Atomistry » Calcium » PDB 2qwd-2rex » 2r8k
Atomistry »
  Calcium »
    PDB 2qwd-2rex »
      2r8k »

Calcium in PDB 2r8k: Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna

Enzymatic activity of Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna

All present enzymatic activity of Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna:
2.7.7.7;

Protein crystallography data

The structure of Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna, PDB code: 2r8k was solved by T.Carell, A.Alt, K.Lammens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.740, 103.740, 292.810, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 26.7

Other elements in 2r8k:

The structure of Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna also contains other interesting chemical elements:

Platinum (Pt) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna (pdb code 2r8k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna, PDB code: 2r8k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2r8k

Go back to Calcium Binding Sites List in 2r8k
Calcium binding site 1 out of 4 in the Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:82.3
occ:1.00
 O1A A:DTP2001 2.1 45.4 1.0
OE1 A:GLU156 2.1 51.7 1.0
OD2 A:ASP30 2.8 37.5 1.0
CD A:GLU156 3.0 47.6 1.0
OD2 A:ASP155 3.1 39.8 1.0
CG A:GLU156 3.4 42.5 1.0
PA A:DTP2001 3.5 44.8 1.0
OD1 A:ASP155 3.7 38.0 1.0
CG A:ASP155 3.8 37.9 1.0
OE2 A:GLU156 4.0 48.1 1.0
CG A:ASP30 4.0 37.4 1.0
O5' A:DTP2001 4.0 44.2 1.0
CA A:CA1002 4.1 36.3 1.0
OG A:SER153 4.2 37.9 1.0
O2A A:DTP2001 4.5 47.2 1.0
O3A A:DTP2001 4.5 46.4 1.0
OD1 A:ASP30 4.7 38.3 1.0
OP1 Q:DC13 4.7 88.5 1.0
CB A:GLU156 4.9 34.6 1.0
OP2 Q:DC13 4.9 88.8 1.0

Calcium binding site 2 out of 4 in 2r8k

Go back to Calcium Binding Sites List in 2r8k
Calcium binding site 2 out of 4 in the Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:36.3
occ:1.00
 OD1 A:ASP30 2.2 38.3 1.0
O1G A:DTP2001 2.2 48.4 1.0
OD1 A:ASP155 2.2 38.0 1.0
O A:MET31 2.4 33.7 1.0
O1B A:DTP2001 2.7 46.5 1.0
CG A:ASP30 2.9 37.4 1.0
OD2 A:ASP30 3.0 37.5 1.0
O3A A:DTP2001 3.1 46.4 1.0
O1A A:DTP2001 3.3 45.4 1.0
PB A:DTP2001 3.4 47.2 1.0
CG A:ASP155 3.4 37.9 1.0
PG A:DTP2001 3.5 48.9 1.0
O5' A:DTP2001 3.5 44.2 1.0
PA A:DTP2001 3.5 44.8 1.0
C A:MET31 3.5 32.5 1.0
O3B A:DTP2001 3.8 48.0 1.0
N A:MET31 4.1 34.1 1.0
OD2 A:ASP155 4.1 39.8 1.0
CA A:CA1001 4.1 82.3 1.0
O3G A:DTP2001 4.1 50.5 1.0
C5' A:DTP2001 4.3 42.9 1.0
CB A:ASP30 4.4 36.1 1.0
CA A:MET31 4.4 32.6 1.0
CB A:ASP155 4.4 34.6 1.0
N A:ASN32 4.5 31.4 1.0
CA A:ASN32 4.6 29.4 1.0
C A:ASP30 4.6 35.4 1.0
N A:ALA33 4.7 26.3 1.0
O2G A:DTP2001 4.7 49.1 1.0
O2B A:DTP2001 4.8 47.0 1.0
C A:ASN32 4.8 27.6 1.0
CA A:ASP30 5.0 35.4 1.0
N A:PHE34 5.0 27.4 1.0
O2A A:DTP2001 5.0 47.2 1.0

