Atomistry » Platinum » PDB 5yky-7bpr » 6f3c
Atomistry »
  Platinum »
    PDB 5yky-7bpr »
      6f3c »

Platinum in PDB 6f3c: The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer

Protein crystallography data

The structure of The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer, PDB code: 6f3c was solved by M.Ferraroni, C.Bazzicalupi, P.Gratteri, F.Papi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 30.090, 30.090, 116.990, 90.00, 90.00, 120.00
R / Rfree (%) 25.7 / 29.2

Other elements in 6f3c:

The structure of The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer (pdb code 6f3c). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer, PDB code: 6f3c:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 6f3c

Go back to Platinum Binding Sites List in 6f3c
Platinum binding site 1 out of 2 in the The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt101

b:46.5
occ:0.50
PT1 A:PT9101 0.0 46.5 0.5
C11 A:PT9102 0.4 45.8 0.5
N4 A:PT9102 1.0 42.3 0.5
C12 A:PT9102 1.6 28.4 0.5
C10 A:PT9102 1.8 42.2 0.5
C15 A:PT9102 1.9 40.8 0.5
N4 A:PT9101 1.9 33.3 0.5
N3 A:PT9101 2.0 35.7 0.5
N1 A:PT9101 2.0 44.6 0.5
N6 A:PT9101 2.0 37.9 0.5
C13 A:PT9102 2.2 32.9 0.5
C14 A:PT9102 2.3 34.9 0.5
N3 A:PT9102 2.5 44.3 0.5
PT1 A:PT9102 2.7 65.4 0.5
C10 A:PT9101 2.8 38.0 0.5
C11 A:PT9101 2.8 36.2 0.5
C9 A:PT9102 2.9 39.0 0.5
C15 A:PT9101 2.9 30.8 0.5
C20 A:PT9101 3.0 38.3 0.5
C1 A:PT9101 3.0 47.6 0.5
C6 A:PT9101 3.0 37.7 0.5
C16 A:PT9101 3.0 33.5 0.5
C5 A:PT9101 3.1 50.7 0.5
N5 A:PT9102 3.2 41.7 0.5
N5 A:PT9101 3.3 30.4 0.5
N2 A:PT9101 3.4 43.2 0.5
N3 B:DG8 3.7 25.8 1.0
C2 B:DG8 3.7 32.3 1.0
C4 B:DG8 3.7 27.6 1.0
C6 A:PT9102 3.8 42.6 0.5
N1 B:DG8 3.8 21.7 1.0
C5 B:DG8 3.9 26.7 1.0
C6 B:DG8 3.9 28.1 1.0
N6 A:PT9102 3.9 45.4 0.5
C16 A:PT9102 4.0 46.4 0.5
C9 A:PT9101 4.1 40.3 0.5
C8 A:PT9102 4.1 42.9 0.5
C12 A:PT9101 4.1 33.5 0.5
C14 A:PT9101 4.2 26.3 0.5
C19 A:PT9101 4.2 39.4 0.5
C2 A:PT9101 4.3 45.5 0.5
C7 A:PT9101 4.3 40.9 0.5
N2 B:DG8 4.3 37.4 1.0
N9 B:DG8 4.3 30.8 1.0
C17 A:PT9101 4.3 36.9 0.5
N2 A:DG6 4.4 35.9 1.0
C4 A:PT9101 4.4 36.6 0.5
C7 A:PT9102 4.4 39.3 0.5
N1 A:PT9102 4.5 42.6 0.5
N7 B:DG8 4.5 30.4 1.0
O6 B:DG8 4.6 41.7 1.0
C13 A:PT9101 4.7 31.3 0.5
C8 A:PT9101 4.7 38.5 0.5
C8 B:DG8 4.8 26.4 1.0
N2 A:PT9102 4.8 38.9 0.5
N3 A:DG6 4.8 42.0 1.0
C18 A:PT9101 4.8 37.1 0.5
C3 A:PT9101 4.8 51.4 0.5
C1' B:DG8 4.9 37.7 1.0
C2 A:DG6 4.9 52.4 1.0

