Atomistry » Calcium » PDB 6m4m-6mr8 » 6mr8
Atomistry »
  Calcium »
    PDB 6m4m-6mr8 »
      6mr8 »

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: Tue Jul 16 11:25:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy