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Platinum in PDB 5bna: The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G

Protein crystallography data

The structure of The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G, PDB code: 5bna was solved by R.M.Wing, P.Pjura, H.R.Drew, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.160, 39.930, 66.120, 90.00, 90.00, 90.00
R / Rfree (%) 10.2 / n/a

Platinum Binding Sites:

The binding sites of Platinum atom in the The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G (pdb code 5bna). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G, PDB code: 5bna:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 5bna

Go back to Platinum Binding Sites List in 5bna
Platinum binding site 1 out of 3 in the The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt25

b:29.1
occ:1.00
PT A:PTN25 0.0 29.1 1.0
N2 A:PTN25 1.8 19.2 1.0
N3 A:PTN25 2.0 10.0 1.0
N1 A:PTN25 2.0 10.0 1.0
N7 B:DG16 2.2 10.0 1.0
C8 B:DG16 3.2 2.1 1.0
C5 B:DG16 3.2 28.9 1.0
O6 B:DG16 3.5 19.3 1.0
O A:HOH33 3.6 17.5 1.0
C6 B:DG16 3.7 1.4 1.0
O A:HOH137 4.0 36.9 1.0
N9 B:DG16 4.4 1.4 1.0
C4 B:DG16 4.4 10.0 1.0
OP2 B:DG16 4.5 23.6 1.0
N6 B:DA17 4.5 36.6 1.0
O B:HOH57 4.6 5.9 1.0
C6 B:DC15 4.7 10.0 1.0
C5 B:DC15 4.8 13.9 1.0
O4 A:DT8 4.9 23.2 1.0
O A:HOH152 4.9 33.4 1.0
O A:HOH71 5.0 27.6 1.0

Platinum binding site 2 out of 3 in 5bna

Go back to Platinum Binding Sites List in 5bna
Platinum binding site 2 out of 3 in the The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt26

b:31.2
occ:1.00
PT A:PTN26 0.0 31.2 1.0
N1 A:PTN26 1.8 10.0 1.0
N3 A:PTN26 2.2 10.0 1.0
N2 A:PTN26 2.2 36.5 1.0
N7 A:DG4 2.3 10.5 1.0
C8 A:DG4 3.2 4.5 1.0
C5 A:DG4 3.4 37.1 1.0
O6 A:DG4 3.7 41.6 1.0
C6 A:DG4 3.9 34.6 1.0
C6 A:DC3 4.2 10.0 1.0
C2' A:DC3 4.2 35.3 1.0
C5 A:DC3 4.4 4.1 1.0
O A:HOH109 4.5 22.7 1.0
N9 A:DG4 4.5 22.3 1.0
C4 A:DG4 4.5 38.9 1.0
N1 A:DC3 4.7 3.8 1.0
N6 A:DA5 4.7 23.6 1.0
OP2 A:DG4 4.7 8.7 1.0
C4 A:DC3 5.0 10.0 1.0

Platinum binding site 3 out of 3 in 5bna

Go back to Platinum Binding Sites List in 5bna
Platinum binding site 3 out of 3 in the The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt27

b:20.8
occ:1.00
PT B:PTN27 0.0 20.8 1.0
N1 B:PTN27 1.8 10.0 1.0
N2 B:PTN27 2.1 0.4 1.0
N3 B:PTN27 2.1 10.0 1.0
N7 A:DG10 2.2 14.9 1.0
C8 A:DG10 3.0 17.5 1.0
C5 A:DG10 3.3 36.1 1.0
O A:HOH139 3.9 47.2 1.0
O6 A:DG10 3.9 48.6 1.0
C6 A:DG10 4.0 35.3 1.0
N9 A:DG10 4.2 30.1 1.0
C4 A:DG10 4.3 39.9 1.0
O B:HOH99 4.6 39.4 1.0

Reference:

R.M.Wing, P.Pjura, H.R.Drew, R.E.Dickerson. The Primary Mode of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G Embo J. V. 3 1201 1984.
ISSN: ISSN 0261-4189
PubMed: 6539674
Page generated: Wed Dec 16 02:05:07 2020

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