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Platinum in PDB 1lu5: 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex

Protein crystallography data

The structure of 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex, PDB code: 1lu5 was solved by A.P.Silverman, W.Bu, S.M.Cohen, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 31.644, 35.638, 46.556, 79.53, 83.02, 81.36
R / Rfree (%) 23.4 / 29.4

Platinum Binding Sites:

The binding sites of Platinum atom in the 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex (pdb code 1lu5). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex, PDB code: 1lu5:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 1lu5

Go back to Platinum Binding Sites List in 1lu5
Platinum binding site 1 out of 2 in the 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt49

b:27.7
occ:1.00
PT A:LPT49 0.0 27.7 1.0
N7 A:DG7 2.0 29.6 1.0
N7 A:DG6 2.0 29.9 1.0
N1 A:LPT49 2.0 18.9 1.0
N2 A:LPT49 2.1 17.4 1.0
C8 A:DG6 2.8 28.0 1.0
C5 A:DG6 2.9 25.7 1.0
C8 A:DG7 2.9 30.0 1.0
C5 A:DG7 3.0 31.2 1.0
C3 A:LPT49 3.0 25.9 1.0
C4 A:LPT49 3.0 27.4 1.0
O A:HOH224 3.3 45.6 1.0
O6 A:DG7 3.4 26.3 1.0
O6 A:DG6 3.4 28.3 1.0
C6 A:DG6 3.5 24.7 1.0
C6 A:DG7 3.5 31.1 1.0
O A:HOH204 3.9 28.4 1.0
N9 A:DG6 4.0 24.5 1.0
C4 A:DG6 4.0 22.9 1.0
OP2 A:DG6 4.1 32.5 1.0
N9 A:DG7 4.1 27.7 1.0
C4 A:DG7 4.1 29.5 1.0
C8 A:LPT49 4.3 24.2 1.0
O A:HOH222 4.4 45.9 1.0
C5 A:LPT49 4.5 28.2 1.0
N1 A:DG6 4.8 25.5 1.0
C4 A:DT5 4.9 27.9 1.0
N1 A:DG7 4.9 32.8 1.0
N3 A:DT5 5.0 29.0 1.0

Platinum binding site 2 out of 2 in 1lu5

Go back to Platinum Binding Sites List in 1lu5
Platinum binding site 2 out of 2 in the 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt50

b:28.7
occ:1.00
PT C:LPT50 0.0 28.7 1.0
N7 C:DG31 2.0 30.3 1.0
N7 C:DG30 2.0 20.2 1.0
N1 C:LPT50 2.0 32.6 1.0
N2 C:LPT50 2.0 13.8 1.0
C5 C:DG30 2.8 20.1 1.0
C8 C:DG31 2.8 28.9 1.0
C8 C:DG30 2.9 19.2 1.0
C5 C:DG31 3.0 32.6 1.0
C3 C:LPT50 3.1 20.6 1.0
C4 C:LPT50 3.1 24.8 1.0
O6 C:DG30 3.2 30.5 1.0
C6 C:DG30 3.4 23.9 1.0
O6 C:DG31 3.6 43.0 1.0
O C:HOH201 3.6 22.3 1.0
C6 C:DG31 3.6 33.7 1.0
C4 C:DG30 4.0 18.4 1.0
OP2 C:DG30 4.0 36.7 1.0
N9 C:DG31 4.0 29.2 1.0
N9 C:DG30 4.0 19.5 1.0
C4 C:DG31 4.1 33.0 1.0
C8 C:LPT50 4.2 28.0 1.0
C5 C:LPT50 4.6 32.9 1.0
N1 C:DG30 4.7 24.3 1.0
C4 C:DT29 4.9 30.4 1.0
N1 C:DG31 5.0 29.8 1.0
N3 C:DT29 5.0 30.8 1.0

Reference:

A.P.Silverman, W.Bu, S.M.Cohen, S.J.Lippard. 2.4-A Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex J.Biol.Chem. V. 277 49743 2002.
ISSN: ISSN 0021-9258
PubMed: 12377787
DOI: 10.1074/JBC.M206979200
Page generated: Wed Dec 16 02:03:37 2020

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