Chlorine in PDB 6ctq: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp, PDB code: 6ctq was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.07 / 1.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.894, 79.789, 55.414, 90.00, 107.65, 90.00
R / Rfree (%)	17.5 / 22.8

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	3 atoms

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp (pdb code 6ctq). 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 Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp, PDB code: 6ctq:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:37.3 occ:1.00 OG1 A:THR297 3.0 24.3 1.0 O A:HOH850 3.2 37.7 1.0 O A:HOH805 3.3 38.0 1.0 ND2 A:ASN294 3.5 23.2 1.0 CG2 A:THR297 3.8 25.2 1.0 OD1 A:ASN294 4.0 24.2 1.0 CB A:THR297 4.0 23.9 1.0 CB A:TYR296 4.0 22.6 1.0 NE A:ARG299 4.1 35.3 1.0 CZ A:ARG299 4.1 44.2 1.0 CG A:ASN294 4.2 21.5 1.0 CD2 A:TYR296 4.2 21.6 1.0 NH2 A:ARG299 4.3 38.5 1.0 CG A:TYR296 4.5 22.6 1.0 NH1 A:ARG299 4.6 38.4 1.0 O A:HOH825 4.6 42.8 1.0 CD A:ARG299 4.6 29.2 1.0 N A:THR297 4.7 21.7 1.0 O A:HOH674 4.7 25.6 1.0 O T:HOH232 4.8 34.8 1.0 CA A:THR297 5.0 17.7 1.0

Chlorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:39.3 occ:1.00 O A:HOH525 2.8 36.7 1.0 O A:HOH608 2.9 25.8 1.0 N A:CYS267 3.0 18.9 1.0 C A:GLN264 3.4 22.9 1.0 N A:TYR266 3.5 23.2 1.0 CA A:GLN264 3.5 22.9 1.0 O A:GLN264 3.5 23.3 1.0 SG A:CYS267 3.6 22.3 1.0 CB A:CYS267 3.7 21.9 1.0 CB A:TYR266 3.7 24.1 1.0 O A:HOH715 3.8 33.5 1.0 CG1 A:VAL313 3.8 22.4 1.0 CA A:TYR266 3.8 20.4 1.0 C A:TYR266 3.9 21.5 1.0 CA A:CYS267 3.9 20.8 1.0 CB A:VAL313 4.0 26.0 1.0 N A:TYR265 4.0 21.9 1.0 O A:HOH740 4.0 33.7 1.0 O A:ASP263 4.1 28.1 1.0 O A:TYR296 4.1 20.9 1.0 CB A:GLN264 4.3 22.1 1.0 C A:TYR265 4.4 22.3 1.0 N A:GLN264 4.6 19.0 1.0 CG2 A:VAL313 4.7 23.5 1.0 CD2 A:TYR266 4.7 33.4 1.0 CG A:TYR266 4.7 29.0 1.0 O A:VAL313 4.7 32.8 1.0 C A:ASP263 4.8 26.7 1.0 CG A:GLN264 4.8 21.0 1.0 CA A:TYR265 4.8 23.6 1.0

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418