693 2010.
ISSN: ISSN 0027-8424
PubMed: 20724659
DOI: 10.1073/PNAS.1007430107