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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: Wed Jul 9 01:36:39 2025

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