Platinum in PDB 4wu8: Structure of Trptnap-NCP145

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

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

Magnesium

(Mg)

1 atom

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 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 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 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

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