Chlorine in PDB 5wny: Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp

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

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp, PDB code: 5wny 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)	24.65 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.480, 79.747, 55.570, 90.00, 107.23, 90.00
R / Rfree (%)	18.1 / 23.7

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

Fluorine	(F)	1 atom
Calcium	(Ca)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp (pdb code 5wny). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp, PDB code: 5wny:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


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-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:55.4 occ:1.00 O A:HOH519 2.9 29.9 1.0 N A:CYS267 3.3 21.3 1.0 CA A:GLN264 3.4 24.9 1.0 CG1 A:VAL313 3.5 33.5 1.0 C A:GLN264 3.5 25.9 1.0 N A:TYR266 3.6 24.5 1.0 O A:ASP263 3.7 33.8 1.0 SG A:CYS267 3.8 28.0 1.0 O A:GLN264 3.8 23.9 1.0 CB A:VAL313 3.8 31.4 1.0 CB A:TYR266 3.9 29.2 1.0 CB A:CYS267 4.0 20.3 1.0 CA A:TYR266 4.0 33.0 1.0 N A:TYR265 4.0 22.6 1.0 C A:TYR266 4.1 28.3 1.0 O A:TYR296 4.2 19.7 1.0 CA A:CYS267 4.3 27.2 1.0 CB A:GLN264 4.3 23.3 1.0 O A:VAL313 4.4 30.1 1.0 N A:GLN264 4.4 24.0 1.0 C A:ASP263 4.5 30.8 1.0 C A:TYR265 4.5 32.3 1.0 CD2 A:TYR266 4.5 32.6 1.0 CG A:TYR266 4.7 24.9 1.0 CG2 A:VAL313 4.7 32.5 1.0 CA A:TYR265 4.9 23.2 1.0 CG A:GLN264 4.9 26.4 1.0 C A:VAL313 5.0 30.6 1.0 CA A:VAL313 5.0 32.2 1.0

Chlorine binding site 2 out of 4 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


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-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:60.6 occ:1.00 C A:ALA32 3.3 31.7 1.0 CA A:ALA32 3.3 41.2 1.0 N A:HIS34 3.4 31.9 1.0 CB A:ALA32 3.4 32.8 1.0 N A:ILE33 3.6 37.5 1.0 O A:ALA32 3.6 35.6 1.0 CB A:HIS34 3.6 43.1 1.0 N A:LYS35 3.7 41.5 1.0 O D:HOH101 3.8 49.0 1.0 CA A:HIS34 3.9 39.9 1.0 ND1 A:HIS34 4.1 47.6 1.0 O A:HOH561 4.1 37.4 1.0 CG A:LYS35 4.3 35.9 1.0 C A:HIS34 4.3 37.3 1.0 CG A:HIS34 4.3 51.8 1.0 C A:ILE33 4.4 40.8 1.0 CA A:ILE33 4.6 37.2 1.0 CB A:LYS35 4.7 27.2 1.0 N A:ALA32 4.7 36.0 1.0 CA A:LYS35 4.8 34.3 1.0

Chlorine binding site 3 out of 4 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


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-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:64.9 occ:1.00 N A:LEU82 3.2 39.0 1.0 CB A:LYS81 3.6 52.6 1.0 CA A:LYS81 3.6 46.8 1.0 C A:LYS81 3.9 41.2 1.0 O A:LEU82 3.9 35.7 1.0 CA A:LEU82 4.1 32.2 1.0 CB A:LEU85 4.1 36.2 1.0 NH2 A:ARG89 4.1 49.5 1.0 CB A:LEU82 4.1 34.5 1.0 CD1 A:LEU85 4.3 38.2 1.0 C A:LEU82 4.4 39.9 1.0 CZ A:ARG89 4.5 48.7 1.0 CG A:GLU86 4.7 58.4 1.0 NE A:ARG89 4.7 40.3 1.0 N A:GLU86 4.8 38.8 1.0 CG A:LEU85 4.9 44.0 1.0 O A:GLY80 5.0 41.9 1.0

Chlorine binding site 4 out of 4 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:43.0 occ:1.00 OG1 A:THR297 3.0 29.6 1.0 NH2 A:ARG299 3.2 30.2 0.4 O A:HOH666 3.3 35.0 1.0 ND2 A:ASN294 3.3 24.2 1.0 NE A:ARG299 3.4 25.2 0.4 CZ A:ARG299 3.7 39.2 0.4 OD1 A:ASN294 3.9 26.4 1.0 CG2 A:THR297 3.9 23.0 1.0 CB A:TYR296 4.0 30.7 1.0 CZ A:ARG299 4.0 33.7 0.6 NE A:ARG299 4.0 21.0 0.6 CG A:ASN294 4.0 24.9 1.0 CB A:THR297 4.1 27.5 1.0 NH2 A:ARG299 4.1 26.1 0.6 CD2 A:TYR296 4.1 25.0 1.0 CG A:TYR296 4.5 26.1 1.0 NH1 A:ARG299 4.5 35.5 0.6 CD A:ARG299 4.6 28.7 0.4 CD A:ARG299 4.6 28.7 0.6 O T:HOH117 4.6 39.6 1.0 O A:HOH501 4.7 50.7 1.0 N A:THR297 4.7 24.2 1.0 O A:HOH557 4.7 25.8 1.0 NH1 A:ARG299 4.9 30.3 0.4 CA A:THR297 5.0 31.6 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