Atomistry » Platinum » PDB 4nsj-5bna » 4wu8
Atomistry »
  Platinum »
    PDB 4nsj-5bna »
      4wu8 »

Platinum in PDB 4wu8: Structure of Trptnap-NCP145

Protein crystallography data

The structure of Structure of Trptnap-NCP145, PDB code: 4wu8 was solved by E.Y.D.Chua, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.05 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.410, 109.630, 183.010, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.3

Other elements in 4wu8:

The structure of Structure of Trptnap-NCP145 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the Structure of Trptnap-NCP145 (pdb code 4wu8). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the Structure of Trptnap-NCP145, PDB code: 4wu8:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 4wu8

Go back to Platinum Binding Sites List in 4wu8
Platinum binding site 1 out of 3 in the Structure of Trptnap-NCP145


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Structure of Trptnap-NCP145 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt100

b:0.8
occ:1.00
PT1 I:CX3100 0.0 0.8 1.0
N2 I:CX3100 2.0 0.3 1.0
N1 I:CX3100 2.0 0.1 1.0
N3 I:CX3100 2.0 0.5 1.0
N7 I:DG-14 2.0 0.8 1.0
C3 I:CX3100 2.8 0.7 1.0
C2 I:CX3100 2.8 0.9 1.0
C5 I:CX3100 2.9 0.3 1.0
C1 I:CX3100 2.9 0.3 1.0
C4 I:CX3100 2.9 0.8 1.0
C6 I:CX3100 3.0 0.5 1.0
C8 I:DG-14 3.0 0.4 1.0
C5 I:DG-14 3.0 0.5 1.0
O1 I:CX3100 3.1 0.2 1.0
O6 I:DG-14 3.4 0.1 1.0
C6 I:DG-14 3.7 0.4 1.0
C8 I:CX3100 3.9 0.0 1.0
C7 I:CX3100 4.1 0.4 1.0
N9 I:DG-14 4.2 0.3 1.0
C4 I:DG-14 4.2 0.8 1.0
N4 I:CX3100 4.3 0.5 1.0
N4 I:DC-13 4.4 88.8 1.0
C2' I:DG-15 4.8 94.1 1.0
C9 I:CX3100 4.9 0.3 1.0
N1 I:DG-14 5.0 0.2 1.0

Platinum binding site 2 out of 3 in 4wu8

Go back to Platinum Binding Sites List in 4wu8
Platinum binding site 2 out of 3 in the Structure of Trptnap-NCP145


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Structure of Trptnap-NCP145 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt101

b:0.1
occ:0.50
PT1 J:CX3101 0.0 0.1 0.5
N2 J:CX3101 2.0 0.1 0.5
N3 J:CX3101 2.0 0.6 0.5
N1 J:CX3101 2.0 0.3 0.5
N7 J:DG-14 2.1 93.6 1.0
C6 J:CX3101 2.7 1.0 0.5
C2 J:CX3101 2.8 0.7 0.5
C5 J:CX3101 2.8 0.6 0.5
C3 J:CX3101 2.8 0.5 0.5
C1 J:CX3101 2.9 0.1 0.5
C4 J:CX3101 2.9 0.1 0.5
C5 J:DG-14 3.0 84.7 1.0
C8 J:DG-14 3.0 82.3 1.0
O6 J:DG-14 3.3 76.7 1.0
O2 J:CX3101 3.3 0.7 0.5
C6 J:DG-14 3.6 81.4 1.0
C7 J:CX3101 3.8 0.2 0.5
C12 J:CX3101 4.1 0.6 0.5
N9 J:DG-14 4.2 75.4 1.0
C4 J:DG-14 4.2 79.5 1.0
N4 J:CX3101 4.3 1.0 0.5
C19 J:CX3101 4.8 0.2 0.5
O1 J:CX3101 4.8 0.5 0.5
N1 J:DG-14 4.9 83.3 1.0
N4 J:DC-13 5.0 52.3 1.0
C2' J:DG-15 5.0 87.5 1.0

Platinum binding site 3 out of 3 in 4wu8

Go back to Platinum Binding Sites List in 4wu8
Platinum binding site 3 out of 3 in the Structure of Trptnap-NCP145


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Structure of Trptnap-NCP145 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt101

b:0.6
occ:0.50
PT1 J:CX3101 0.0 0.6 0.5
N2 J:CX3101 2.0 0.5 0.5
N1 J:CX3101 2.0 0.4 0.5
N3 J:CX3101 2.0 0.1 0.5
C2 J:CX3101 2.8 0.7 0.5
C3 J:CX3101 2.8 0.7 0.5
C1 J:CX3101 2.9 0.8 0.5
C4 J:CX3101 2.9 0.1 0.5
C5 J:CX3101 2.9 0.1 0.5
O6 J:DG-15 3.7 0.7 1.0
C6 J:CX3101 4.1 0.1 0.5
N4 I:DC15 4.1 84.9 1.0
N6 J:DA-16 4.6 0.6 1.0
O2 J:CX3101 4.7 0.9 0.5
N7 J:DA-16 4.8 1.0 1.0
C6 J:DG-15 4.9 97.5 1.0

Reference:

E.Y.Chua, G.E.Davey, C.F.Chin, P.Droge, W.H.Ang, C.A.Davey. Stereochemical Control of Nucleosome Targeting By Platinum-Intercalator Antitumor Agents. Nucleic Acids Res. V. 43 5284 2015.
ISSN: ESSN 1362-4962
PubMed: 25916851
DOI: 10.1093/NAR/GKV356
Page generated: Wed Dec 16 02:05:04 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy