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Chlorine in PDB 4rpx: Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2, PDB code: 4rpx was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.43 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.660, 79.360, 55.650, 90.00, 106.34, 90.00
R / Rfree (%) 18.9 / 22.7

Other elements in 4rpx:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2 (pdb code 4rpx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2, PDB code: 4rpx:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4rpx

Go back to Chlorine Binding Sites List in 4rpx
Chlorine binding site 1 out of 3 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:40.0
occ:1.00
 N A:HIS135 3.0 17.6 1.0
O A:HOH632 3.1 28.7 1.0
CB A:HIS135 3.4 18.1 1.0
OD1 A:ASN133 3.6 19.5 1.0
N A:HIS134 3.6 17.4 1.0
CG A:ASN133 3.6 18.5 1.0
CB A:HIS134 3.8 18.4 1.0
CA A:HIS135 3.8 17.8 1.0
CB A:ASN133 3.9 17.9 1.0
C A:HIS134 3.9 17.5 1.0
CA A:HIS134 3.9 17.5 1.0
ND2 A:ASN133 4.1 18.1 1.0
C A:ASN133 4.3 17.4 1.0
CA A:ASN133 4.7 17.7 1.0
CG A:HIS135 4.8 18.2 1.0
CG A:HIS134 4.8 19.0 1.0
ND1 A:HIS134 4.8 19.7 1.0
O T:HOH136 4.8 42.0 1.0
O A:LEU228 4.8 19.0 1.0

Chlorine binding site 2 out of 3 in 4rpx

Go back to Chlorine Binding Sites List in 4rpx
Chlorine binding site 2 out of 3 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:26.9
occ:1.00
 O A:HOH636 3.2 28.7 1.0
NH2 A:ARG299 3.2 21.4 0.5
OG1 A:THR297 3.3 20.2 1.0
NE A:ARG299 3.4 21.8 0.5
ND2 A:ASN294 3.5 16.1 1.0
NH1 A:ARG299 3.5 28.3 0.5
CZ A:ARG299 3.8 21.9 0.5
CG2 A:THR297 3.9 19.7 1.0
CB A:TYR296 4.0 18.0 1.0
OD1 A:ASN294 4.0 16.2 1.0
CG A:ASN294 4.2 15.9 1.0
CZ A:ARG299 4.2 27.9 0.5
CD2 A:TYR296 4.2 19.0 1.0
CB A:THR297 4.2 19.4 1.0
O T:HOH109 4.2 38.3 1.0
CD A:ARG299 4.4 26.0 0.5
CG A:TYR296 4.5 18.8 1.0
NE A:ARG299 4.6 27.4 0.5
CD A:ARG299 4.7 22.2 0.5
O A:HOH608 4.8 19.0 1.0
N A:THR297 4.8 18.4 1.0
O A:HOH667 4.8 36.6 1.0

Chlorine binding site 3 out of 3 in 4rpx

Go back to Chlorine Binding Sites List in 4rpx
Chlorine binding site 3 out of 3 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:27.8
occ:1.00
 N A:HIS34 3.3 18.5 1.0
C A:ALA32 3.4 18.7 1.0
CA A:ALA32 3.4 18.7 1.0
CB A:ALA32 3.5 18.8 1.0
CB A:HIS34 3.6 20.1 1.0
N A:LYS35 3.6 16.5 1.0
N A:ILE33 3.7 18.2 1.0
CA A:HIS34 3.8 18.5 1.0
O A:ALA32 3.9 19.6 1.0
CD2 A:HIS34 4.0 21.4 1.0
CG A:HIS34 4.1 20.8 1.0
O A:HOH646 4.2 23.9 1.0
C A:HIS34 4.2 17.7 1.0
CG A:LYS35 4.3 16.5 1.0
C A:ILE33 4.4 18.6 1.0
CA A:ILE33 4.6 18.7 1.0
CB A:LYS35 4.7 16.2 1.0
CA A:LYS35 4.7 16.0 1.0
O6 D:DG1 4.8 16.6 1.0
N A:ALA32 4.9 19.1 1.0

Reference:

R.Vyas, A.J.Reed, E.J.Tokarsky, Z.Suo. Viewing Human Dna Polymerase Beta Faithfully and Unfaithfully Bypass An Oxidative Lesion By Time-Dependent Crystallography. J.Am.Chem.Soc. V. 137 5225 2015.
ISSN: ISSN 0002-7863
PubMed: 25825995
DOI: 10.1021/JACS.5B02109
Page generated: Fri Jul 26 01:22:53 2024

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