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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

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