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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: Wed Dec 16 02:05:30 2020

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