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Calcium in PDB 6dic: D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

Enzymatic activity of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

All present enzymatic activity of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog:
2.7.7.7;

Protein crystallography data

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dic was solved by B.D.Freudenthal, M.R.Smith, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.66 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 17.5 / 23.2

Other elements in 6dic:

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog (pdb code 6dic). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dic:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6dic

Go back to Calcium Binding Sites List in 6dic
Calcium binding site 1 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:15.8
occ:1.00
 OD2 A:ASP256 2.2 18.3 1.0
OD1 A:ASP192 2.3 16.9 1.0
O A:HOH630 2.3 16.3 1.0
OD2 A:ASP190 2.4 20.8 1.0
O3' P:DC10 2.4 22.1 1.0
O1A A:GKS403 2.5 13.1 1.0
OD1 A:ASP190 2.6 14.4 1.0
CG A:ASP190 2.8 16.5 1.0
CG A:ASP192 3.3 14.9 1.0
CG A:ASP256 3.4 22.3 1.0
PA A:GKS403 3.5 16.5 1.0
C3' P:DC10 3.5 22.4 1.0
OD2 A:ASP192 3.7 18.6 1.0
CA A:CA410 3.8 14.4 1.0
O2A A:GKS403 3.9 19.4 1.0
O5' A:GKS403 3.9 21.1 1.0
C4' P:DC10 4.2 21.8 1.0
C5' P:DC10 4.2 17.8 1.0
C5' A:GKS403 4.2 15.1 1.0
CB A:ASP256 4.2 21.3 1.0
O A:HOH684 4.3 23.2 1.0
CB A:ASP190 4.4 16.4 1.0
OD1 A:ASP256 4.4 18.1 1.0
O A:HOH571 4.6 24.8 1.0
O A:MET191 4.6 16.6 1.0
CB A:ASP192 4.6 15.6 1.0
O5' P:DC10 4.7 16.7 1.0
C2' P:DC10 4.8 21.5 1.0
OP1 P:DC10 4.8 24.0 1.0
O3A A:GKS403 4.8 20.1 1.0
NH2 A:ARG254 4.9 14.2 1.0
C A:MET191 5.0 14.4 1.0

Calcium binding site 2 out of 3 in 6dic

Go back to Calcium Binding Sites List in 6dic
Calcium binding site 2 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:14.4
occ:1.00
 OD2 A:ASP192 2.3 18.6 1.0
OD1 A:ASP190 2.3 14.4 1.0
O2G A:GKS403 2.3 21.8 1.0
O2B A:GKS403 2.4 15.4 1.0
O A:HOH537 2.4 17.0 1.0
O1A A:GKS403 2.4 13.1 1.0
O A:ASP190 2.9 19.5 1.0
CG A:ASP192 3.3 14.9 1.0
PB A:GKS403 3.5 15.2 1.0
CG A:ASP190 3.5 16.5 1.0
C A:ASP190 3.5 14.3 1.0
PG A:GKS403 3.6 19.8 1.0
OD1 A:ASP192 3.6 16.9 1.0
PA A:GKS403 3.7 16.5 1.0
N A:ASP190 3.7 12.8 1.0
O3A A:GKS403 3.7 20.1 1.0
CA A:CA402 3.8 15.8 1.0
O3B A:GKS403 3.8 16.9 1.0
CA A:ASP190 4.0 8.7 1.0
O A:HOH684 4.1 23.2 1.0
O A:HOH631 4.2 15.1 1.0
O1G A:GKS403 4.3 16.3 1.0
CB A:ASP190 4.4 16.4 1.0
OD2 A:ASP190 4.4 20.8 1.0
N A:MET191 4.4 12.7 1.0
N A:SER180 4.5 18.0 1.0
C5' A:GKS403 4.5 15.1 1.0
OG A:SER180 4.5 19.6 1.0
CA A:GLY179 4.6 12.2 1.0
CB A:ASP192 4.6 15.6 1.0
O5' A:GKS403 4.6 21.1 1.0
O3G A:GKS403 4.7 15.2 1.0
C A:GLY189 4.8 19.4 1.0
O2A A:GKS403 4.8 19.4 1.0
N A:ASP192 4.8 19.2 1.0
C A:MET191 4.8 14.4 1.0
O1B A:GKS403 4.8 19.5 1.0
CA A:MET191 4.9 17.7 1.0
N A:GLY189 4.9 17.5 1.0
O A:HOH630 4.9 16.3 1.0

Calcium binding site 3 out of 3 in 6dic

Go back to Calcium Binding Sites List in 6dic
Calcium binding site 3 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca411

b:40.6
occ:1.00
 O A:HOH738 2.3 33.4 1.0
O A:HOH661 2.4 27.7 1.0
OD2 A:ASP145 2.5 21.1 1.0
O A:HOH530 2.8 24.7 1.0
OD1 A:ASP145 2.9 26.9 1.0
CG A:ASP145 3.0 22.9 1.0
O A:HOH744 4.2 32.8 1.0
O A:HOH643 4.3 26.8 1.0
O A:HOH665 4.4 26.4 1.0
O A:HOH507 4.4 31.7 1.0
ND1 A:HIS252 4.4 19.9 1.0
CB A:ASP145 4.5 19.8 1.0
CA A:PRO251 4.6 15.5 1.0
N A:HIS252 4.6 11.7 1.0

Reference:

M.R.Smith, D.D.Shock, W.A.Beard, M.M.Greenberg, B.D.Freudenthal, S.H.Wilson. A Guardian Residue Hinders Insertion of A Fapy•Dgtp Analog By Modulating the Open-Closed Dna Polymerase Transition. Nucleic Acids Res. V. 47 3197 2019.
ISSN: ESSN 1362-4962
PubMed: 30649431
DOI: 10.1093/NAR/GKZ002
Page generated: Wed Jul 9 13:26:21 2025

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