Atomistry » Platinum » PDB 1uas-3az7 » 2dyw
Atomistry »
  Platinum »
    PDB 1uas-3az7 »
      2dyw »

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

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy