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Chlorine in PDB 5j2h: Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus

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

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus, PDB code: 5j2h 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 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 79.700, 55.400, 90.00, 107.50, 90.00
R / Rfree (%) 20.5 / 26.6

Other elements in 5j2h:

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

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus (pdb code 5j2h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus, PDB code: 5j2h:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5j2h

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Chlorine binding site 1 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T 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 G:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:39.6
occ:1.00
 N A:CYS267 3.3 23.1 1.0
O A:HOH560 3.3 19.6 1.0
C A:GLN264 3.5 27.4 1.0
CA A:GLN264 3.5 27.7 1.0
N A:TYR266 3.5 25.4 1.0
O A:GLN264 3.6 29.1 1.0
CB A:TYR266 3.6 27.2 1.0
SG A:CYS267 3.7 24.6 1.0
CB A:VAL313 3.8 29.6 1.0
O A:ASP263 3.9 31.8 1.0
CA A:TYR266 3.9 25.0 1.0
CB A:CYS267 3.9 25.4 1.0
C A:TYR266 4.0 24.1 1.0
CG1 A:VAL313 4.0 30.5 1.0
N A:TYR265 4.0 26.9 1.0
CA A:CYS267 4.2 23.2 1.0
C A:TYR265 4.4 26.8 1.0
CB A:GLN264 4.5 28.4 1.0
N A:GLN264 4.5 29.7 1.0
CD2 A:TYR266 4.5 29.6 1.0
O A:VAL313 4.5 30.1 1.0
O A:TYR296 4.5 23.7 1.0
O A:HOH585 4.5 37.8 1.0
CG2 A:VAL313 4.5 28.6 1.0
C A:ASP263 4.6 30.1 1.0
CG A:TYR266 4.6 29.0 1.0
CA A:TYR265 4.8 26.3 1.0
CG A:GLN264 4.9 26.1 1.0
C A:VAL313 4.9 31.7 1.0
CA A:VAL313 5.0 30.3 1.0

Chlorine binding site 2 out of 5 in 5j2h

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Chlorine binding site 2 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T 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 G:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:37.0
occ:1.00
 N A:HIS34 3.2 29.3 1.0
CB A:HIS34 3.3 31.5 1.0
C A:ALA32 3.4 29.6 1.0
N A:LYS35 3.4 28.2 1.0
O A:ALA32 3.4 30.4 1.0
CB A:ALA32 3.5 26.1 1.0
CA A:ALA32 3.5 28.9 1.0
CA A:HIS34 3.6 31.0 1.0
N A:ILE33 3.9 29.9 1.0
CG A:LYS35 3.9 26.0 1.0
C A:HIS34 3.9 31.1 1.0
CG A:HIS34 4.0 33.0 1.0
CD2 A:HIS34 4.1 34.0 1.0
C A:ILE33 4.2 30.2 1.0
CB A:LYS35 4.3 26.6 1.0
CA A:LYS35 4.4 27.1 1.0
CA A:ILE33 4.6 31.1 1.0
CD A:LYS35 4.8 27.2 1.0
O6 D:DG1 4.9 26.7 1.0
N A:ALA32 5.0 27.7 1.0

Chlorine binding site 3 out of 5 in 5j2h

Go back to Chlorine Binding Sites List in 5j2h
Chlorine binding site 3 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T 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 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:43.6
occ:1.00
 N A:LEU82 3.0 28.8 1.0
CA A:LYS81 3.7 31.7 1.0
NH2 A:ARG89 3.7 45.3 1.0
NH1 A:ARG89 3.7 44.2 1.0
CB A:LYS81 3.8 33.4 1.0
C A:LYS81 3.8 30.9 1.0
O A:LEU82 3.8 31.2 1.0
CA A:LEU82 3.9 30.8 1.0
CB A:LEU82 3.9 30.2 1.0
CB A:LEU85 4.0 33.3 1.0
CZ A:ARG89 4.1 44.6 1.0
CD1 A:LEU85 4.2 32.7 1.0
C A:LEU82 4.3 31.1 1.0
CG A:LEU85 4.7 33.7 1.0
O A:LYS81 5.0 28.3 1.0
N A:GLU86 5.0 35.3 1.0

Chlorine binding site 4 out of 5 in 5j2h

Go back to Chlorine Binding Sites List in 5j2h
Chlorine binding site 4 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T 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 4 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:41.2
occ:1.00
 O A:HOH663 2.8 29.3 1.0
NH2 A:ARG299 3.0 32.2 1.0
ND2 A:ASN294 3.4 25.9 1.0
NE A:ARG299 3.4 32.6 1.0
OG1 A:THR297 3.4 30.1 1.0
CZ A:ARG299 3.6 35.0 1.0
CB A:TYR296 4.1 24.8 1.0
CD2 A:TYR296 4.1 24.3 1.0
CG A:ASN294 4.3 27.9 1.0
OD1 A:ASN294 4.3 28.4 1.0
CG A:TYR296 4.6 23.7 1.0
CD A:ARG299 4.7 31.9 1.0
CB A:THR297 4.7 29.6 1.0
O T:HOH123 4.8 43.2 1.0
CG2 A:THR297 4.9 29.5 1.0
N A:THR297 4.9 25.7 1.0
NH1 A:ARG299 5.0 36.4 1.0

Chlorine binding site 5 out of 5 in 5j2h

Go back to Chlorine Binding Sites List in 5j2h
Chlorine binding site 5 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T 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 5 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:46.1
occ:1.00
 OH A:TYR271 3.2 28.1 1.0
NH1 A:ARG258 3.3 15.6 1.0
O3' P:DT10 3.3 46.8 1.0
O T:HOH114 3.8 37.9 1.0
CE1 A:PHE272 4.0 20.9 1.0
CD A:LYS234 4.0 22.7 1.0
C3' P:DT10 4.1 47.2 1.0
CZ A:TYR271 4.2 22.8 1.0
C2' P:DT10 4.2 46.6 1.0
CE2 A:TYR271 4.2 20.2 1.0
C4' P:DT10 4.2 45.6 1.0
CZ A:ARG258 4.5 16.0 1.0
CZ A:PHE272 4.6 21.2 1.0
CD A:ARG258 4.7 20.2 1.0
CD1 A:PHE272 4.8 20.7 1.0
CG A:LYS234 4.9 20.7 1.0
O P:HOH102 4.9 20.6 1.0
NZ A:LYS234 5.0 27.2 1.0

Reference:

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
Page generated: Sat Jul 12 03:23:48 2025

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