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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

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