Chlorine in PDB 7s9p: Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog:
2.7.7.7;

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog, PDB code: 7s9p was solved by B.D.Freudenthal, B.J.Ryan, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.50 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.673, 79.621, 55.347, 90, 108.02, 90
R / Rfree (%)	17.6 / 22.8

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog also contains other interesting chemical elements:

Manganese	(Mn)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog (pdb code 7s9p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog, PDB code: 7s9p:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:42.6 occ:1.00 N A:HIS34 3.1 26.1 1.0 C A:ALA32 3.2 22.9 1.0 CA A:ALA32 3.3 26.1 1.0 CB A:ALA32 3.4 23.6 1.0 CB A:HIS34 3.4 27.8 1.0 N A:ILE33 3.4 24.9 1.0 N A:LYS35 3.5 21.9 1.0 O A:ALA32 3.6 21.7 1.0 CA A:HIS34 3.7 26.2 1.0 O A:HOH664 3.7 31.3 1.0 CG A:HIS34 3.9 31.9 1.0 CD2 A:HIS34 4.0 34.3 1.0 C A:HIS34 4.1 23.2 1.0 C A:ILE33 4.1 24.4 1.0 CG A:LYS35 4.4 25.1 1.0 CA A:ILE33 4.4 24.2 1.0 CB A:LYS35 4.5 15.9 1.0 CA A:LYS35 4.6 15.3 1.0 N A:ALA32 4.8 24.6 1.0 CG2 A:ILE33 4.8 25.7 1.0

Chlorine binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:54.3 occ:1.00 O A:HOH815 2.8 36.0 1.0 ND2 A:ASN294 3.3 20.7 1.0 OG1 A:THR297 3.4 18.7 1.0 O A:HOH776 3.7 36.0 1.0 CG2 A:THR297 3.9 20.2 1.0 NE A:ARG299 4.0 30.7 1.0 CZ A:ARG299 4.0 28.6 1.0 OD1 A:ASN294 4.1 21.4 1.0 NH2 A:ARG299 4.1 29.4 1.0 CG A:ASN294 4.1 22.0 1.0 CB A:TYR296 4.2 21.2 1.0 CB A:THR297 4.3 20.9 1.0 CD2 A:TYR296 4.3 19.4 1.0 NH1 A:ARG299 4.6 30.8 1.0 CD A:ARG299 4.7 26.6 1.0 CG A:TYR296 4.7 19.8 1.0 O A:HOH665 4.8 22.6 1.0 N A:THR297 4.9 17.8 1.0

B.J.Ryan, H.Yang, J.H.T.Bacurio, M.R.Smith, A.K.Basu, M.M.Greenberg, B.D.Freudenthal. Structural Dynamics of A Common Mutagenic Oxidative Dna Lesion in Duplex Dna and During Dna Replication. J.Am.Chem.Soc. V. 144 8054 2022.
ISSN: ESSN 1520-5126
PubMed: 35499923
DOI: 10.1021/JACS.2C00193