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

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

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

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dia 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) 22.57 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.947, 80.584, 55.314, 90.00, 109.94, 90.00
R / Rfree (%) 19.6 / 24.6

Other elements in 6dia:

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

Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 3 in 6dia

Go back to Calcium Binding Sites List in 6dia
Calcium binding site 1 out of 3 in the 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 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:Ca403

b:34.9
occ:1.00
 O1A A:GKS401 2.3 32.1 1.0
OD2 A:ASP192 2.4 36.3 1.0
O A:HOH512 2.4 29.0 1.0
OD1 A:ASP190 2.5 27.1 1.0
O3G A:GKS401 2.6 38.2 1.0
O2B A:GKS401 2.6 31.9 1.0
O A:HOH649 2.7 29.3 1.0
OD1 A:ASP192 2.8 39.6 1.0
CG A:ASP192 3.0 33.8 1.0
CG A:ASP190 3.4 30.7 1.0
PA A:GKS401 3.5 40.6 1.0
OD2 A:ASP190 3.7 38.1 1.0
PB A:GKS401 3.7 39.5 1.0
O3A A:GKS401 3.7 40.3 1.0
N2 A:GKS401 3.8 32.2 1.0
PG A:GKS401 3.8 41.9 1.0
O A:HOH519 4.1 48.5 1.0
O2G A:GKS401 4.1 45.8 1.0
O3B A:GKS401 4.1 46.9 1.0
O A:HOH507 4.2 34.8 1.0
O2A A:GKS401 4.3 43.9 1.0
O A:HOH584 4.4 30.4 1.0
CB A:ASP192 4.5 27.2 1.0
O3' P:DC10 4.6 32.2 1.0
NA P:NA101 4.6 46.3 1.0
O A:ASP190 4.6 22.9 1.0
O A:HOH520 4.7 39.2 1.0
O5' A:GKS401 4.7 40.9 1.0
CA A:GLY179 4.8 28.0 1.0
O A:HOH598 4.8 28.7 1.0
CB A:ASP190 4.8 18.8 1.0
C A:ASP190 4.9 20.6 1.0
C2 A:GKS401 5.0 42.6 1.0
N A:ASP190 5.0 23.3 1.0

Calcium binding site 2 out of 3 in 6dia

Go back to Calcium Binding Sites List in 6dia
Calcium binding site 2 out of 3 in the 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 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:Ca404

b:34.9
occ:1.00
 O A:HOH720 2.3 33.5 1.0
O A:HOH652 2.3 25.9 1.0
OD1 A:ASP145 2.5 21.0 1.0
OD2 A:ASP145 2.6 23.0 1.0
O A:HOH576 2.6 28.6 1.0
O A:HOH679 2.6 32.4 1.0
CG A:ASP145 2.9 26.1 1.0
O A:HOH712 3.6 38.3 1.0
O A:HOH710 3.9 35.6 1.0
O A:HOH642 4.3 22.0 1.0
CB A:ASP145 4.4 18.9 1.0
O A:HOH681 4.5 40.5 1.0
CA A:PRO251 4.6 27.8 1.0
ND1 A:HIS252 4.6 32.7 1.0
OE1 A:GLU249 4.7 44.2 1.0
N A:HIS252 4.9 26.1 1.0

Calcium binding site 3 out of 3 in 6dia

Go back to Calcium Binding Sites List in 6dia
Calcium binding site 3 out of 3 in the 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 Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca101

b:51.2
occ:1.00
 O T:HOH208 2.3 26.2 1.0
O A:HOH522 2.3 35.2 1.0
O A:HOH505 2.3 35.7 1.0
O T:HOH219 2.4 35.6 1.0
O A:HOH517 2.5 43.1 1.0
O A:HOH530 2.6 30.5 1.0
O2 T:DC6 2.9 31.4 1.0
OE1 A:GLU295 3.6 40.5 1.0
C2 T:DC6 4.0 29.4 1.0
O4' T:DG7 4.0 23.4 1.0
O T:HOH256 4.3 35.2 1.0
N3 T:DG7 4.3 22.6 1.0
N3 T:DC6 4.5 28.7 1.0
OH A:TYR271 4.5 39.2 1.0
O4' T:DC8 4.5 22.9 1.0
C4' T:DG7 4.5 29.0 1.0
CD A:GLU295 4.7 38.9 1.0
O A:HOH577 4.7 37.6 1.0
N2 T:DG7 4.8 23.7 1.0
C1' T:DG7 4.8 25.4 1.0
C5' T:DC8 4.9 28.6 1.0
C2 T:DG7 4.9 24.1 1.0
OH A:TYR296 4.9 33.9 1.0
C4' T:DC8 5.0 29.1 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: Sat Dec 12 06:03:27 2020

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