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Platinum in PDB 3rek: 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin

Protein crystallography data

The structure of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin, PDB code: 3rek was solved by B.Wu, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.001, 109.436, 176.357, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 28.1

Other elements in 3rek:

The structure of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Platinum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Platinum atom in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin (pdb code 3rek). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 40 binding sites of Platinum where determined in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin, PDB code: 3rek:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 40 in 3rek

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Platinum binding site 1 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt74

b:0.3
occ:1.00
N7 I:DA-72 0.3 0.7 1.0
C5 I:DA-72 1.4 0.5 1.0
C8 I:DA-72 1.6 0.8 1.0
C4 I:DA-72 2.4 0.9 1.0
C6 I:DA-72 2.5 0.9 1.0
N9 I:DA-72 2.5 0.4 1.0
N6 I:DA-72 3.0 0.1 1.0
N1 I:DA-72 3.6 0.0 1.0
N3 I:DA-72 3.7 0.8 1.0
C1' I:DA-72 4.0 0.8 1.0
C2 I:DA-72 4.1 0.8 1.0
O4' I:DA-72 4.5 0.7 1.0
O4 I:DT-71 4.7 0.7 1.0
C2' I:DA-72 4.8 0.1 1.0
C4 I:DT-71 5.0 0.6 1.0

Platinum binding site 2 out of 40 in 3rek

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Platinum binding site 2 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt73

b:0.7
occ:0.68
N7 J:DG-3 1.7 89.7 1.0
C5 J:DG-3 2.6 90.0 1.0
C8 J:DG-3 2.9 90.2 1.0
O6 J:DG-3 2.9 90.3 1.0
C6 J:DG-3 3.1 90.2 1.0
N6 J:DA-2 3.8 93.9 1.0
C4 J:DG-3 3.9 89.9 1.0
N9 J:DG-3 4.0 89.7 1.0
C2' J:DT-4 4.1 85.9 1.0
C6 J:DT-4 4.5 88.1 1.0
N1 J:DG-3 4.5 90.0 1.0
OP2 J:DG-3 4.7 81.1 1.0
C6 J:DA-2 4.7 93.6 1.0
N7 J:DA-2 4.8 92.9 1.0
C5 J:DT-4 4.8 88.7 1.0
N1 J:DT-4 4.8 87.5 1.0

Platinum binding site 3 out of 40 in 3rek

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Platinum binding site 3 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt74

b:0.6
occ:0.79
N7 J:DA-73 1.4 0.4 1.0
C8 J:DA-73 2.5 0.1 1.0
C5 J:DA-73 2.6 0.1 1.0
N6 J:DA-73 3.2 0.4 1.0
C6 J:DA-73 3.3 0.3 1.0
N9 J:DA-73 3.6 0.3 1.0
C4 J:DA-73 3.7 0.3 1.0
N1 J:DA-73 4.6 0.3 1.0
N3 J:DA-73 5.0 0.4 1.0
C1' J:DA-73 5.0 0.5 1.0

Platinum binding site 4 out of 40 in 3rek

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Platinum binding site 4 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt75

b:0.1
occ:0.54
N7 J:DG-46 2.5 0.1 1.0
O6 J:DG-46 3.2 0.4 1.0
C5 J:DG-46 3.4 0.5 1.0
C8 J:DG-46 3.6 0.5 1.0
C6 J:DG-46 3.7 0.3 1.0
C8 J:DA-47 3.9 0.5 1.0
N7 J:DA-47 4.1 0.4 1.0
C4 J:DG-46 4.7 0.5 1.0
N6 J:DA-45 4.7 92.8 1.0
N9 J:DG-46 4.8 0.4 1.0
N9 J:DA-47 4.8 0.6 1.0
C2' J:DA-47 4.9 0.0 1.0
C5 J:DA-47 5.0 0.6 1.0

Platinum binding site 5 out of 40 in 3rek

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Platinum binding site 5 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt76

b:0.4
occ:0.41
N7 J:DG7 2.0 73.2 1.0
C5 J:DG7 3.0 72.8 1.0
C8 J:DG7 3.1 73.1 1.0
O6 J:DG7 3.3 72.9 1.0
C6 J:DG7 3.5 72.7 1.0
C2' J:DT6 4.1 79.7 1.0
C4 J:DG7 4.2 72.6 1.0
C6 J:DT6 4.3 82.5 1.0
N9 J:DG7 4.3 72.7 1.0
N6 J:DA8 4.7 67.9 1.0
C5 J:DT6 4.7 82.3 1.0
N1 J:DT6 4.8 81.5 1.0
C7 J:DT6 4.8 82.0 1.0
N1 J:DG7 4.9 72.8 1.0
C1' J:DT6 4.9 81.3 1.0

