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Calcium in PDB 2wtf: Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link

Enzymatic activity of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link

All present enzymatic activity of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link, PDB code: 2wtf was solved by T.Reissner, S.Schneider, O.Ziv, S.Schorr, Z.Livneh, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 2.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.240, 103.240, 292.740, 90.00, 90.00, 90.00
R / Rfree (%) 22.712 / 26.871

Other elements in 2wtf:

The structure of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link also contains other interesting chemical elements:

Platinum (Pt) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link (pdb code 2wtf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link, PDB code: 2wtf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 2wtf

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Calcium binding site 1 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1511

b:24.1
occ:1.00
OD1 A:ASP30 2.1 35.4 1.0
O1G A:DTP1510 2.2 25.6 1.0
O1A A:DTP1510 2.3 23.4 1.0
O A:MET31 2.3 23.7 1.0
O1B A:DTP1510 2.3 20.7 1.0
OD1 A:ASP155 2.4 25.7 1.0
OD2 A:ASP30 2.8 34.2 1.0
CG A:ASP30 2.8 27.9 1.0
CG A:ASP155 3.4 27.7 1.0
PB A:DTP1510 3.4 22.1 1.0
CA A:CA1512 3.4 57.5 1.0
C A:MET31 3.5 23.7 1.0
PG A:DTP1510 3.5 24.1 1.0
PA A:DTP1510 3.6 19.9 1.0
OD2 A:ASP155 3.8 28.8 1.0
O3A A:DTP1510 3.8 22.2 1.0
O3B A:DTP1510 3.8 22.0 1.0
N A:MET31 4.0 24.5 1.0
O2G A:DTP1510 4.0 24.6 1.0
C5' A:DTP1510 4.3 22.9 1.0
CB A:ASP30 4.3 24.9 1.0
CA A:MET31 4.3 24.6 1.0
C A:ASP30 4.4 24.4 1.0
N A:ASN32 4.4 22.8 1.0
N A:ALA33 4.4 21.9 1.0
O5' A:DTP1510 4.5 23.1 1.0
CA A:ASN32 4.5 22.3 1.0
CB A:ASP155 4.7 27.8 1.0
C A:ASN32 4.7 21.6 1.0
N A:PHE34 4.7 22.2 1.0
CB A:MET31 4.7 25.5 1.0
O3G A:DTP1510 4.7 28.7 1.0
O2B A:DTP1510 4.8 24.9 1.0
CB A:PHE34 4.8 22.2 1.0
O2A A:DTP1510 4.8 25.6 1.0
CA A:ASP30 4.8 24.2 1.0
O A:ASP155 4.9 26.5 1.0
OE1 A:GLU156 4.9 45.1 1.0
O A:ASP30 5.0 25.0 1.0

Calcium binding site 2 out of 10 in 2wtf

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Calcium binding site 2 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1512

b:57.5
occ:1.00
OE1 A:GLU156 2.0 45.1 1.0
O1A A:DTP1510 2.3 23.4 1.0
OD2 A:ASP30 2.7 34.2 1.0
OD2 A:ASP155 2.7 28.8 1.0
CD A:GLU156 3.0 38.0 1.0
PA A:DTP1510 3.3 19.9 1.0
CA A:CA1511 3.4 24.1 1.0
CG A:GLU156 3.5 33.5 1.0
CG A:ASP155 3.5 27.7 1.0
OD1 A:ASP155 3.6 25.7 1.0
O2A A:DTP1510 3.7 25.6 1.0
CG A:ASP30 3.8 27.9 1.0
O5' A:DTP1510 3.9 23.1 1.0
C5' A:DTP1510 4.1 22.9 1.0
OE2 A:GLU156 4.1 38.7 1.0
OD1 A:ASP30 4.3 35.4 1.0
OG A:SER153 4.3 31.3 1.0
O1G A:DTP1510 4.5 25.6 1.0
O3A A:DTP1510 4.7 22.2 1.0
CB A:GLU156 4.8 28.9 1.0
OP1 P:DC9 4.9 52.5 1.0
O1B A:DTP1510 4.9 20.7 1.0
CB A:ASP30 5.0 24.9 1.0

Calcium binding site 3 out of 10 in 2wtf

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Calcium binding site 3 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1513

b:88.6
occ:1.00
OD2 A:ASP321 2.8 79.5 1.0
OD1 A:ASP318 2.9 85.9 1.0
O A:ASP318 2.9 84.5 1.0
C A:ASP318 3.9 83.9 1.0
CG A:ASP321 3.9 80.4 1.0
CG A:ASP318 4.1 85.0 1.0
CA A:ASP318 4.3 84.3 1.0
CB A:ASP321 4.5 80.5 1.0
CA A:ASP321 4.5 80.6 1.0
N A:ASP321 4.7 80.7 1.0
CB A:ASP318 4.8 84.3 1.0
OD1 A:ASP321 4.9 79.3 1.0
N A:VAL319 5.0 83.2 1.0

Calcium binding site 4 out of 10 in 2wtf

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Calcium binding site 4 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1514

b:74.1
occ:1.00
O A:HOH2033 2.3 34.3 1.0
OD1 A:ASP289 2.9 35.0 1.0
OD2 A:ASP289 3.0 33.6 1.0
CG A:ASP289 3.3 38.3 1.0
OD2 A:ASP234 4.0 33.8 1.0
OG1 A:THR231 4.2 41.8 1.0
OD1 A:ASP234 4.4 34.0 1.0
CB A:ASP232 4.5 40.8 1.0
CG A:ASP234 4.6 34.4 1.0
CB A:ASP289 4.7 39.8 1.0
CD A:LYS3 4.8 55.8 1.0

Calcium binding site 5 out of 10 in 2wtf

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Calcium binding site 5 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1509

b:41.7
occ:1.00
OE1 B:GLU156 2.4 27.4 1.0
O1A B:DTP1511 2.5 27.1 1.0
O B:HOH2020 2.5 32.5 1.0
OD2 B:ASP155 2.6 24.5 1.0
OD2 B:ASP30 2.6 26.6 1.0
CD B:GLU156 3.2 25.1 1.0
OD1 B:ASP155 3.2 24.0 1.0
CG B:ASP155 3.3 21.5 1.0
CG B:GLU156 3.3 25.2 1.0
PA B:DTP1511 3.5 24.6 1.0
CA B:CA1510 3.5 24.3 1.0
CG B:ASP30 3.8 24.0 1.0
O2A B:DTP1511 3.8 25.0 1.0
O5' B:DTP1511 4.0 21.8 1.0
C5' B:DTP1511 4.2 25.7 1.0
OD1 B:ASP30 4.2 28.3 1.0
OG B:SER153 4.2 27.7 1.0
OE2 B:GLU156 4.4 27.7 1.0
CB B:ASP155 4.7 20.5 1.0
O2G B:DTP1511 4.7 22.3 1.0
CB B:GLU156 4.8 22.9 1.0
O3A B:DTP1511 4.9 25.4 1.0
O1B B:DTP1511 4.9 24.3 1.0
C B:ASP155 4.9 20.1 1.0
CB B:ASP30 5.0 22.6 1.0

Calcium binding site 6 out of 10 in 2wtf

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Calcium binding site 6 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1510

b:24.3
occ:1.00
O1A B:DTP1511 2.2 27.1 1.0
O B:MET31 2.3 20.7 1.0
O1B B:DTP1511 2.3 24.3 1.0
OD1 B:ASP30 2.3 28.3 1.0
O2G B:DTP1511 2.4 22.3 1.0
OD1 B:ASP155 2.4 24.0 1.0
CG B:ASP30 3.0 24.0 1.0
OD2 B:ASP30 3.0 26.6 1.0
PB B:DTP1511 3.4 25.4 1.0
C B:MET31 3.4 21.3 1.0
CA B:CA1509 3.5 41.7 1.0
PG B:DTP1511 3.5 26.4 1.0
CG B:ASP155 3.5 21.5 1.0
PA B:DTP1511 3.5 24.6 1.0
O3A B:DTP1511 3.7 25.4 1.0
O B:HOH2001 3.7 30.3 1.0
O3B B:DTP1511 3.8 23.4 1.0
N B:MET31 4.0 22.7 1.0
O3G B:DTP1511 4.1 21.5 1.0
OD2 B:ASP155 4.1 24.5 1.0
C5' B:DTP1511 4.2 25.7 1.0
CA B:MET31 4.2 22.8 1.0
N B:ASN32 4.4 20.3 1.0
N B:ALA33 4.4 21.0 1.0
O5' B:DTP1511 4.4 21.8 1.0
CB B:ASP30 4.5 22.6 1.0
CA B:ASN32 4.5 20.1 1.0
C B:ASP30 4.6 22.2 1.0
O2A B:DTP1511 4.6 25.0 1.0
CB B:ASP155 4.7 20.5 1.0
C B:ASN32 4.7 21.0 1.0
O2B B:DTP1511 4.7 25.0 1.0
CB B:MET31 4.8 23.9 1.0
N B:PHE34 4.8 21.7 1.0
O1G B:DTP1511 4.9 28.4 1.0
CB B:PHE34 4.9 20.3 1.0
CA B:ASP30 5.0 21.8 1.0

Calcium binding site 7 out of 10 in 2wtf

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Calcium binding site 7 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1512

b:59.7
occ:0.77
OE2 B:GLU417 2.5 43.4 1.0
O B:GLY98 2.6 40.0 1.0
OE1 B:GLU417 3.0 47.6 1.0
CD B:GLU417 3.2 41.4 1.0
C B:GLY98 3.5 39.1 1.0
CA B:GLY98 3.8 38.5 1.0
N B:GLU99 4.6 39.1 1.0
CG B:GLU417 4.7 33.8 1.0
OG B:SER414 4.8 29.4 1.0

Calcium binding site 8 out of 10 in 2wtf

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Calcium binding site 8 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1513

b:64.3
occ:1.00
OD2 B:ASP289 2.7 29.0 1.0
OD1 B:ASP289 2.9 23.9 1.0
CG B:ASP289 3.2 23.7 1.0
OG1 B:THR231 3.9 25.6 1.0
O B:HOH2042 4.3 22.9 1.0
CB B:ASP232 4.3 23.5 1.0
OD2 B:ASP234 4.5 16.9 1.0
OD1 B:ASP234 4.6 22.0 1.0
CB B:ASP289 4.7 22.6 1.0
CD B:LYS3 4.7 42.3 1.0
OD2 B:ASP232 4.9 27.1 1.0
CG B:ASP234 5.0 18.3 1.0

Calcium binding site 9 out of 10 in 2wtf

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Calcium binding site 9 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1514

b:67.1
occ:0.91
O B:ASP318 2.4 51.4 1.0
OD2 B:ASP321 2.5 55.2 1.0
C B:ASP318 3.5 50.6 1.0
CG B:ASP321 3.5 52.7 1.0
OD1 B:ASP318 3.9 59.1 1.0
CG B:ASP318 4.0 55.0 1.0
OD2 B:ASP318 4.0 57.0 1.0
CA B:ASP318 4.2 51.1 1.0
CA B:ASP321 4.3 49.5 1.0
N B:ASP321 4.3 49.2 1.0
OD1 B:ASP321 4.3 58.8 1.0
CB B:ASP321 4.3 49.8 1.0
O B:VAL319 4.4 51.2 1.0
N B:VAL319 4.5 50.1 1.0
C B:VAL319 4.6 50.5 1.0
CA B:VAL319 4.6 50.0 1.0
CB B:ASP318 4.7 51.8 1.0
CE B:LYS349 4.7 64.0 1.0
OD2 B:ASP354 4.9 68.5 1.0

Calcium binding site 10 out of 10 in 2wtf

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Calcium binding site 10 out of 10 in the Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Dna Polymerase Eta in Complex with the Cis-Diammineplatinum (II) 1,3-Gtg Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1515

b:48.6
occ:1.00
O B:GLY298 2.7 30.1 1.0
OE1 B:GLU325 3.0 58.8 1.0
CD B:GLU325 3.9 54.7 1.0
OE2 B:GLU301 3.9 32.2 1.0
C B:GLY298 3.9 29.4 1.0
CG B:GLU325 4.6 48.9 1.0
OE2 B:GLU325 4.6 58.3 1.0
CA B:GLY298 4.7 27.8 1.0
N B:LYS299 4.9 30.7 1.0

Reference:

T.Reissner, S.Schneider, S.Schorr, T.Carell. Crystal Structure of A Cisplatin-(1,3-Gtg) Cross- Link Within Dna Polymerase Eta. Angew.Chem.Int.Ed.Engl. V. 49 3077 2010.
ISSN: ISSN 1433-7851
PubMed: 20333640
DOI: 10.1002/ANIE.201000414
Page generated: Wed Oct 28 08:00:02 2020

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