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Platinum in PDB 2dyw: A Backbone Binding Dna Complex

Protein crystallography data

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

Other elements in 2dyw:

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

Sodium (Na) 1 atom

Platinum Binding Sites:

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 2dyw

Go back to Platinum Binding Sites List in 2dyw
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 2dyw

Go back to Platinum Binding Sites List in 2dyw
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 2dyw

Go back to Platinum Binding Sites List in 2dyw
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 2dyw

Go back to Platinum Binding Sites List in 2dyw
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

Reference:

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
Page generated: Wed Dec 16 02:03:59 2020

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