Platinum in PDB 2dyw: A Backbone Binding Dna Complex

The structure of A Backbone Binding Dna Complex, PDB code: 2dyw was solved by S.Komeda, T.Moulaei, K.K.Woods, M.Chikuma, N.P.Farrell, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	5.50 / 1.13
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	23.675, 41.692, 65.651, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / 23.2

The structure of A Backbone Binding Dna Complex also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Platinum atom in the A Backbone Binding Dna Complex (pdb code 2dyw). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 4 binding sites of Platinum where determined in the A Backbone Binding Dna Complex, PDB code: 2dyw:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in the A Backbone Binding Dna Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of A Backbone Binding Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt301 b:19.1 occ:0.60 PT A:A71301 0.0 19.1 0.6 N8 A:A71301 2.0 30.2 0.6 N10 A:A71301 2.0 16.6 0.6 N9 A:A71301 2.0 15.3 0.6 N11 A:A71301 2.0 15.5 0.6 C7 A:A71301 2.9 23.4 0.6 OP1 A:DG4 3.8 27.0 1.0 C6 A:A71301 4.2 20.3 0.6 O A:HOH2106 4.5 35.6 1.0 C5' A:DG4 4.5 14.5 1.0 P A:DG4 4.9 20.0 1.0

Platinum binding site 2 out of 4 in the A Backbone Binding Dna Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of A Backbone Binding Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt201 b:11.2 occ:0.75 PT B:A71201 0.0 11.2 0.8 N9 B:A71201 2.0 9.9 0.8 N10 B:A71201 2.0 10.1 0.8 N11 B:A71201 2.0 12.9 0.8 N8 B:A71201 2.0 9.4 0.8 C7 B:A71201 2.9 15.2 0.8 C12 B:A72202 3.0 8.5 0.8 C6 B:A71201 3.2 23.7 0.8 C13 B:A72202 3.4 14.4 0.8 O B:HOH2006 4.0 16.2 1.0 O B:HOH2046 4.2 24.0 1.0 C5 B:A71201 4.2 20.0 0.8 C14 B:A72202 4.8 12.4 0.8 OP1 B:DC3 5.0 12.0 1.0

Platinum binding site 3 out of 4 in the A Backbone Binding Dna Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of A Backbone Binding Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt202 b:14.3 occ:0.75 PT B:A72202 0.0 14.3 0.8 N18 B:A72202 2.0 8.8 0.8 N21 B:A72202 2.0 12.1 0.8 N19 B:A72202 2.0 14.1 0.8 N20 B:A72202 2.0 13.7 0.8 C22 B:A72202 2.9 21.2 0.8 C17 B:A72202 3.0 12.7 0.8 OP1 B:DG4 4.0 12.6 1.0 C23 B:A72202 4.2 30.7 0.8 C5' B:DG4 4.3 11.3 1.0 C16 B:A72202 4.4 9.3 0.8 O B:HOH2086 4.5 31.6 1.0 P B:DG4 5.0 11.8 1.0

Platinum binding site 4 out of 4 in the A Backbone Binding Dna Complex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of A Backbone Binding Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt203 b:24.1 occ:0.75 PT B:A71203 0.0 24.1 0.8 N11 B:A71203 2.0 18.6 0.8 N9 B:A71203 2.0 19.0 0.8 N10 B:A71203 2.0 25.2 0.8 N8 B:A71203 2.0 16.1 0.8 C7 B:A71203 2.9 19.2 0.8 C27 B:A72202 2.9 28.7 0.8 OP1 B:DA5 3.9 16.6 1.0 C26 B:A72202 4.1 34.7 0.8 C6 B:A71203 4.2 24.6 0.8 C25 B:A72202 4.8 33.7 0.8

S.Komeda, T.Moulaei, K.K.Woods, M.Chikuma, N.P.Farrell, L.D.Williams. A Third Mode of Dna Binding: Phosphate Clamps By A Polynuclear Platinum Complex J.Am.Chem.Soc. V. 128 16092 2006.
ISSN: ISSN 0002-7863
PubMed: 17165762
DOI: 10.1021/JA062851Y