Chlorine in PDB 5j2b: Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus, PDB code: 5j2b 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)	50.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.710, 79.880, 55.470, 90.00, 107.58, 90.00
R / Rfree (%)	21 / 28.8

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus also contains other interesting chemical elements:

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

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus (pdb code 5j2b). 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:C Mismatch at the Primer Terminus, PDB code: 5j2b:
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:C Mismatch at the Primer Terminus


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:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:37.1 occ:1.00 NH2 A:ARG299 2.8 46.4 1.0 ND2 A:ASN294 3.2 24.9 1.0 OG1 A:THR297 3.2 28.0 1.0 CZ A:ARG299 3.5 47.1 1.0 NE A:ARG299 3.6 44.8 1.0 O A:HOH573 3.8 27.1 1.0 CB A:TYR296 4.0 24.0 1.0 OD1 A:ASN294 4.0 20.6 1.0 CG A:ASN294 4.0 21.2 1.0 CD2 A:TYR296 4.2 21.9 1.0 CG A:TYR296 4.5 22.8 1.0 CB A:THR297 4.6 26.0 1.0 NH1 A:ARG299 4.6 47.7 1.0 N A:THR297 4.7 25.4 1.0 O A:HOH577 4.8 30.6 1.0 CD A:ARG299 4.9 41.8 1.0 O T:HOH105 4.9 31.4 1.0 CG2 A:THR297 4.9 25.9 1.0

Chlorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus


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:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:46.4 occ:1.00 N A:HIS34 3.3 27.1 1.0 C A:ALA32 3.3 25.3 1.0 CB A:HIS34 3.4 29.6 1.0 CA A:ALA32 3.4 25.1 1.0 CB A:ALA32 3.5 23.1 1.0 O A:ALA32 3.5 26.5 1.0 N A:LYS35 3.6 25.4 1.0 CA A:HIS34 3.8 27.4 1.0 N A:ILE33 3.9 26.2 1.0 CD2 A:HIS34 4.1 32.9 1.0 CG A:HIS34 4.1 32.2 1.0 CG A:LYS35 4.2 25.1 1.0 C A:HIS34 4.2 26.7 1.0 C A:ILE33 4.3 27.8 1.0 O D:HOH107 4.4 43.6 1.0 O A:HOH686 4.5 28.3 1.0 CA A:ILE33 4.6 28.8 1.0 CB A:LYS35 4.7 24.4 1.0 CA A:LYS35 4.8 24.6 1.0 N A:ALA32 4.9 24.3 1.0 O6 D:DG1 5.0 22.5 1.0

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006