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Chlorine in PDB 5j2e: Ternary Complex Crystal Structure of Dna Polymerase Beta with C:T Mismatch at the Primer Terminus

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:T Mismatch at the Primer Terminus, PDB code: 5j2e 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 (°) 50.940, 79.940, 55.500, 90.00, 107.68, 90.00
R / Rfree (%) 23.9 / 29.2

Other elements in 5j2e:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:T Mismatch at the Primer Terminus (pdb code 5j2e). 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 C:T Mismatch at the Primer Terminus, PDB code: 5j2e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5j2e

Go back to Chlorine Binding Sites List in 5j2e
Chlorine binding site 1 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:30.3
occ:1.00
 NH1 A:ARG258 3.1 12.5 1.0
O3' P:DT10 3.1 39.2 1.0
OH A:TYR271 3.2 20.8 1.0
O T:HOH114 3.8 25.9 1.0
CE2 A:TYR271 3.9 18.7 1.0
C2' P:DT10 3.9 40.1 1.0
C3' P:DT10 4.0 38.2 1.0
CE1 A:PHE272 4.0 16.4 1.0
CD A:LYS234 4.0 17.1 1.0
CZ A:TYR271 4.0 17.5 1.0
CZ A:ARG258 4.3 13.2 1.0
CD A:ARG258 4.3 16.1 1.0
C4' P:DT10 4.4 36.9 1.0
O A:HOH541 4.4 22.3 1.0
C1' P:DT10 4.5 40.0 1.0
CG A:ARG258 4.6 14.0 1.0
CD1 A:PHE272 4.7 13.1 1.0
CZ A:PHE272 4.7 17.9 1.0
CG A:LYS234 4.7 13.8 1.0
NE A:ARG258 4.7 16.1 1.0
CB A:ARG258 5.0 14.4 1.0

Chlorine binding site 2 out of 5 in 5j2e

Go back to Chlorine Binding Sites List in 5j2e
Chlorine binding site 2 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:33.8
occ:1.00
 ND2 A:ASN294 3.0 18.3 1.0
OG1 A:THR297 3.1 23.0 1.0
NH2 A:ARG299 3.3 32.7 1.0
O A:HOH663 3.4 32.5 1.0
NE A:ARG299 3.4 30.6 1.0
O A:HOH775 3.5 33.8 1.0
CZ A:ARG299 3.8 33.2 1.0
CG A:ASN294 3.9 19.3 1.0
OD1 A:ASN294 3.9 20.4 1.0
CB A:TYR296 3.9 22.8 1.0
CD2 A:TYR296 4.0 24.1 1.0
CB A:THR297 4.4 23.6 1.0
CG A:TYR296 4.5 23.1 1.0
O T:HOH146 4.5 32.0 1.0
O T:HOH119 4.5 38.2 1.0
O A:HOH600 4.6 25.6 1.0
N A:THR297 4.6 22.3 1.0
CD A:ARG299 4.6 25.7 1.0
CG2 A:THR297 4.7 22.5 1.0

Chlorine binding site 3 out of 5 in 5j2e

Go back to Chlorine Binding Sites List in 5j2e
Chlorine binding site 3 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:32.3
occ:1.00
 N A:HIS34 3.2 23.0 1.0
CB A:HIS34 3.2 23.3 1.0
C A:ALA32 3.5 27.5 1.0
N A:LYS35 3.6 22.6 1.0
CD2 A:HIS34 3.6 27.8 1.0
CA A:HIS34 3.6 24.1 1.0
CA A:ALA32 3.6 27.0 1.0
CB A:ALA32 3.7 26.1 1.0
CG A:HIS34 3.7 27.6 1.0
O A:ALA32 3.8 28.3 1.0
N A:ILE33 3.8 26.0 1.0
C A:HIS34 4.1 22.5 1.0
C A:ILE33 4.2 24.6 1.0
CG2 A:ILE33 4.2 26.2 1.0
CA A:ILE33 4.5 26.2 1.0
CG A:LYS35 4.6 23.9 1.0
CB A:LYS35 4.7 21.9 1.0
CA A:LYS35 4.7 23.7 1.0
NE2 A:HIS34 4.9 30.1 1.0
O6 D:DG1 5.0 25.6 1.0

Chlorine binding site 4 out of 5 in 5j2e

Go back to Chlorine Binding Sites List in 5j2e
Chlorine binding site 4 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:39.5
occ:1.00
 N A:LEU82 3.0 24.0 1.0
O A:HOH746 3.1 44.7 1.0
NH1 A:ARG89 3.6 38.0 1.0
O A:HOH569 3.6 34.1 1.0
CA A:LYS81 3.7 26.8 1.0
CB A:LYS81 3.8 29.3 1.0
C A:LYS81 3.8 24.8 1.0
CD1 A:LEU85 3.8 23.9 1.0
NH2 A:ARG89 3.9 38.9 1.0
CB A:LEU82 3.9 26.9 1.0
O A:LEU82 3.9 25.2 1.0
CA A:LEU82 3.9 26.4 1.0
CB A:LEU85 3.9 26.6 1.0
CZ A:ARG89 4.2 36.8 1.0
C A:LEU82 4.3 26.4 1.0
CG A:LEU85 4.5 26.5 1.0
OE1 A:GLU86 4.7 43.2 1.0
CE1 A:PHE76 4.8 18.8 1.0
CD1 A:PHE76 4.9 19.1 1.0
O A:LYS81 5.0 24.9 1.0

Chlorine binding site 5 out of 5 in 5j2e

Go back to Chlorine Binding Sites List in 5j2e
Chlorine binding site 5 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:T Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:46.5
occ:1.00
 O A:HOH647 2.9 23.3 1.0
N A:CYS267 3.4 18.9 1.0
CA A:GLN264 3.5 20.7 1.0
CG1 A:VAL313 3.6 28.9 1.0
C A:GLN264 3.6 20.0 1.0
SG A:CYS267 3.7 22.3 1.0
N A:TYR266 3.7 22.1 1.0
CB A:VAL313 3.7 29.8 1.0
O A:ASP263 3.7 25.3 1.0
CB A:TYR266 3.8 23.8 1.0
O A:GLN264 3.9 20.4 1.0
CB A:CYS267 4.0 19.6 1.0
CA A:TYR266 4.1 20.5 1.0
N A:TYR265 4.1 21.7 1.0
C A:TYR266 4.1 19.6 1.0
O A:VAL313 4.3 32.3 1.0
CA A:CYS267 4.3 18.2 1.0
O A:HOH697 4.4 36.3 1.0
O A:TYR296 4.4 21.2 1.0
CD2 A:TYR266 4.5 29.0 1.0
CB A:GLN264 4.5 21.9 1.0
N A:GLN264 4.5 22.6 1.0
C A:ASP263 4.5 22.9 1.0
C A:TYR265 4.6 21.8 1.0
CG2 A:VAL313 4.6 26.8 1.0
CG A:TYR266 4.6 27.1 1.0
C A:VAL313 4.7 31.6 1.0
CA A:VAL313 4.8 31.0 1.0
CG A:GLN264 4.9 20.0 1.0
CA A:TYR265 4.9 22.2 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: Fri Jul 26 09:41:39 2024

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