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Calcium in PDB 6mr8: D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog

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

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

Protein crystallography data

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr8 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) 24.80 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.015, 80.282, 55.564, 90.00, 110.46, 90.00
R / Rfree (%) 19.6 / 23.9

Other elements in 6mr8:

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

Sodium (Na) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog (pdb code 6mr8). 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 Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6mr8

Go back to Calcium Binding Sites List in 6mr8
Calcium binding site 1 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:45.1
occ:0.85
 O A:HOH512 2.2 34.5 1.0
O1A A:GKS401 2.3 50.9 0.8
OD2 A:ASP192 2.3 31.7 0.5
OD1 A:ASP190 2.5 28.3 1.0
O A:HOH662 2.7 33.6 1.0
PA A:GKS401 3.1 57.4 0.8
O2A A:GKS401 3.2 53.6 0.8
CG A:ASP192 3.2 26.6 0.5
O1B A:GKS401 3.2 48.1 0.8
CA A:CA407 3.2 64.5 0.8
CG A:ASP190 3.3 30.8 1.0
OD1 A:ASP192 3.4 33.0 0.5
O A:HOH537 3.4 44.0 1.0
OD2 A:ASP190 3.5 34.8 1.0
O2G A:GKS401 3.8 42.6 0.8
O A:HOH564 3.8 41.6 1.0
O3A A:GKS401 3.9 53.8 0.8
PB A:GKS401 4.2 55.3 0.8
O A:HOH597 4.3 36.8 1.0
O5' A:GKS401 4.4 53.1 0.8
O A:HOH689 4.5 45.8 1.0
CB A:ASP192 4.6 28.0 0.5
CB A:ASP192 4.7 28.1 0.5
O A:ASP190 4.7 23.1 1.0
CA A:GLY179 4.7 30.1 1.0
PG A:GKS401 4.8 59.2 0.8
CB A:ASP190 4.8 20.5 1.0
O3B A:GKS401 4.8 59.3 0.8
OD1 A:ASP192 4.9 33.0 0.5
C A:ASP190 4.9 22.9 1.0

Calcium binding site 2 out of 3 in 6mr8

Go back to Calcium Binding Sites List in 6mr8
Calcium binding site 2 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:64.5
occ:0.85
 O3A A:GKS401 2.6 53.8 0.8
O1G A:GKS401 2.7 57.7 0.8
O A:HOH537 2.7 44.0 1.0
O2A A:GKS401 2.7 53.6 0.8
O A:HOH689 2.8 45.8 1.0
PA A:GKS401 2.9 57.4 0.8
O3B A:GKS401 3.1 59.3 0.8
O P:HOH235 3.1 42.7 0.5
O A:HOH703 3.1 30.0 1.0
PG A:GKS401 3.2 59.2 0.8
CA A:CA406 3.2 45.1 0.8
PB A:GKS401 3.3 55.3 0.8
O2G A:GKS401 3.4 42.6 0.8
O1A A:GKS401 3.5 50.9 0.8
O1B A:GKS401 3.6 48.1 0.8
O A:HOH501 3.6 30.0 1.0
O P:HOH235 4.0 37.3 0.5
N2 A:GKS401 4.2 57.0 0.8
O A:HOH512 4.2 34.5 1.0
OD2 A:ASP190 4.4 34.8 1.0
O5' A:GKS401 4.5 53.1 0.8
OD1 A:ASP190 4.6 28.3 1.0
O2B A:GKS401 4.6 48.3 0.8
O3G A:GKS401 4.7 50.4 0.8
CG A:ASP190 4.8 30.8 1.0
O A:HOH662 4.9 33.6 1.0

Calcium binding site 3 out of 3 in 6mr8

Go back to Calcium Binding Sites List in 6mr8
Calcium binding site 3 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:25.0
occ:1.00
 O A:HOH666 2.3 23.7 1.0
O A:HOH717 2.4 25.7 1.0
OD1 A:ASP145 2.5 19.1 1.0
O A:HOH677 2.5 28.7 1.0
OD2 A:ASP145 2.6 21.0 1.0
O A:HOH550 2.7 25.3 1.0
CG A:ASP145 2.9 22.7 1.0
O A:HOH720 3.3 32.2 1.0
O A:HOH718 3.6 32.0 1.0
O A:HOH613 4.3 22.7 1.0
O A:HOH639 4.3 19.1 1.0
O A:HOH524 4.4 39.2 1.0
CB A:ASP145 4.4 19.4 1.0
ND1 A:HIS252 4.4 24.0 1.0
OE1 A:GLU249 4.5 36.7 1.0
CA A:PRO251 4.5 24.4 1.0
O A:HOH634 4.6 32.8 1.0
O A:HOH746 4.8 43.2 1.0
N A:HIS252 4.9 23.2 1.0
O A:TYR250 4.9 26.6 1.0
CE1 A:HIS252 5.0 29.6 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 16:09:28 2025

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