Platinum binding site 2 out of 2 in 6f3c

Go back to Platinum Binding Sites List in 6f3c
Platinum binding site 2 out of 2 in the The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The Cytotoxic [Pt(H2BAPBPY)] Platinum Complex Interacting with the Cgtacg Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt102

b:65.4
occ:0.50
PT1 A:PT9102 0.0 65.4 0.5
C5 A:PT9101 0.5 50.7 0.5
N1 A:PT9101 1.0 44.6 0.5
N2 A:PT9101 1.6 43.2 0.5
C4 A:PT9101 1.8 36.6 0.5
N4 A:PT9102 2.0 42.3 0.5
N1 A:PT9102 2.0 42.6 0.5
C1 A:PT9101 2.0 47.6 0.5
N3 A:PT9102 2.0 44.3 0.5
N6 A:PT9102 2.1 45.4 0.5
C6 A:PT9101 2.3 37.7 0.5
C3 A:PT9101 2.5 51.4 0.5
C2 A:PT9101 2.6 45.5 0.5
N3 A:PT9101 2.6 35.7 0.5
PT1 A:PT9101 2.7 46.5 0.5
C11 A:PT9102 2.9 45.8 0.5
C10 A:PT9102 2.9 42.2 0.5
C1 A:PT9102 2.9 42.7 0.5
C15 A:PT9102 2.9 40.8 0.5
C5 A:PT9102 2.9 49.8 0.5
C6 A:PT9102 3.0 42.6 0.5
C16 A:PT9102 3.0 46.4 0.5
C20 A:PT9102 3.0 44.2 0.5
N5 A:PT9102 3.2 41.7 0.5
N2 A:DG6 3.2 35.9 1.0
N2 A:PT9102 3.3 38.9 0.5
O6 B:DG8 3.3 41.7 1.0
C6 B:DG8 3.4 28.1 1.0
C7 A:PT9101 3.6 40.9 0.5
C2 A:DG6 3.8 52.4 1.0
C5 B:DG8 3.8 26.7 1.0
C10 A:PT9101 3.9 38.0 0.5
N1 B:DG8 4.0 21.7 1.0
N7 B:DG8 4.0 30.4 1.0
N6 A:PT9101 4.1 37.9 0.5
C9 A:PT9102 4.2 39.0 0.5
C20 A:PT9101 4.2 38.3 0.5
C14 A:PT9102 4.2 34.9 0.5
C2 A:PT9102 4.2 39.2 0.5
C12 A:PT9102 4.2 28.4 0.5
C4 A:PT9102 4.2 42.3 0.5
C7 A:PT9102 4.2 39.3 0.5
N3 A:DG6 4.3 42.0 1.0
C17 A:PT9102 4.3 40.5 0.5
C19 A:PT9102 4.3 46.2 0.5
N1 A:DG6 4.3 51.6 1.0
N3 A:DC5 4.4 29.5 1.0
N4 A:PT9101 4.4 33.3 0.5
C4 B:DG8 4.5 27.6 1.0
N4 A:DC5 4.6 47.5 1.0
C8 A:PT9101 4.6 38.5 0.5
C13 A:PT9102 4.7 32.9 0.5
C8 A:PT9102 4.7 42.9 0.5
C3 A:PT9102 4.7 45.1 0.5
C11 A:PT9101 4.8 36.2 0.5
C9 A:PT9101 4.8 40.3 0.5
C4 A:DC5 4.8 35.2 1.0
C2 B:DG8 4.8 32.3 1.0
C18 A:PT9102 4.8 45.9 0.5
C8 B:DG8 4.8 26.4 1.0

Reference:

V.H.S.Van Rixel, A.Busemann, M.F.Wissingh, S.L.Hopkins, B.Siewert, C.Van De Griend, M.A.Siegler, T.Marzo, F.Papi, M.Ferraroni, P.Gratteri, C.Bazzicalupi, L.Messori, S.Bonnet. Induction of A Four-Way Junction Structure in the Dna Palindromic Hexanucleotide 5'-D(Cgtacg)-3' By A Mononuclear Platinum Complex. Angew.Chem.Int.Ed.Engl. V. 58 9378 2019.
ISSN: ESSN 1521-3773
PubMed: 31046177
DOI: 10.1002/ANIE.201814532
Page generated: Thu Oct 10 11:42:44 2024

Last articles

Ca in 9CM2
Ca in 9CGR
Ca in 9BBF
Ca in 9BAR
Ca in 9BB8
Ca in 9BCF
Ca in 9BHU
Ca in 9BHV
Ca in 9BI0
Ca in 8XNI
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy