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Chlorine in PDB 5j2k: Ternary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus, PDB code: 5j2k 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 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.820, 80.170, 55.380, 90.00, 107.86, 90.00
R / Rfree (%) 22 / 28.4

Other elements in 5j2k:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus (pdb code 5j2k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus, PDB code: 5j2k:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5j2k

Go back to Chlorine Binding Sites List in 5j2k
Chlorine binding site 1 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:58.7
occ:1.00
O A:HOH613 3.1 27.2 1.0
N A:CYS267 3.3 16.8 1.0
CA A:GLN264 3.4 23.5 1.0
C A:GLN264 3.4 23.4 1.0
N A:TYR266 3.5 21.6 1.0
O A:HOH602 3.7 35.1 1.0
O A:ASP263 3.7 26.6 1.0
O A:GLN264 3.7 23.8 1.0
CG1 A:VAL313 3.8 22.6 1.0
CB A:TYR266 3.8 23.4 1.0
N A:TYR265 3.8 23.6 1.0
CB A:VAL313 3.9 23.5 1.0
CA A:TYR266 3.9 20.6 1.0
CB A:CYS267 4.0 20.0 1.0
SG A:CYS267 4.0 20.9 1.0
C A:TYR266 4.1 19.2 1.0
O A:VAL313 4.2 26.9 1.0
CA A:CYS267 4.3 16.7 1.0
CD2 A:TYR266 4.3 28.5 1.0
CB A:GLN264 4.3 23.8 1.0
C A:TYR265 4.3 22.9 1.0
N A:GLN264 4.3 24.5 1.0
O A:TYR296 4.4 22.4 1.0
C A:ASP263 4.4 25.3 1.0
CG A:TYR266 4.5 26.2 1.0
CA A:TYR265 4.6 23.3 1.0
CG2 A:VAL313 4.7 23.9 1.0
CG A:GLN264 4.8 25.3 1.0
C A:VAL313 4.9 25.9 1.0
O A:HOH565 5.0 25.4 1.0
CA A:VAL313 5.0 26.2 1.0

Chlorine binding site 2 out of 4 in 5j2k

Go back to Chlorine Binding Sites List in 5j2k
Chlorine binding site 2 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:33.1
occ:1.00
N A:HIS34 3.2 26.3 1.0
CB A:HIS34 3.4 28.0 1.0
C A:ALA32 3.5 29.2 1.0
CB A:ALA32 3.6 28.5 1.0
CA A:ALA32 3.6 29.4 1.0
CA A:HIS34 3.7 25.4 1.0
N A:LYS35 3.7 22.4 1.0
O A:ALA32 3.8 30.8 1.0
N A:ILE33 3.8 28.6 1.0
CD2 A:HIS34 3.9 32.5 1.0
CG A:HIS34 4.0 30.9 1.0
C A:HIS34 4.1 23.8 1.0
CG A:LYS35 4.3 20.8 1.0
C A:ILE33 4.3 28.7 1.0
CA A:ILE33 4.6 29.5 1.0
CB A:LYS35 4.7 20.7 1.0
CA A:LYS35 4.8 21.6 1.0
CG2 A:ILE33 4.9 32.7 1.0
O6 D:DG1 5.0 26.8 1.0

Chlorine binding site 3 out of 4 in 5j2k

Go back to Chlorine Binding Sites List in 5j2k
Chlorine binding site 3 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:43.5
occ:1.00
O A:HOH684 3.2 41.1 1.0
N A:LEU82 3.2 26.1 1.0
NH1 A:ARG89 3.5 41.5 1.0
CB A:LYS81 3.7 31.9 1.0
CA A:LYS81 3.7 29.8 1.0
NH2 A:ARG89 3.8 42.3 1.0
O A:LEU82 3.8 29.4 1.0
C A:LYS81 3.9 28.1 1.0
CZ A:ARG89 4.1 41.4 1.0
CA A:LEU82 4.1 28.1 1.0
CB A:LEU82 4.1 27.1 1.0
CB A:LEU85 4.2 27.3 1.0
CD1 A:LEU85 4.3 27.9 1.0
C A:LEU82 4.4 29.0 1.0
CG A:LEU85 4.9 26.8 1.0
CE1 A:PHE76 4.9 24.0 1.0

Chlorine binding site 4 out of 4 in 5j2k

Go back to Chlorine Binding Sites List in 5j2k
Chlorine binding site 4 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T: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 T:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:27.1
occ:1.00
NH2 A:ARG299 2.9 23.6 0.5
OG1 A:THR297 3.2 25.5 1.0
ND2 A:ASN294 3.3 21.3 1.0
NE A:ARG299 3.3 26.5 0.5
CZ A:ARG299 3.4 25.4 0.5
CZ A:ARG299 3.9 25.4 0.5
NH1 A:ARG299 4.0 24.3 0.5
OD1 A:ASN294 4.1 21.1 1.0
NE A:ARG299 4.1 24.6 0.5
CB A:TYR296 4.1 23.0 1.0
CG A:ASN294 4.1 20.5 1.0
NH2 A:ARG299 4.2 24.5 0.5
CG2 A:THR297 4.2 23.7 1.0
CD2 A:TYR296 4.3 21.4 1.0
CB A:THR297 4.3 23.7 1.0
CD A:ARG299 4.5 25.8 0.5
CD A:ARG299 4.6 27.0 0.5
NH1 A:ARG299 4.6 25.7 0.5
CG A:TYR296 4.6 23.6 1.0
N A:THR297 4.7 21.8 1.0
O A:HOH631 4.7 22.6 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 Dec 12 11:52:09 2020

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