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:
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
|