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Calcium 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:

Chlorine (Cl) 3 atoms
Sodium (Na) 7 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 Dctp in the Presence of CACL2 (pdb code 4rpx). 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 Dctp in the Presence of CACL2, PDB code: 4rpx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4rpx

Go back to Calcium Binding Sites List in 4rpx
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 Dctp 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 Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:18.3
occ:1.00
 OD2 A:ASP256 2.3 17.1 1.0
OD1 A:ASP192 2.3 14.2 1.0
OD2 A:ASP190 2.4 18.3 1.0
O P:HOH201 2.4 16.2 1.0
O3' P:DC10 2.5 16.3 1.0
O2A A:DCP401 2.5 16.1 1.0
OD1 A:ASP190 2.6 17.4 1.0
CG A:ASP190 2.8 18.2 1.0
CG A:ASP192 3.4 15.0 1.0
CG A:ASP256 3.5 17.3 1.0
C3' P:DC10 3.5 16.3 1.0
PA A:DCP401 3.6 16.2 1.0
OD2 A:ASP192 3.7 14.5 1.0
CA A:CA403 3.8 18.7 1.0
O5' A:DCP401 4.0 15.4 1.0
O1A A:DCP401 4.0 15.5 1.0
C5' P:DC10 4.1 16.7 1.0
C4' P:DC10 4.1 16.4 1.0
CB A:ASP256 4.2 15.9 1.0
C5' A:DCP401 4.2 15.6 1.0
CB A:ASP190 4.3 17.6 1.0
OD1 A:ASP256 4.5 17.6 1.0
O A:MET191 4.6 17.0 1.0
OP1 P:DC10 4.6 16.6 1.0
CB A:ASP192 4.7 14.6 1.0
O5' P:DC10 4.7 17.2 1.0
C2' P:DC10 4.8 16.2 1.0
NH2 A:ARG254 4.8 16.0 1.0
O3G A:DCP401 4.9 17.1 1.0
C A:MET191 5.0 17.4 1.0

Calcium binding site 2 out of 2 in 4rpx

Go back to Calcium Binding Sites List in 4rpx
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 Dctp 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 Dctp in the Presence of CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:18.7
occ:1.00
 O3G A:DCP401 2.2 17.1 1.0
O2B A:DCP401 2.3 15.6 1.0
OD1 A:ASP190 2.3 17.4 1.0
O2A A:DCP401 2.3 16.1 1.0
OD2 A:ASP192 2.3 14.5 1.0
O A:HOH501 2.4 17.7 1.0
O A:ASP190 3.0 19.4 1.0
CG A:ASP192 3.3 15.0 1.0
PB A:DCP401 3.4 16.3 1.0
PG A:DCP401 3.5 18.5 1.0
CG A:ASP190 3.5 18.2 1.0
PA A:DCP401 3.6 16.2 1.0
OD1 A:ASP192 3.7 14.2 1.0
C A:ASP190 3.7 18.7 1.0
O3A A:DCP401 3.8 16.3 1.0
CA A:CA402 3.8 18.3 1.0
O3B A:DCP401 3.8 16.8 1.0
N A:ASP190 3.8 17.3 1.0
O A:HOH502 4.1 14.9 1.0
CA A:ASP190 4.2 17.8 1.0
O1G A:DCP401 4.2 17.6 1.0
C5' A:DCP401 4.3 15.6 1.0
OD2 A:ASP190 4.4 18.3 1.0
CB A:ASP190 4.4 17.6 1.0
OG A:SER180 4.5 18.9 1.0
O5' A:DCP401 4.5 15.4 1.0
N A:SER180 4.5 17.5 1.0
N A:MET191 4.6 18.3 1.0
CA A:GLY179 4.6 16.8 1.0
O2G A:DCP401 4.6 17.4 1.0
CB A:ASP192 4.7 14.6 1.0
O1B A:DCP401 4.7 16.6 1.0
O1A A:DCP401 4.7 15.5 1.0
N A:ASP192 4.8 15.4 1.0
C A:MET191 4.9 17.4 1.0
C A:GLY189 4.9 17.0 1.0
N A:GLY189 5.0 17.7 1.0
CA A:MET191 5.0 18.7 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 12:45:40 2024

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