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Chlorine in PDB 5j2j: Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G 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:G Mismatch at the Primer Terminus, PDB code: 5j2j 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 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.820, 80.170, 55.510, 90.00, 107.85, 90.00
R / Rfree (%) 20.1 / 26.6

Other elements in 5j2j:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G 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:G Mismatch at the Primer Terminus (pdb code 5j2j). 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:G Mismatch at the Primer Terminus, PDB code: 5j2j:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5j2j

Go back to Chlorine Binding Sites List in 5j2j
Chlorine binding site 1 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:33.2
occ:1.00
 O A:HOH565 3.1 30.0 1.0
N A:CYS267 3.3 20.1 1.0
CA A:GLN264 3.5 22.2 1.0
C A:GLN264 3.5 22.1 1.0
N A:TYR266 3.5 21.0 1.0
CG1 A:VAL313 3.7 25.6 1.0
O A:ASP263 3.8 23.7 1.0
O A:GLN264 3.8 22.8 1.0
CB A:TYR266 3.8 22.8 1.0
CB A:VAL313 3.8 26.0 1.0
SG A:CYS267 3.9 22.2 1.0
N A:TYR265 3.9 21.6 1.0
CB A:CYS267 4.0 20.4 1.0
CA A:TYR266 4.0 21.9 1.0
C A:TYR266 4.1 21.8 1.0
CA A:CYS267 4.2 18.9 1.0
O A:TYR296 4.4 18.1 1.0
C A:TYR265 4.4 21.4 1.0
O A:VAL313 4.4 27.8 1.0
CB A:GLN264 4.4 22.4 1.0
N A:GLN264 4.5 24.1 1.0
CD2 A:TYR266 4.5 29.8 1.0
C A:ASP263 4.5 24.2 1.0
CG A:TYR266 4.6 27.0 1.0
CG2 A:VAL313 4.7 24.3 1.0
CA A:TYR265 4.7 21.0 1.0
C A:VAL313 4.8 27.8 1.0
CA A:VAL313 4.9 27.1 1.0
CG A:GLN264 5.0 23.6 1.0

Chlorine binding site 2 out of 4 in 5j2j

Go back to Chlorine Binding Sites List in 5j2j
Chlorine binding site 2 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:32.5
occ:1.00
 N A:HIS34 3.3 22.9 1.0
C A:ALA32 3.5 23.0 1.0
CB A:HIS34 3.5 23.4 1.0
CA A:ALA32 3.6 24.5 1.0
CB A:ALA32 3.6 23.1 1.0
O A:ALA32 3.7 22.5 1.0
N A:LYS35 3.8 20.7 1.0
CA A:HIS34 3.8 23.9 1.0
N A:ILE33 3.9 24.1 1.0
CD2 A:HIS34 3.9 25.4 1.0
CG A:HIS34 4.0 25.5 1.0
C A:HIS34 4.3 23.7 1.0
CG A:LYS35 4.3 19.7 1.0
C A:ILE33 4.3 25.7 1.0
O A:HOH707 4.4 27.0 1.0
CA A:ILE33 4.6 25.9 1.0
CG2 A:ILE33 4.6 28.2 1.0
CB A:LYS35 4.8 17.8 1.0
CA A:LYS35 4.8 19.4 1.0

Chlorine binding site 3 out of 4 in 5j2j

Go back to Chlorine Binding Sites List in 5j2j
Chlorine binding site 3 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:42.5
occ:1.00
 NH2 A:ARG89 3.2 42.4 1.0
O A:HOH715 3.3 36.0 1.0
N A:LEU82 3.4 21.8 1.0
NH1 A:ARG89 3.7 40.8 1.0
CA A:LYS81 3.7 23.9 1.0
CB A:LYS81 3.8 26.9 1.0
CZ A:ARG89 3.9 40.5 1.0
C A:LYS81 4.1 22.4 1.0
O A:LEU82 4.3 26.2 1.0
CD1 A:LEU85 4.3 17.8 1.0
CB A:LEU82 4.4 23.3 1.0
CA A:LEU82 4.4 23.4 1.0
CB A:LEU85 4.5 22.4 1.0
O A:GLY80 4.8 26.5 1.0
C A:LEU82 4.8 24.8 1.0
OE1 A:GLU21 4.8 33.5 1.0
CE1 A:PHE76 4.8 21.6 1.0
CD1 A:PHE76 4.9 18.6 1.0
O A:HOH648 4.9 19.8 1.0
N A:LYS81 5.0 24.0 1.0

Chlorine binding site 4 out of 4 in 5j2j

Go back to Chlorine Binding Sites List in 5j2j
Chlorine binding site 4 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:29.8
occ:1.00
 O A:HOH755 3.0 31.0 1.0
OG1 A:THR297 3.2 18.7 1.0
ND2 A:ASN294 3.3 21.8 1.0
O A:HOH618 3.4 30.9 1.0
CZ A:ARG299 3.7 38.1 1.0
NH2 A:ARG299 3.8 37.8 1.0
NH1 A:ARG299 4.0 38.0 1.0
NE A:ARG299 4.0 35.6 1.0
CB A:TYR296 4.1 18.4 1.0
OD1 A:ASN294 4.1 20.9 1.0
CG A:ASN294 4.1 19.8 1.0
CG2 A:THR297 4.3 19.0 1.0
CB A:THR297 4.3 20.6 1.0
CD2 A:TYR296 4.3 18.4 1.0
O A:HOH586 4.6 10.6 1.0
CG A:TYR296 4.6 19.6 1.0
N A:THR297 4.6 18.3 1.0
CD A:ARG299 4.7 32.3 1.0
O A:HOH771 4.8 41.8 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: Fri Jul 26 09:41:58 2024

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