Chlorine in PDB 5wo0: Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp, PDB code: 5wo0 was solved by M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.79 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.728, 79.637, 55.289, 90.00, 107.28, 90.00
R / Rfree (%)	20 / 23.1

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp (pdb code 5wo0). 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 Substrate Complex with Incoming 5-Fodutp, PDB code: 5wo0:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp


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 Substrate Complex with Incoming 5-Fodutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:29.1 occ:0.00 N A:HIS34 3.4 26.2 1.0 CB A:HIS34 3.5 27.1 1.0 N A:LYS35 3.5 25.7 1.0 CB A:ALA32 3.5 25.4 1.0 C A:ALA32 3.5 30.4 1.0 CA A:ALA32 3.6 29.8 1.0 CA A:HIS34 3.8 30.1 1.0 O A:ALA32 3.9 23.2 1.0 N A:ILE33 3.9 25.2 1.0 C A:HIS34 4.0 23.8 1.0 CG A:LYS35 4.1 27.2 1.0 CG A:HIS34 4.2 32.5 1.0 CD2 A:HIS34 4.2 36.4 1.0 C A:ILE33 4.4 26.3 1.0 CB A:LYS35 4.5 19.1 1.0 CA A:LYS35 4.6 23.7 1.0 O6 D:DG1 4.7 26.4 1.0 CA A:ILE33 4.8 27.9 1.0 CD A:LYS35 4.9 27.0 1.0 O A:HOH627 4.9 33.6 1.0

Chlorine binding site 2 out of 3 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp


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 Substrate Complex with Incoming 5-Fodutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:35.0 occ:0.00 N A:LEU82 3.3 20.2 1.0 OE2 A:GLU86 3.3 53.4 1.0 CA A:LYS81 3.9 25.2 1.0 O A:LEU82 4.0 23.6 1.0 CB A:LEU85 4.0 23.7 1.0 C A:LYS81 4.0 20.8 1.0 CA A:LEU82 4.2 24.2 1.0 CB A:LEU82 4.2 26.2 1.0 CD1 A:LEU85 4.2 25.6 1.0 NH1 A:ARG89 4.2 54.1 1.0 CB A:LYS81 4.3 30.7 1.0 CD A:GLU86 4.3 53.2 1.0 CZ A:ARG89 4.3 37.2 1.0 NH2 A:ARG89 4.4 41.6 1.0 C A:LEU82 4.5 26.6 1.0 CG A:GLU86 4.5 36.1 1.0 CG A:LEU85 4.7 26.1 1.0 N A:GLU86 4.9 29.2 1.0 CG A:LYS81 4.9 41.5 1.0 NE A:ARG89 4.9 37.8 1.0 O A:GLY80 5.0 25.4 1.0

Chlorine binding site 3 out of 3 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp


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 Substrate Complex with Incoming 5-Fodutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:26.6 occ:0.00 O A:HOH711 3.1 39.5 1.0 OG1 A:THR297 3.3 23.0 1.0 ND2 A:ASN294 3.6 21.7 1.0 CG2 A:THR297 4.0 19.8 1.0 CZ A:ARG299 4.0 35.9 1.0 NE A:ARG299 4.2 28.4 1.0 CB A:TYR296 4.2 17.7 1.0 NH1 A:ARG299 4.2 35.2 1.0 CB A:THR297 4.3 18.8 1.0 CD2 A:TYR296 4.3 19.6 1.0 NH2 A:ARG299 4.3 33.2 1.0 OD1 A:ASN294 4.4 18.3 1.0 CG A:ASN294 4.5 20.3 1.0 CD A:ARG299 4.6 29.7 1.0 CG A:TYR296 4.7 20.6 1.0 N A:THR297 5.0 20.1 1.0

M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal. Structures of A Dna Polymerase Inserting Therapeutic Nucleotide Analogues. Chem. Res. Toxicol. V. 30 1993 2017.
ISSN: ISSN 1520-5010
PubMed: 28862449
DOI: 10.1021/ACS.CHEMRESTOX.7B00173