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Calcium in PDB 2r8j: 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: 2r8j 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) 20.00 / 3.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.090, 104.090, 293.050, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.7

Other elements in 2r8j:

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 2r8j). 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: 2r8j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2r8j

Go back to Calcium Binding Sites List in 2r8j
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:Ca1501

b:91.4
occ:1.00
 OE1 A:GLU156 2.6 39.6 1.0
O A:HOH2004 2.7 61.3 1.0
OD2 A:ASP30 2.7 31.5 1.0
O1A A:DCP2001 3.1 35.0 1.0
OP1 Q:DG13 3.4 53.6 1.0
O1G A:DCP2001 3.7 40.4 1.0
CD A:GLU156 3.8 37.4 1.0
CG A:ASP30 3.9 31.1 1.0
O2A A:DCP2001 4.0 33.7 1.0
PA A:DCP2001 4.2 34.0 1.0
NZ A:LYS272 4.2 47.8 1.0
ND2 A:ASN276 4.3 44.6 1.0
OD1 A:ASP30 4.5 32.1 1.0
CA A:CA1502 4.6 21.2 1.0
OE2 A:GLU156 4.6 37.7 1.0
P Q:DG13 4.6 51.5 1.0
CG A:GLU156 4.7 33.2 1.0
CB A:ASP30 4.9 27.7 1.0

Calcium binding site 2 out of 4 in 2r8j

Go back to Calcium Binding Sites List in 2r8j
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:Ca1502

b:21.2
occ:1.00
 OD1 A:ASP30 2.1 32.1 1.0
OD1 A:ASP155 2.3 29.2 1.0
O1A A:DCP2001 2.3 35.0 1.0
O A:MET31 2.5 20.3 1.0
O2B A:DCP2001 2.7 35.2 1.0
O3G A:DCP2001 2.7 38.2 1.0
CG A:ASP30 3.0 31.1 1.0
OD2 A:ASP30 3.2 31.5 1.0
CG A:ASP155 3.2 28.6 1.0
O1G A:DCP2001 3.4 40.4 1.0
PA A:DCP2001 3.4 34.0 1.0
PB A:DCP2001 3.5 35.3 1.0
PG A:DCP2001 3.5 35.4 1.0
OD2 A:ASP155 3.6 29.5 1.0
C A:MET31 3.7 22.4 1.0
C5' A:DCP2001 3.8 34.4 1.0
O3A A:DCP2001 3.8 34.8 1.0
O3B A:DCP2001 3.9 36.0 1.0
O5' A:DCP2001 4.0 33.6 1.0
N A:MET31 4.2 25.3 1.0
C A:ASP30 4.4 27.4 1.0
CB A:ASP30 4.4 27.7 1.0
CA A:MET31 4.5 24.0 1.0
CB A:ASP155 4.5 25.8 1.0
CA A:CA1501 4.6 91.4 1.0
N A:ALA33 4.6 18.4 1.0
N A:ASN32 4.6 21.3 1.0
O A:ASP30 4.7 31.1 1.0
O A:ASP155 4.7 27.8 1.0
CA A:ASN32 4.7 21.2 1.0
N A:PHE34 4.8 16.3 1.0
O2A A:DCP2001 4.8 33.7 1.0
CA A:ASP30 4.8 26.9 1.0
CB A:MET31 4.9 25.2 1.0
C A:ASN32 4.9 20.1 1.0
O1B A:DCP2001 4.9 39.1 1.0
CB A:PHE34 5.0 16.8 1.0
O2G A:DCP2001 5.0 37.9 1.0

Calcium binding site 3 out of 4 in 2r8j

Go back to Calcium Binding Sites List in 2r8j
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:Ca1701

b:39.4
occ:1.00
 OE1 B:GLU156 2.5 28.1 1.0
O1A B:DCP3001 2.6 41.2 1.0
OD2 B:ASP155 2.7 26.2 1.0
OD2 B:ASP30 2.8 28.8 1.0
OD1 B:ASP155 2.8 28.7 1.0
CG B:ASP155 3.1 26.2 1.0
CD B:GLU156 3.3 24.8 1.0
CA B:CA1702 3.4 21.3 1.0
CG B:GLU156 3.4 22.3 1.0
O5' B:DCP3001 3.5 38.8 1.0
PA B:DCP3001 3.6 39.1 1.0
CG B:ASP30 3.9 29.8 1.0
O2A B:DCP3001 4.2 40.9 1.0
C5' B:DCP3001 4.3 42.7 1.0
OE2 B:GLU156 4.4 25.8 1.0
OG B:SER153 4.5 21.8 1.0
OD1 B:ASP30 4.5 32.7 1.0
CB B:ASP155 4.6 22.5 1.0
CB B:GLU156 4.9 18.5 1.0
O1G B:DCP3001 4.9 33.3 1.0

Calcium binding site 4 out of 4 in 2r8j

Go back to Calcium Binding Sites List in 2r8j
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:Ca1702

b:21.3
occ:1.00
 OD1 B:ASP155 2.2 28.7 1.0
OD1 B:ASP30 2.4 32.7 1.0
O1A B:DCP3001 2.4 41.2 1.0
O2B B:DCP3001 2.4 34.2 1.0
O1G B:DCP3001 2.5 33.3 1.0
O B:MET31 2.6 20.3 1.0
OD2 B:ASP30 2.9 28.8 1.0
CG B:ASP30 3.0 29.8 1.0
PB B:DCP3001 3.3 33.4 1.0
CG B:ASP155 3.4 26.2 1.0
CA B:CA1701 3.4 39.4 1.0
PA B:DCP3001 3.4 39.1 1.0
PG B:DCP3001 3.6 32.7 1.0
O3A B:DCP3001 3.7 37.7 1.0
O3B B:DCP3001 3.8 32.7 1.0
C B:MET31 3.8 21.5 1.0
O5' B:DCP3001 3.9 38.8 1.0
C5' B:DCP3001 3.9 42.7 1.0
O3G B:DCP3001 4.1 33.7 1.0
OD2 B:ASP155 4.2 26.2 1.0
N B:MET31 4.2 20.7 1.0
CB B:ASP155 4.3 22.5 1.0
CB B:ASP30 4.5 25.4 1.0
CA B:MET31 4.6 21.0 1.0
C B:ASP30 4.7 21.5 1.0
O1B B:DCP3001 4.7 34.6 1.0
N B:ASN32 4.8 21.1 1.0
N B:ALA33 4.8 21.6 1.0
O2A B:DCP3001 4.8 40.9 1.0
CA B:ASN32 4.9 21.4 1.0
CB B:MET31 5.0 21.8 1.0
O2G B:DCP3001 5.0 35.2 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 15:47:11 2024

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