Atomistry » Chlorine » PDB 5uwu-5v49 » 5v1i
Atomistry »
  Chlorine »
    PDB 5uwu-5v49 »
      5v1i »

Chlorine in PDB 5v1i: Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp

Enzymatic activity of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp

All present enzymatic activity of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp, PDB code: 5v1i was solved by B.D.Freudenthal, M.R.Smith, A.M.Whitaker, M.A.Schaich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.60 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.564, 79.798, 55.539, 90.00, 107.62, 90.00
R / Rfree (%) 18.4 / 23.7

Other elements in 5v1i:

The structure of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp (pdb code 5v1i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp, PDB code: 5v1i:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5v1i

Go back to Chlorine Binding Sites List in 5v1i
Chlorine binding site 1 out of 4 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:37.1
occ:1.00
 O A:HOH520 3.2 23.2 1.0
N A:CYS267 3.3 14.2 1.0
N A:TYR266 3.5 18.1 1.0
CA A:GLN264 3.5 20.3 1.0
C A:GLN264 3.5 21.2 1.0
CG1 A:VAL313 3.6 25.5 1.0
O A:ASP263 3.8 24.8 1.0
SG A:CYS267 3.8 22.8 1.0
CB A:TYR266 3.8 17.4 1.0
O A:GLN264 3.8 20.7 1.0
CB A:VAL313 3.9 23.8 1.0
CA A:TYR266 3.9 17.5 1.0
N A:TYR265 4.0 17.9 1.0
CB A:CYS267 4.0 18.1 1.0
C A:TYR266 4.1 14.7 1.0
CA A:CYS267 4.2 12.8 1.0
O A:VAL313 4.3 26.8 1.0
O A:TYR296 4.3 19.3 1.0
C A:TYR265 4.4 18.5 1.0
CB A:GLN264 4.4 21.9 1.0
CD2 A:TYR266 4.5 30.4 1.0
N A:GLN264 4.5 19.8 1.0
C A:ASP263 4.5 21.7 1.0
CG A:TYR266 4.6 26.1 1.0
CG2 A:VAL313 4.7 25.2 1.0
CA A:TYR265 4.8 23.3 1.0
C A:VAL313 4.9 28.2 1.0
CG A:GLN264 4.9 21.9 1.0
CA A:VAL313 5.0 28.3 1.0

Chlorine binding site 2 out of 4 in 5v1i

Go back to Chlorine Binding Sites List in 5v1i
Chlorine binding site 2 out of 4 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:42.1
occ:1.00
 N A:HIS34 3.2 26.1 1.0
C A:ALA32 3.3 27.3 1.0
CB A:HIS34 3.4 32.5 1.0
CA A:ALA32 3.4 32.1 1.0
CB A:ALA32 3.5 23.6 1.0
N A:ILE33 3.6 24.0 1.0
N A:LYS35 3.7 22.4 1.0
CD2 A:HIS34 3.7 34.2 1.0
O A:ALA32 3.8 28.4 1.0
CA A:HIS34 3.8 26.9 1.0
CG A:HIS34 3.9 37.9 1.0
O A:HOH551 4.1 34.6 1.0
C A:HIS34 4.2 22.1 1.0
C A:ILE33 4.2 29.2 1.0
CG A:LYS35 4.4 25.1 1.0
CA A:ILE33 4.5 31.9 1.0
CB A:LYS35 4.7 23.2 1.0
CA A:LYS35 4.8 21.6 1.0
CG2 A:ILE33 4.8 30.3 1.0
O6 D:DG1 4.9 34.0 1.0
N A:ALA32 4.9 26.0 1.0

Chlorine binding site 3 out of 4 in 5v1i

Go back to Chlorine Binding Sites List in 5v1i
Chlorine binding site 3 out of 4 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:46.1
occ:1.00
 NH1 A:ARG89 3.1 50.7 1.0
N A:LEU82 3.4 29.7 1.0
OE1 A:GLU86 3.7 60.3 1.0
CA A:LYS81 3.9 31.0 1.0
C A:LYS81 4.0 35.4 1.0
CB A:LEU85 4.1 25.1 1.0
CZ A:ARG89 4.1 49.9 1.0
O A:LEU82 4.2 25.8 1.0
CB A:LEU82 4.2 32.1 1.0
CA A:LEU82 4.2 27.4 1.0
CB A:LYS81 4.3 30.9 1.0
CD1 A:LEU85 4.3 28.8 1.0
NH2 A:ARG89 4.4 37.2 1.0
C A:LEU82 4.7 33.0 1.0
CD A:GLU86 4.7 58.0 1.0
CG A:LEU85 4.8 27.1 1.0
CG A:GLU86 4.9 44.0 1.0
O A:GLY80 4.9 33.7 1.0

Chlorine binding site 4 out of 4 in 5v1i

Go back to Chlorine Binding Sites List in 5v1i
Chlorine binding site 4 out of 4 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:28.6
occ:1.00
 NH2 A:ARG299 3.1 19.5 0.6
OG1 A:THR297 3.2 17.8 1.0
O A:HOH651 3.3 28.5 1.0
ND2 A:ASN294 3.3 25.1 1.0
NE A:ARG299 3.6 18.7 0.6
CZ A:ARG299 3.7 21.3 0.6
CG2 A:THR297 3.9 14.7 1.0
OD1 A:ASN294 3.9 21.6 1.0
CB A:TYR296 3.9 25.7 1.0
CD2 A:TYR296 4.0 16.6 1.0
CG A:ASN294 4.0 16.6 1.0
CZ A:ARG299 4.1 25.1 0.4
CB A:THR297 4.2 18.7 1.0
NH2 A:ARG299 4.2 19.3 0.4
NE A:ARG299 4.2 19.2 0.4
CG A:TYR296 4.4 17.1 1.0
NH1 A:ARG299 4.6 18.4 0.4
O T:HOH115 4.7 32.9 1.0
O A:HOH607 4.8 18.5 1.0
N A:THR297 4.8 14.9 1.0
CD A:ARG299 4.8 20.3 0.6
O T:HOH129 4.8 42.0 1.0
CD A:ARG299 4.9 20.3 0.4
NH1 A:ARG299 4.9 22.3 0.6

Reference:

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293
Page generated: Fri Jul 26 18:32:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy