Atomistry » Calcium » PDB 4pkg-4q1l » 4ptf
Atomistry »
  Calcium »
    PDB 4pkg-4q1l »
      4ptf »

Calcium in PDB 4ptf: Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G

Enzymatic activity of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G

All present enzymatic activity of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G, PDB code: 4ptf was solved by R.Jain, K.R.Rajashankar, A.Buku, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 2.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.293, 68.478, 149.079, 90.00, 109.60, 90.00
R / Rfree (%) 18.3 / 24.7

Other elements in 4ptf:

The structure of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G (pdb code 4ptf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G, PDB code: 4ptf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4ptf

Go back to Calcium Binding Sites List in 4ptf
Calcium binding site 1 out of 4 in the Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1202

b:49.3
occ:1.00
 O3G A:DCP1201 2.1 33.3 1.0
O2B A:DCP1201 2.2 33.4 1.0
O1A A:DCP1201 2.2 34.1 1.0
OD1 A:ASP640 2.2 35.8 1.0
O A:VAL641 2.4 34.7 1.0
OD2 A:ASP877 2.4 34.8 1.0
PB A:DCP1201 3.1 31.9 1.0
CG A:ASP640 3.2 38.5 1.0
PA A:DCP1201 3.2 35.6 1.0
PG A:DCP1201 3.3 36.9 1.0
O3B A:DCP1201 3.4 37.0 1.0
CG A:ASP877 3.4 31.2 1.0
OD2 A:ASP640 3.4 48.6 1.0
O3A A:DCP1201 3.5 29.3 1.0
CA A:CA1203 3.6 68.2 1.0
C A:VAL641 3.6 32.0 1.0
OD1 A:ASP877 3.6 27.7 1.0
O A:HOH1309 3.8 51.0 1.0
O2G A:DCP1201 4.2 41.5 1.0
N A:VAL641 4.3 32.1 1.0
C5' A:DCP1201 4.3 27.5 1.0
O1G A:DCP1201 4.3 38.1 1.0
O2A A:DCP1201 4.3 37.2 1.0
O5' A:DCP1201 4.3 31.5 1.0
O A:HOH1310 4.4 40.5 1.0
N A:SER643 4.5 33.5 1.0
CA A:VAL641 4.5 30.0 1.0
CB A:ASP640 4.5 35.9 1.0
O1B A:DCP1201 4.5 33.0 1.0
N A:ALA642 4.5 32.4 1.0
C A:ASP640 4.5 37.3 1.0
CA A:ALA642 4.6 30.6 1.0
CB A:ASP877 4.7 29.1 1.0
N A:MET644 4.8 24.5 1.0
C A:ALA642 4.8 33.0 1.0
O A:ASP640 4.9 35.5 1.0
NZ A:LYS824 5.0 39.4 1.0
CA A:ASP640 5.0 35.4 1.0
CB A:VAL641 5.0 27.5 1.0

Calcium binding site 2 out of 4 in 4ptf

Go back to Calcium Binding Sites List in 4ptf
Calcium binding site 2 out of 4 in the Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1203

b:68.2
occ:1.00
 OD1 A:ASP877 2.4 27.7 1.0
OD2 A:ASP640 2.5 48.6 1.0
O1A A:DCP1201 2.7 34.1 1.0
CG A:ASP640 3.1 38.5 1.0
OD1 A:ASP640 3.2 35.8 1.0
O A:HOH1309 3.3 51.0 1.0
O A:HOH1308 3.3 36.4 1.0
CG A:ASP877 3.4 31.2 1.0
CA A:CA1202 3.6 49.3 1.0
C3' P:DOC12 3.7 26.7 1.0
C5' P:DOC12 3.7 29.2 1.0
OD2 A:ASP877 3.8 34.8 1.0
PA A:DCP1201 3.8 35.6 1.0
O2A A:DCP1201 4.1 37.2 1.0
C4' P:DOC12 4.1 30.2 1.0
N A:GLY878 4.2 32.5 1.0
O A:ASP875 4.3 32.7 1.0
C A:ASP877 4.4 27.3 1.0
O5' A:DCP1201 4.4 31.5 1.0
CB A:ASP640 4.4 35.9 1.0
O5' P:DOC12 4.4 22.3 1.0
CA A:GLY878 4.5 30.3 1.0
O A:ASP877 4.6 30.4 1.0
CB A:ASP877 4.7 29.1 1.0
O P:HOH104 4.8 43.3 1.0
C5' A:DCP1201 4.8 27.5 1.0
N A:ASP877 4.8 26.8 1.0
CA A:ASP877 4.9 26.5 1.0

Calcium binding site 3 out of 4 in 4ptf

Go back to Calcium Binding Sites List in 4ptf
Calcium binding site 3 out of 4 in the Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1204

b:64.3
occ:1.00
 O A:HOH1365 2.4 37.4 1.0
OD1 A:ASP290 2.4 43.9 1.0
O A:HOH1366 3.2 36.6 1.0
CG A:ASP290 3.4 42.8 1.0
OD2 A:ASP290 3.6 48.8 1.0
OD1 A:ASP383 3.8 46.1 1.0
OD2 A:ASP383 4.3 39.6 1.0
O A:ILE291 4.4 51.6 1.0
O A:PHE377 4.4 38.8 1.0
CG A:ASP383 4.5 37.7 1.0
OD2 A:ASP477 4.5 52.1 1.0
CD2 A:PHE382 4.7 34.8 1.0
CB A:ASP290 4.8 32.6 1.0

Calcium binding site 4 out of 4 in 4ptf

Go back to Calcium Binding Sites List in 4ptf
Calcium binding site 4 out of 4 in the Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca101

b:67.2
occ:1.00
 O T:HOH215 2.4 34.1 1.0
O T:HOH214 2.5 42.1 1.0
O T:HOH213 3.0 36.5 1.0
N7 T:DG9 3.4 32.1 1.0
C8 T:DG9 4.1 32.0 1.0
O6 T:DG10 4.3 39.1 1.0
C2' T:DG8 4.4 25.5 1.0
C5 T:DG9 4.5 24.5 1.0
N7 T:DG10 4.6 30.7 1.0
C8 T:DG8 4.6 26.4 1.0
O6 T:DG9 4.7 27.2 1.0
N9 T:DG8 4.9 27.7 1.0
N7 T:DG8 4.9 28.1 1.0
C6 T:DG9 5.0 26.6 1.0

Reference:

R.Jain, K.R.Rajashankar, A.Buku, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Crystal Structure of Yeast Dna Polymerase Epsilon Catalytic Domain. Plos One V. 9 94835 2014.
ISSN: ESSN 1932-6203
PubMed: 24733111
DOI: 10.1371/JOURNAL.PONE.0094835
Page generated: Sun Jul 14 12:15:00 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