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Chlorine in PDB 8vfi: Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da

Enzymatic activity of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da

All present enzymatic activity of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da:
2.7.7.7;

Protein crystallography data

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da, PDB code: 8vfi was solved by P.N.Oden, B.J.Ryan, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.65 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.8, 80.4, 55.5, 90, 107.9, 90
R / Rfree (%) 18.1 / 22.9

Other elements in 8vfi:

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da 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 Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da (pdb code 8vfi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da, PDB code: 8vfi:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8vfi

Go back to Chlorine Binding Sites List in 8vfi
Chlorine binding site 1 out of 3 in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:33.8
occ:1.00
 N A:HIS34 3.2 18.9 1.0
C A:ALA32 3.4 25.8 1.0
CB A:HIS34 3.4 27.4 1.0
CA A:ALA32 3.5 26.2 1.0
CB A:ALA32 3.5 20.1 1.0
N A:LYS35 3.6 22.2 1.0
N A:ILE33 3.6 21.7 1.0
CA A:HIS34 3.7 22.6 1.0
O A:ALA32 3.8 23.9 1.0
CD2 A:HIS34 3.9 32.3 1.0
CG A:HIS34 4.0 34.3 1.0
C A:HIS34 4.1 22.5 1.0
C A:ILE33 4.2 24.1 1.0
CG A:LYS35 4.4 25.8 1.0
CA A:ILE33 4.5 27.3 1.0
O A:HOH639 4.5 31.1 1.0
CB A:LYS35 4.6 19.1 1.0
CA A:LYS35 4.7 20.7 1.0
O6 D:DG1 4.9 31.4 1.0
N A:ALA32 4.9 20.6 1.0

Chlorine binding site 2 out of 3 in 8vfi

Go back to Chlorine Binding Sites List in 8vfi
Chlorine binding site 2 out of 3 in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:48.5
occ:1.00
 O A:HOH732 3.1 38.6 1.0
N A:LEU82 3.3 19.7 1.0
OE2 A:GLU86 3.4 43.4 1.0
CA A:LYS81 3.9 23.0 1.0
O A:HOH788 4.0 36.8 1.0
O A:LEU82 4.0 22.3 1.0
C A:LYS81 4.1 23.7 1.0
NH1 A:ARG89 4.1 47.8 1.0
CB A:LEU85 4.1 26.1 1.0
CD A:GLU86 4.2 53.4 1.0
CB A:LYS81 4.2 27.4 1.0
CA A:LEU82 4.2 20.4 1.0
CZ A:ARG89 4.3 41.6 1.0
CB A:LEU82 4.3 26.2 1.0
CD1 A:LEU85 4.3 24.4 1.0
CG A:GLU86 4.4 32.0 1.0
NH2 A:ARG89 4.4 34.7 1.0
C A:LEU82 4.6 23.1 1.0
N A:GLU86 4.8 22.8 1.0
CG A:LYS81 4.8 35.5 1.0
CG A:LEU85 4.9 26.1 1.0
NE A:ARG89 4.9 35.2 1.0
O A:GLY80 5.0 27.5 1.0

Chlorine binding site 3 out of 3 in 8vfi

Go back to Chlorine Binding Sites List in 8vfi
Chlorine binding site 3 out of 3 in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:34.8
occ:1.00
 NH2 A:ARG299 2.9 21.1 0.5
O A:HOH766 3.2 34.7 1.0
OG1 A:THR297 3.3 22.6 1.0
ND2 A:ASN294 3.3 18.8 1.0
NE A:ARG299 3.4 22.7 0.5
O T:HOH142 3.6 42.8 1.0
CZ A:ARG299 3.6 25.0 0.5
CG2 A:THR297 3.9 20.1 1.0
CB A:TYR296 4.0 23.2 1.0
OD1 A:ASN294 4.0 20.8 1.0
CG A:ASN294 4.1 17.0 1.0
CD2 A:TYR296 4.1 20.1 1.0
CZ A:ARG299 4.2 25.2 0.5
CB A:THR297 4.2 22.7 1.0
NE A:ARG299 4.2 22.7 0.5
NH2 A:ARG299 4.3 24.5 0.5
CG A:TYR296 4.5 20.6 1.0
NH1 A:ARG299 4.6 19.8 0.5
CD A:ARG299 4.7 22.0 0.5
CD A:ARG299 4.7 21.6 0.5
O T:HOH119 4.7 32.8 1.0
O A:HOH683 4.8 43.7 1.0
N A:THR297 4.8 18.8 1.0
O A:HOH695 4.9 20.9 1.0
NH1 A:ARG299 4.9 27.2 0.5

Reference:

S.Gao, P.N.Oden, B.J.Ryan, H.Yang, B.D.Freudenthal, M.M.Greenberg. Biochemical and Structural Characterization of Fapy•Dg Replication By Human Dna Polymerase Beta. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38634780
DOI: 10.1093/NAR/GKAE277
Page generated: Sun Jul 13 15:18:19 2025

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