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Platinum in PDB 4wu9: Structure of Cisptnap-NCP145

Protein crystallography data

The structure of Structure of Cisptnap-NCP145, PDB code: 4wu9 was solved by E.Y.D.Chua, G.E.Davey, C.F.Chin, P.Droge, W.H.Ang, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.33 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.570, 109.330, 181.280, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 27.3

Other elements in 4wu9:

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

Magnesium (Mg) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the Structure of Cisptnap-NCP145 (pdb code 4wu9). 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 Cisptnap-NCP145, PDB code: 4wu9:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 4wu9

Go back to Platinum Binding Sites List in 4wu9
Platinum binding site 1 out of 3 in the Structure of Cisptnap-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 Cisptnap-NCP145 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt101

b:0.7
occ:1.00
PT1 I:CX8101 0.0 0.7 1.0
N2 I:CX8101 1.9 0.6 1.0
N1 I:CX8101 2.0 0.8 1.0
N7 I:DG-14 2.0 0.4 1.0
N3 I:CX8101 2.1 0.8 1.0
C4 I:CX8101 2.8 0.1 1.0
C1 I:CX8101 2.9 0.9 1.0
C3 I:CX8101 2.9 0.6 1.0
C2 I:CX8101 2.9 0.6 1.0
C5 I:CX8101 3.0 0.9 1.0
C8 I:DG-14 3.0 0.8 1.0
C5 I:DG-14 3.0 0.4 1.0
O6 I:DG-14 3.3 0.1 1.0
C6 I:DG-14 3.6 0.4 1.0
C2' I:DG-15 4.1 0.8 1.0
N9 I:DG-14 4.2 0.9 1.0
C4 I:DG-14 4.2 0.8 1.0
C6 I:CX8101 4.3 0.8 1.0
O1 I:CX8101 4.4 0.0 1.0
C3' I:DG-15 4.5 0.0 1.0
O3' I:DG-15 4.6 0.5 1.0
N1 I:DG-14 4.9 0.9 1.0

Platinum binding site 2 out of 3 in 4wu9

Go back to Platinum Binding Sites List in 4wu9
Platinum binding site 2 out of 3 in the Structure of Cisptnap-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 Cisptnap-NCP145 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt102

b:1.0
occ:1.00
PT1 I:CX8102 0.0 1.0 1.0
N2 I:CX8102 1.9 0.9 1.0
N1 I:CX8102 2.0 0.0 1.0
N3 I:CX8102 2.1 0.1 1.0
O1 I:CX8102 2.6 0.1 1.0
C8 I:CX8102 2.6 0.7 1.0
C4 I:CX8102 2.9 0.9 1.0
C1 I:CX8102 2.9 0.3 1.0
C2 I:CX8102 2.9 0.3 1.0
C3 I:CX8102 2.9 0.7 1.0
C5 I:CX8102 3.1 0.8 1.0
N4 I:CX8102 3.1 1.0 1.0
C9 I:CX8102 3.3 0.4 1.0
C6 I:CX8102 3.3 0.2 1.0
C7 I:CX8102 3.5 0.2 1.0
C19 I:CX8102 3.8 0.7 1.0
C12 I:CX8102 3.9 0.0 1.0
C10 I:CX8102 4.1 0.3 1.0
C11 I:CX8102 4.4 0.4 1.0
O2 I:CX8102 4.8 0.5 1.0
C18 I:CX8102 4.9 0.8 1.0

Platinum binding site 3 out of 3 in 4wu9

Go back to Platinum Binding Sites List in 4wu9
Platinum binding site 3 out of 3 in the Structure of Cisptnap-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 Cisptnap-NCP145 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Pt100

b:0.7
occ:1.00
PT1 J:CX8100 0.0 0.7 1.0
N2 J:CX8100 1.9 0.5 1.0
N1 J:CX8100 2.0 0.8 1.0
N7 J:DG-14 2.0 0.5 1.0
N3 J:CX8100 2.0 0.3 1.0
C1 J:CX8100 2.7 0.0 1.0
C3 J:CX8100 2.7 0.8 1.0
C2 J:CX8100 2.8 0.0 1.0
C4 J:CX8100 2.8 0.2 1.0
C5 J:CX8100 2.9 0.3 1.0
C8 J:DG-14 3.0 0.9 1.0
C5 J:DG-14 3.0 0.7 1.0
O6 J:DG-14 3.4 1.0 1.0
C6 J:DG-14 3.6 0.5 1.0
N9 J:DG-14 4.2 0.8 1.0
O1 J:CX8100 4.2 0.8 1.0
C4 J:DG-14 4.2 0.0 1.0
C6 J:CX8100 4.2 0.6 1.0
N4 J:DC-13 4.7 92.0 1.0
C8 J:CX8100 4.9 0.6 1.0
N1 J:DG-14 5.0 0.6 1.0
OP2 J:DG-14 5.0 95.2 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 02:05:05 2020

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