Platinum binding site 6 out of 40 in 3rek

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Platinum binding site 6 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt75

b:0.6
occ:0.57
N7 I:DG71 2.2 90.4 1.0
C8 I:DG71 3.2 90.3 1.0
C5 I:DG71 3.2 90.6 1.0
O6 I:DG71 3.5 90.4 1.0
C6 I:DG71 3.7 90.5 1.0
N6 I:DA72 4.0 94.5 1.0
N7 I:DA70 4.1 88.0 1.0
C8 I:DA70 4.2 87.9 1.0
N9 I:DG71 4.4 90.5 1.0
C4 I:DG71 4.4 90.7 1.0
C5 I:DA70 4.8 88.2 1.0
C6 I:DA72 4.8 94.6 1.0
N9 I:DA70 4.9 87.9 1.0

Platinum binding site 7 out of 40 in 3rek

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Platinum binding site 7 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt103

b:0.8
occ:0.56
OH B:TYR88 2.9 54.4 1.0
CG B:MET84 3.2 50.6 1.0
CE B:MET84 3.3 58.1 1.0
SD B:MET84 3.6 59.3 1.0
PT B:PT104 3.8 0.8 0.3
CZ B:TYR88 4.0 53.0 1.0
CB B:MET84 4.1 47.3 1.0
CE1 B:TYR88 4.7 53.4 1.0
CE2 B:TYR88 4.9 53.3 1.0
N B:GLY102 5.0 58.9 1.0

Platinum binding site 8 out of 40 in 3rek

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Platinum binding site 8 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt76

b:0.2
occ:0.63
N7 I:DG-53 0.6 0.5 1.0
C5 I:DG-53 1.7 0.9 1.0
C8 I:DG-53 1.8 0.0 1.0
C6 I:DG-53 2.6 1.0 1.0
C4 I:DG-53 2.8 0.9 1.0
N9 I:DG-53 2.8 0.1 1.0
O6 I:DG-53 2.9 0.0 1.0
C6 I:DC-54 3.5 0.2 1.0
C5 I:DC-54 3.8 0.0 1.0
N1 I:DG-53 3.9 0.9 1.0
C2' I:DC-54 3.9 0.3 1.0
N3 I:DG-53 4.0 0.7 1.0
N1 I:DC-54 4.1 0.3 1.0
C1' I:DG-53 4.2 0.1 1.0
O6 I:DG-52 4.2 1.0 1.0
C2 I:DG-53 4.4 0.7 1.0
C1' I:DC-54 4.5 0.2 1.0
C4 I:DC-54 4.6 0.9 1.0
OP2 I:DC-54 4.7 0.5 1.0
N7 I:DG-52 4.8 0.2 1.0
C2 I:DC-54 4.8 0.4 1.0
C2' I:DG-53 4.9 0.9 1.0
O4' I:DG-53 4.9 0.9 1.0
C6 I:DG-52 4.9 1.0 1.0

Platinum binding site 9 out of 40 in 3rek

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Platinum binding site 9 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt77

b:0.5
occ:0.49
N7 I:DG-14 2.0 77.3 1.0
C5 I:DG-14 2.9 77.4 1.0
C8 I:DG-14 3.1 77.5 1.0
O6 I:DG-14 3.1 78.2 1.0
C6 I:DG-14 3.4 77.6 1.0
C8 I:DG-15 3.8 0.9 1.0
N7 I:DG-15 4.1 0.5 1.0
C4 I:DG-14 4.2 77.5 1.0
N9 I:DG-14 4.2 76.8 1.0
PT I:PT84 4.4 0.2 0.4
N9 I:DG-15 4.4 0.9 1.0
C2' I:DG-15 4.6 0.4 1.0
N6 I:DA-13 4.7 72.9 1.0
N1 I:DG-14 4.8 76.9 1.0
C5 I:DG-15 4.9 0.7 1.0
C1' I:DG-15 4.9 0.6 1.0

Platinum binding site 10 out of 40 in 3rek

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Platinum binding site 10 out of 40 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt78

b:0.5
occ:0.34
N7 I:DA-46 2.8 0.6 1.0
C8 I:DA-46 3.7 0.6 1.0
N6 I:DA-46 3.8 0.7 1.0
C5 I:DA-46 3.8 0.6 1.0
O6 I:DG-45 4.1 0.4 1.0
C6 I:DA-46 4.2 0.7 1.0
PT I:PT89 4.4 0.7 0.3
C2' I:DT-47 4.7 0.7 1.0
N9 I:DA-46 4.9 0.5 1.0
C6 I:DG-45 5.0 0.2 1.0
C4 I:DA-46 5.0 0.6 1.0

Reference:

B.Wu, G.E.Davey, A.A.Nazarov, P.J.Dyson, C.A.Davey. Specific Dna Structural Attributes Modulate Platinum Anticancer Drug Site Selection and Cross-Link Generation. Nucleic Acids Res. V. 39 8200 2011.
ISSN: ISSN 0305-1048
PubMed: 21724603
DOI: 10.1093/NAR/GKR491
Page generated: Wed Dec 16 02:04:22 2020

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