Atomistry » Platinum » PDB 3co3-3wu9 » 3rei
Atomistry »
  Platinum »
    PDB 3co3-3wu9 »
      3rei »

Platinum in PDB 3rei: 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride

Protein crystallography data

The structure of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride, PDB code: 3rei 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) 58.00 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.877, 109.904, 181.701, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 27.6

Other elements in 3rei:

The structure of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride 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; Page 5, Binding sites: 41 - 49;

Binding sites:

The binding sites of Platinum atom in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride (pdb code 3rei). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 49 binding sites of Platinum where determined in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride, PDB code: 3rei:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 1 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt73

b:89.8
occ:1.00
N7 I:DG60 2.0 0.4 1.0
O6 I:DG60 2.3 0.5 1.0
C5 I:DG60 2.5 0.1 1.0
C6 I:DG60 2.6 0.2 1.0
C8 I:DG60 3.2 0.0 1.0
O6 I:DG61 3.8 0.9 1.0
C4 I:DG60 3.8 0.3 1.0
N1 I:DG60 4.0 0.8 1.0
N7 I:DA59 4.1 0.2 1.0
N9 I:DG60 4.2 0.3 1.0
C8 I:DA59 4.2 0.1 1.0
C6 I:DG61 4.8 0.8 1.0
N4 J:DC-61 4.9 0.1 1.0
N7 I:DG61 4.9 0.8 1.0
N3 I:DG60 5.0 0.3 1.0
C2 I:DG60 5.0 0.9 1.0
C5 I:DA59 5.0 0.5 1.0

Platinum binding site 2 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 2 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt73

b:95.2
occ:0.89
O6 J:DG60 1.9 0.9 1.0
N7 J:DG60 2.1 0.7 1.0
C6 J:DG60 2.3 0.0 1.0
C5 J:DG60 2.4 0.8 1.0
C8 J:DG60 3.4 0.9 1.0
O6 J:DG61 3.6 0.9 1.0
N1 J:DG60 3.7 0.6 1.0
C4 J:DG60 3.8 0.5 1.0
N7 J:DA59 3.9 0.5 1.0
C8 J:DA59 4.1 0.6 1.0
N9 J:DG60 4.3 0.8 1.0
C2 J:DG60 4.7 0.8 1.0
C6 J:DG61 4.7 0.8 1.0
C5 J:DA59 4.7 0.4 1.0
N3 J:DG60 4.8 0.6 1.0
N4 I:DC-61 4.9 0.7 1.0

Platinum binding site 3 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 3 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt74

b:77.1
occ:0.70
N7 I:DG7 2.1 77.6 1.0
C8 I:DG7 3.0 75.6 1.0
C5 I:DG7 3.1 76.9 1.0
O6 I:DG7 3.5 75.6 1.0
C6 I:DG7 3.7 75.9 1.0
C2' I:DT6 4.1 82.6 1.0
C6 I:DT6 4.2 87.2 1.0
N9 I:DG7 4.2 74.2 1.0
C4 I:DG7 4.3 75.2 1.0
C7 I:DT6 4.6 86.3 1.0
C5 I:DT6 4.6 87.2 1.0
N6 I:DA8 4.6 68.1 1.0
N1 I:DT6 4.8 86.9 1.0
O4 J:DT-8 4.9 93.4 1.0
C1' I:DT6 4.9 85.0 1.0

Platinum binding site 4 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 4 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt74

b:85.0
occ:0.60
N7 J:DG7 2.0 85.2 1.0
C8 J:DG7 2.9 84.6 1.0
C5 J:DG7 3.2 85.2 1.0
O6 J:DG7 3.7 84.8 1.0
C6 J:DG7 3.8 84.7 1.0
C2' J:DT6 4.0 91.7 1.0
N9 J:DG7 4.1 83.8 1.0
C4 J:DG7 4.3 84.2 1.0
C6 J:DT6 4.8 96.2 1.0
C1' J:DT6 4.8 94.4 1.0
N6 J:DA8 4.9 79.8 1.0
N1 J:DT6 5.0 95.6 1.0

Platinum binding site 5 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 5 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt75

b:91.5
occ:0.75
N7 J:DG-55 1.5 0.0 1.0
C5 J:DG-55 2.5 0.5 1.0
C8 J:DG-55 2.5 0.7 1.0
O6 J:DG-55 3.1 0.6 1.0
C6 J:DG-55 3.1 0.6 1.0
N6 J:DA-54 3.6 0.1 1.0
C4 J:DG-55 3.6 0.5 1.0
N9 J:DG-55 3.7 0.5 1.0
N1 J:DG-55 4.5 0.6 1.0
C8 J:DA-56 4.5 0.3 1.0
N7 J:DA-56 4.5 0.5 1.0
C6 J:DA-54 4.5 0.1 1.0
N7 J:DA-54 4.7 0.5 1.0
N3 J:DG-55 4.9 0.6 1.0
C5 J:DA-54 5.0 0.3 1.0

Platinum binding site 6 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 6 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt76

b:0.6
occ:0.71
N7 J:DG-33 1.4 0.8 1.0
C8 J:DG-33 2.4 0.0 1.0
C5 J:DG-33 2.4 0.1 1.0
O6 J:DG-33 3.1 1.0 1.0
C6 J:DG-33 3.1 0.0 1.0
N9 J:DG-33 3.6 0.9 1.0
C4 J:DG-33 3.6 0.9 1.0
C8 J:DG-34 4.0 0.8 1.0
N7 J:DG-34 4.2 0.1 1.0
PT J:PT89 4.4 0.6 0.2
N6 J:DA-32 4.4 0.1 1.0
N1 J:DG-33 4.5 0.2 1.0
N9 J:DG-34 4.6 0.4 1.0
O4 I:DT32 4.8 0.8 1.0
C2' J:DG-34 4.8 0.6 1.0
N3 J:DG-33 4.9 0.9 1.0
C5 J:DG-34 5.0 1.0 1.0
C1' J:DG-33 5.0 0.9 1.0

Platinum binding site 7 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 7 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt77

b:0.8
occ:0.59
N7 J:DG47 2.1 0.2 1.0
C8 J:DG47 3.0 0.1 1.0
C5 J:DG47 3.2 0.4 1.0
O6 J:DG47 3.5 0.4 1.0
C6 J:DG47 3.7 0.4 1.0
PT J:PT88 4.0 0.7 0.4
C2' J:DT46 4.0 0.1 1.0
N9 J:DG47 4.2 0.0 1.0
C4 J:DG47 4.3 0.3 1.0
OP2 J:DG47 4.5 0.6 1.0
O6 J:DG48 4.5 0.1 1.0
C3' J:DT46 5.0 0.7 1.0
C1' J:DT46 5.0 0.8 1.0

Platinum binding site 8 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 8 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt75

b:0.6
occ:0.53
N7 I:DG-55 1.5 0.1 1.0
C5 I:DG-55 2.2 0.4 1.0
O6 I:DG-55 2.5 0.3 1.0
C6 I:DG-55 2.6 0.4 1.0
C8 I:DG-55 2.7 0.4 1.0
C4 I:DG-55 3.5 0.3 1.0
N9 I:DG-55 3.7 0.4 1.0
N1 I:DG-55 4.0 0.4 1.0
N6 I:DA-54 4.1 0.5 1.0
N7 I:DA-56 4.1 0.6 1.0
C8 I:DA-56 4.2 0.6 1.0
N3 I:DG-55 4.6 0.2 1.0
N7 I:DA-54 4.7 0.5 1.0
C2 I:DG-55 4.8 0.4 1.0
C5 I:DA-56 4.8 0.3 1.0
N9 I:DA-56 4.9 0.5 1.0
C6 I:DA-54 4.9 0.7 1.0

Platinum binding site 9 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 9 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt76

b:88.2
occ:0.26
N7 I:DG-34 2.1 0.4 1.0
C8 I:DG-34 2.9 0.5 1.0
C5 I:DG-34 3.2 0.7 1.0
O6 I:DG-33 3.5 0.8 1.0
C2' I:DT-35 3.7 0.7 1.0
O6 I:DG-34 3.7 0.7 1.0
C6 I:DG-34 3.9 0.2 1.0
PT I:PT77 3.9 0.5 0.6
C6 I:DG-33 4.2 0.5 1.0
N9 I:DG-34 4.2 0.5 1.0
OP2 I:DG-34 4.2 0.3 1.0
O3' I:DT-35 4.3 0.5 1.0
C4 I:DG-34 4.3 0.1 1.0
C3' I:DT-35 4.4 0.3 1.0
N4 J:DC33 4.4 0.6 1.0
N7 I:DG-33 4.5 0.1 1.0
C5 I:DG-33 4.6 0.5 1.0
P I:DG-34 5.0 0.6 1.0
C1' I:DT-35 5.0 0.3 1.0

Platinum binding site 10 out of 49 in 3rei

Go back to Platinum Binding Sites List in 3rei
Platinum binding site 10 out of 49 in the 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 145 Bp Alpha-Satellite Dna (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt77

b:0.5
occ:0.55
N7 I:DG-33 1.9 0.1 1.0
C5 I:DG-33 2.9 0.5 1.0
C8 I:DG-33 2.9 0.6 1.0
O6 I:DG-33 3.2 0.8 1.0
C6 I:DG-33 3.4 0.5 1.0
C8 I:DG-34 3.8 0.5 1.0
N7 I:DG-34 3.9 0.4 1.0
PT I:PT76 3.9 88.2 0.3
C4 I:DG-33 4.1 0.7 1.0
N9 I:DG-33 4.1 0.4 1.0
O4 J:DT32 4.2 0.0 1.0
N6 I:DA-32 4.4 0.3 1.0
N9 I:DG-34 4.6 0.5 1.0
N1 I:DG-33 4.7 0.4 1.0
C5 I:DG-34 4.7 0.7 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

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy