Atomistry » Chlorine » PDB 5ivs-5j7f » 5j2d
Atomistry »
  Chlorine »
    PDB 5ivs-5j7f »
      5j2d »

Chlorine in PDB 5j2d: Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C 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:C Mismatch at the Primer Terminus, PDB code: 5j2d 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 (°) 50.740, 79.940, 55.480, 90.00, 107.63, 90.00
R / Rfree (%) 20.1 / 25.6

Other elements in 5j2d:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C 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:C Mismatch at the Primer Terminus (pdb code 5j2d). 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 C:C Mismatch at the Primer Terminus, PDB code: 5j2d:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5j2d

Go back to Chlorine Binding Sites List in 5j2d
Chlorine binding site 1 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:C Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:30.3
occ:1.00
 O3' P:DC10 2.7 50.0 0.5
OH A:TYR271 3.0 18.8 1.0
O P:HOH101 3.2 28.3 1.0
NH1 A:ARG258 3.3 13.4 1.0
O A:HOH599 3.3 30.5 1.0
CE1 A:PHE272 3.7 16.6 1.0
C1' P:DC10 3.8 49.3 0.5
CD A:LYS234 3.8 22.0 1.0
C3' P:DC10 3.9 49.4 0.5
CZ A:TYR271 3.9 16.5 1.0
CE2 A:TYR271 4.0 15.6 1.0
C2' P:DC10 4.1 49.4 0.5
O4' P:DC10 4.2 49.2 0.5
CD A:ARG258 4.2 18.4 1.0
C4' P:DC10 4.3 49.5 0.5
CZ A:PHE272 4.4 15.3 1.0
O2 P:DC10 4.4 48.6 1.0
CZ A:ARG258 4.4 15.6 1.0
CD1 A:PHE272 4.4 13.9 1.0
CG A:ARG258 4.6 15.6 1.0
CG A:LYS234 4.7 17.7 1.0
NE A:ARG258 4.7 16.5 1.0
NZ A:LYS234 4.8 26.1 1.0
CB A:ARG258 4.8 13.6 1.0
CE A:LYS234 5.0 25.5 1.0
O P:HOH109 5.0 11.7 1.0
N1 P:DC10 5.0 48.5 1.0

Chlorine binding site 2 out of 4 in 5j2d

Go back to Chlorine Binding Sites List in 5j2d
Chlorine binding site 2 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:C Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:35.1
occ:1.00
 O A:HOH756 2.9 42.7 1.0
NH1 A:ARG299 2.9 39.8 1.0
O A:HOH746 3.0 40.2 1.0
O A:HOH792 3.0 32.2 1.0
ND2 A:ASN294 3.1 23.0 1.0
OG1 A:THR297 3.2 20.9 1.0
CZ A:ARG299 3.8 37.5 1.0
CB A:TYR296 3.9 22.8 1.0
CG A:ASN294 4.0 22.4 1.0
OD1 A:ASN294 4.0 24.3 1.0
CG2 A:THR297 4.1 21.3 1.0
CD2 A:TYR296 4.2 22.4 1.0
CB A:THR297 4.3 23.7 1.0
NH2 A:ARG299 4.4 38.5 1.0
CG A:TYR296 4.5 22.2 1.0
N A:THR297 4.6 22.2 1.0
NE A:ARG299 4.6 35.3 1.0
O T:HOH114 4.8 34.2 1.0
CD A:ARG299 4.8 31.8 1.0
O A:HOH518 4.9 25.4 1.0

Chlorine binding site 3 out of 4 in 5j2d

Go back to Chlorine Binding Sites List in 5j2d
Chlorine binding site 3 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:55.4
occ:1.00
 O A:HOH668 2.8 23.1 1.0
CA A:GLN264 3.4 20.4 1.0
N A:CYS267 3.4 17.1 1.0
C A:GLN264 3.5 19.9 1.0
N A:TYR266 3.7 19.3 1.0
O A:HOH695 3.7 44.9 1.0
O A:GLN264 3.7 20.3 1.0
SG A:CYS267 3.8 20.8 1.0
O A:ASP263 3.8 24.3 1.0
CG1 A:VAL313 3.8 29.4 1.0
CB A:VAL313 3.9 29.5 1.0
CB A:TYR266 3.9 23.6 1.0
CB A:CYS267 3.9 19.3 1.0
N A:TYR265 4.0 19.8 1.0
CA A:TYR266 4.1 19.2 1.0
C A:TYR266 4.2 18.3 1.0
CB A:GLN264 4.2 21.3 1.0
CA A:CYS267 4.3 17.5 1.0
CD2 A:TYR266 4.3 31.1 1.0
N A:GLN264 4.4 21.6 1.0
O A:TYR296 4.4 19.9 1.0
C A:ASP263 4.5 22.1 1.0
C A:TYR265 4.5 19.2 1.0
O A:VAL313 4.5 29.9 1.0
CG A:TYR266 4.6 27.6 1.0
CG2 A:VAL313 4.6 26.9 1.0
CG A:GLN264 4.7 23.3 1.0
CA A:TYR265 4.8 20.0 1.0
C A:VAL313 4.9 30.6 1.0

Chlorine binding site 4 out of 4 in 5j2d

Go back to Chlorine Binding Sites List in 5j2d
Chlorine binding site 4 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 4 of Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:52.7
occ:1.00
 O A:HOH597 3.1 33.1 1.0
N A:LEU82 3.2 22.5 1.0
OE2 A:GLU86 3.3 39.8 1.0
CA A:LYS81 3.7 24.9 1.0
CB A:LYS81 3.7 28.2 1.0
O A:HOH550 3.7 35.0 1.0
C A:LYS81 3.9 23.9 1.0
NH2 A:ARG89 3.9 41.7 1.0
O A:LEU82 3.9 25.7 1.0
CB A:LEU85 4.1 21.4 1.0
CA A:LEU82 4.1 24.9 1.0
CZ A:ARG89 4.2 41.1 1.0
CB A:LEU82 4.2 25.4 1.0
CD1 A:LEU85 4.3 18.7 1.0
O A:HOH697 4.3 34.1 1.0
CD A:GLU86 4.3 39.4 1.0
NH1 A:ARG89 4.3 43.4 1.0
C A:LEU82 4.5 25.2 1.0
CG A:GLU86 4.6 36.1 1.0
CG A:LEU85 4.8 18.4 1.0
NE A:ARG89 4.9 38.3 1.0
O A:GLY80 5.0 24.6 1.0
N A:GLU86 5.0 27.6 1.0
N A:LYS81 5.0 23.6 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: Fri Jul 26 09:41:10 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy