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Chlorine in PDB 4rq3: Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp 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 Datp 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 Datp 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 Datp in the Presence of CACL2, PDB code: 4rq3 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) 47.29 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.320, 79.680, 55.450, 90.00, 106.51, 90.00
R / Rfree (%) 19.2 / 24.6

Other elements in 4rq3:

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 Datp in the Presence of CACL2 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 4 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 Datp in the Presence of CACL2 (pdb code 4rq3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 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 Datp in the Presence of CACL2, PDB code: 4rq3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4rq3

Go back to Chlorine Binding Sites List in 4rq3
Chlorine binding site 1 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp 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 Datp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:32.7
occ:1.00
 O A:HOH536 3.1 22.4 1.0
N A:CYS267 3.2 20.0 1.0
N A:TYR266 3.3 20.7 1.0
C A:GLN264 3.4 21.0 1.0
O A:GLN264 3.5 20.2 1.0
CA A:GLN264 3.5 20.1 1.0
CB A:TYR266 3.6 22.6 1.0
CA A:TYR266 3.7 21.1 1.0
CG1 A:VAL313 3.8 30.1 1.0
SG A:CYS267 3.9 22.5 1.0
CB A:VAL313 3.9 29.9 1.0
O A:ASP263 3.9 20.5 1.0
C A:TYR266 3.9 21.0 1.0
O A:HOH590 4.0 50.5 1.0
N A:TYR265 4.0 21.6 1.0
CB A:CYS267 4.0 19.6 1.0
CA A:CYS267 4.2 19.8 1.0
CD2 A:TYR266 4.3 24.7 1.0
C A:TYR265 4.3 21.1 1.0
CG A:TYR266 4.5 23.4 1.0
CB A:GLN264 4.5 19.7 1.0
N A:GLN264 4.5 19.6 1.0
O A:TYR296 4.5 21.6 1.0
O A:VAL313 4.5 26.0 1.0
C A:ASP263 4.6 20.5 1.0
CG2 A:VAL313 4.7 29.6 1.0
CA A:TYR265 4.8 21.2 1.0
C A:VAL313 5.0 29.0 1.0

Chlorine binding site 2 out of 4 in 4rq3

Go back to Chlorine Binding Sites List in 4rq3
Chlorine binding site 2 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp 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 Datp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:41.2
occ:1.00
 OG1 A:THR227 2.9 20.6 1.0
NE2 A:GLN219 3.4 26.4 1.0
CD A:LYS230 3.5 25.4 1.0
CB A:THR227 3.7 20.2 1.0
CG2 A:THR227 3.7 20.6 1.0
CE A:LYS230 4.1 26.4 1.0
CD A:GLN219 4.5 25.7 1.0
O A:HOH531 4.5 19.4 1.0
CE1 A:PHE235 4.6 16.0 1.0
OE1 A:GLN219 4.7 27.9 1.0
CG1 A:VAL215 4.8 17.4 1.0
CG A:LYS230 4.9 23.6 1.0
NZ A:LYS230 4.9 26.7 1.0
CB A:LYS230 5.0 22.4 1.0

Chlorine binding site 3 out of 4 in 4rq3

Go back to Chlorine Binding Sites List in 4rq3
Chlorine binding site 3 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp 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 Datp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:23.6
occ:1.00
 NH2 A:ARG299 2.9 35.4 1.0
O A:HOH621 3.0 24.7 1.0
OG1 A:THR297 3.4 22.9 1.0
ND2 A:ASN294 3.4 19.9 1.0
NE A:ARG299 3.5 35.9 1.0
CZ A:ARG299 3.6 36.3 1.0
CG2 A:THR297 3.8 22.2 1.0
CB A:TYR296 3.9 21.2 1.0
OD1 A:ASN294 4.1 18.7 1.0
CG A:ASN294 4.2 19.2 1.0
CD2 A:TYR296 4.2 21.6 1.0
CB A:THR297 4.2 22.9 1.0
CG A:TYR296 4.5 21.4 1.0
O T:HOH106 4.7 41.3 1.0
CD A:ARG299 4.8 33.5 1.0
N A:THR297 4.8 22.0 1.0
O A:HOH594 4.9 21.4 1.0
NH1 A:ARG299 4.9 38.1 1.0
O A:HOH566 5.0 24.4 1.0

Chlorine binding site 4 out of 4 in 4rq3

Go back to Chlorine Binding Sites List in 4rq3
Chlorine binding site 4 out of 4 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp 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 4 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine (8-Oxog) and Datp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:39.8
occ:1.00
 CB A:ALA32 3.3 22.0 1.0
CA A:ALA32 3.3 22.1 1.0
C A:ALA32 3.4 21.8 1.0
N A:HIS34 3.5 22.4 1.0
CB A:HIS34 3.6 24.6 1.0
N A:LYS35 3.6 20.8 1.0
O D:HOH104 3.7 46.2 1.0
N A:ILE33 3.8 22.1 1.0
O A:ALA32 3.8 21.3 1.0
CA A:HIS34 3.9 23.2 1.0
CD2 A:HIS34 4.0 27.0 1.0
CG A:LYS35 4.1 20.8 1.0
CG A:HIS34 4.1 25.6 1.0
C A:HIS34 4.2 21.7 1.0
O A:HOH631 4.4 29.4 1.0
C A:ILE33 4.5 23.4 1.0
CB A:LYS35 4.5 21.4 1.0
CA A:LYS35 4.7 20.8 1.0
O6 D:DG1 4.7 27.9 1.0
CA A:ILE33 4.8 22.9 1.0
N A:ALA32 4.8 21.7 1.0
CD A:LYS35 4.8 21.9 1.0
CE A:LYS35 4.9 22.8 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 01:24:45 2024

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