Calcium binding site 3 out of 4 in 2r8k

Go back to Calcium Binding Sites List in 2r8k
Calcium binding site 3 out of 4 in the Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3001

b:52.2
occ:1.00
 O1A B:DTP4001 2.1 44.7 1.0
OE1 B:GLU156 2.2 36.1 1.0
OD2 B:ASP30 2.5 34.9 1.0
OD2 B:ASP155 2.7 29.8 1.0
CD B:GLU156 3.0 33.5 1.0
OD1 B:ASP155 3.3 27.5 1.0
CG B:GLU156 3.3 31.2 1.0
CG B:ASP155 3.4 28.2 1.0
PA B:DTP4001 3.5 42.5 1.0
CG B:ASP30 3.7 34.1 1.0
O5' B:DTP4001 3.9 42.2 1.0
CA B:CA3002 3.9 33.8 1.0
OG B:SER153 4.1 32.3 1.0
OE2 B:GLU156 4.1 34.4 1.0
O3A B:DTP4001 4.2 40.0 1.0
OD1 B:ASP30 4.4 35.1 1.0
CB B:GLU156 4.7 27.2 1.0
O2A B:DTP4001 4.7 41.2 1.0
CB B:ASP30 4.8 30.2 1.0
CB B:ASP155 4.9 27.9 1.0

Calcium binding site 4 out of 4 in 2r8k

Go back to Calcium Binding Sites List in 2r8k
Calcium binding site 4 out of 4 in the Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Eukaryotic Dna Polymerase Eta in Complex with 1,2- D(Gpg)-Cisplatin Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3002

b:33.8
occ:1.00
 O3A B:DTP4001 2.3 40.0 1.0
OD1 B:ASP30 2.3 35.1 1.0
OD1 B:ASP155 2.3 27.5 1.0
O B:MET31 2.5 29.7 1.0
O3B B:DTP4001 2.8 40.6 1.0
O3G B:DTP4001 2.9 42.8 1.0
CG B:ASP30 3.0 34.1 1.0
OD2 B:ASP30 3.0 34.9 1.0
PB B:DTP4001 3.2 40.0 1.0
PA B:DTP4001 3.3 42.5 1.0
O1A B:DTP4001 3.4 44.7 1.0
PG B:DTP4001 3.5 41.8 1.0
CG B:ASP155 3.5 28.2 1.0
C B:MET31 3.7 29.2 1.0
O5' B:DTP4001 3.7 42.2 1.0
O1B B:DTP4001 3.9 40.5 1.0
CA B:CA3001 3.9 52.2 1.0
OD2 B:ASP155 4.2 29.8 1.0
O1G B:DTP4001 4.2 41.2 1.0
N B:MET31 4.3 28.9 1.0
C5' B:DTP4001 4.4 40.8 1.0
O2B B:DTP4001 4.4 43.7 1.0
CB B:ASP30 4.5 30.2 1.0
N B:ASN32 4.6 29.1 1.0
CA B:MET31 4.6 28.5 1.0
CA B:ASN32 4.6 28.6 1.0
O2G B:DTP4001 4.6 42.7 1.0
CB B:ASP155 4.6 27.9 1.0
O2A B:DTP4001 4.6 41.2 1.0
N B:ALA33 4.7 28.4 1.0
C B:ASN32 4.8 28.0 1.0
C B:ASP30 4.9 28.5 1.0
N B:PHE34 4.9 28.2 1.0

Reference:

A.Alt, K.Lammens, C.Chiocchini, A.Lammens, J.C.Pieck, D.Kuch, K.P.Hopfner, T.Carell. Bypass of Dna Lesions Generated During Anticancer Treatment with Cisplatin By Dna Polymerase Eta Science V. 318 967 2007.
ISSN: ISSN 0036-8075
PubMed: 17991862
DOI: 10.1126/SCIENCE.1148242
Page generated: Fri Jul 12 15:47:39 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy