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Calcium 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:

Chlorine (Cl) 4 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4rq3

Go back to Calcium Binding Sites List in 4rq3
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca402

b:26.6
occ:1.00
 OD2 A:ASP190 2.1 21.1 1.0
OD1 A:ASP192 2.2 16.6 1.0
OD2 A:ASP256 2.4 18.8 1.0
O P:HOH101 2.4 25.7 1.0
O3' P:DC10 2.4 27.8 1.0
O2A A:DTP401 2.5 24.9 1.0
CG A:ASP190 3.0 18.9 1.0
OD1 A:ASP190 3.1 18.1 1.0
CG A:ASP192 3.2 17.5 1.0
C3' P:DC10 3.4 26.9 1.0
CG A:ASP256 3.5 18.3 1.0
PA A:DTP401 3.5 28.7 1.0
OD2 A:ASP192 3.6 17.5 1.0
O1A A:DTP401 3.9 26.0 1.0
CA A:CA403 3.9 24.6 1.0
O5' A:DTP401 3.9 25.4 1.0
C5' P:DC10 3.9 27.8 1.0
C4' P:DC10 3.9 27.2 1.0
CB A:ASP256 4.1 17.1 1.0
C5' A:DTP401 4.2 23.6 1.0
CB A:ASP190 4.4 18.3 1.0
OD1 A:ASP256 4.5 19.9 1.0
O5' P:DC10 4.5 27.9 1.0
CB A:ASP192 4.5 17.5 1.0
OP1 P:DC10 4.6 23.3 1.0
C2' P:DC10 4.7 26.2 1.0
O A:MET191 4.7 18.8 1.0
NH2 A:ARG254 4.8 15.9 1.0
O2G A:DTP401 5.0 26.2 1.0
O3A A:DTP401 5.0 27.4 1.0

Calcium binding site 2 out of 2 in 4rq3

Go back to Calcium Binding Sites List in 4rq3
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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:Ca403

b:24.6
occ:1.00
 OD1 A:ASP190 2.2 18.1 1.0
O A:HOH501 2.2 24.1 1.0
O2B A:DTP401 2.2 25.0 1.0
OD2 A:ASP192 2.2 17.5 1.0
O2G A:DTP401 2.2 26.2 1.0
O2A A:DTP401 2.2 24.9 1.0
PB A:DTP401 3.2 26.2 1.0
CG A:ASP192 3.3 17.5 1.0
CG A:ASP190 3.4 18.9 1.0
PA A:DTP401 3.4 28.7 1.0
PG A:DTP401 3.5 27.8 1.0
O3A A:DTP401 3.5 27.4 1.0
O A:ASP190 3.6 19.9 1.0
OD1 A:ASP192 3.7 16.6 1.0
O3B A:DTP401 3.7 27.0 1.0
CA A:CA402 3.9 26.6 1.0
O A:HOH502 4.0 25.6 1.0
C A:ASP190 4.0 18.4 1.0
OD2 A:ASP190 4.0 21.1 1.0
O1G A:DTP401 4.1 26.0 1.0
N A:ASP190 4.1 17.9 1.0
C5' A:DTP401 4.2 23.6 1.0
O5' A:DTP401 4.3 25.4 1.0
CA A:ASP190 4.4 18.0 1.0
CB A:ASP190 4.5 18.3 1.0
CA A:GLY179 4.5 19.4 1.0
N A:SER180 4.5 19.9 1.0
CB A:ASP192 4.6 17.5 1.0
OG A:SER180 4.6 23.0 1.0
O1B A:DTP401 4.6 26.5 1.0
O1A A:DTP401 4.7 26.0 1.0
N A:MET191 4.7 18.5 1.0
O3G A:DTP401 4.7 28.6 1.0
N A:ASP192 4.8 18.1 1.0
O P:HOH101 4.8 25.7 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: Sun Jul 14 12:45:57 2024

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