Atomistry » Gold » PDB 3l47-5ix6 » 5dnn
Atomistry »
  Gold »
    PDB 3l47-5ix6 »
      5dnn »

Gold in PDB 5dnn: Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes

Protein crystallography data

The structure of Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes, PDB code: 5dnn was solved by Z.Adhireksan, Z.Ma, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.87 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.726, 109.948, 182.041, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.6

Other elements in 5dnn:

The structure of Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Ruthenium (Ru) 2 atoms

Gold Binding Sites:

The binding sites of Gold atom in the Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes (pdb code 5dnn). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 2 binding sites of Gold where determined in the Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes, PDB code: 5dnn:
Jump to Gold binding site number: 1; 2;

Gold binding site 1 out of 2 in 5dnn

Go back to Gold Binding Sites List in 5dnn
Gold binding site 1 out of 2 in the Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au201

b:65.2
occ:0.70
AU1 A:AUF201 0.0 65.2 0.7
P1 A:AUF201 1.9 73.8 0.7
ND1 A:HIS113 2.1 54.6 1.0
CE1 A:HIS113 3.0 54.3 1.0
C3 A:AUF201 3.0 66.0 0.7
C5 A:AUF201 3.1 66.9 0.7
CG A:HIS113 3.1 57.4 1.0
C1 A:AUF201 3.1 64.7 0.7
C4 A:AUF201 3.2 62.0 0.7
CB A:HIS113 3.5 61.3 1.0
C2 A:AUF201 3.5 69.4 0.7
CA A:HIS113 3.8 59.1 1.0
O E:LYS122 4.1 54.2 1.0
CB E:LEU126 4.2 44.4 1.0
NE2 A:HIS113 4.2 51.9 1.0
CD2 A:HIS113 4.2 53.6 1.0
CB E:LYS122 4.4 57.1 1.0
C6 A:AUF201 4.4 85.8 0.7
CD2 E:LEU126 4.6 48.0 1.0
CE E:LYS122 4.6 68.1 1.0
CG E:LYS122 4.6 55.1 1.0
CD1 E:LEU126 4.7 47.6 1.0
CG E:LEU126 4.7 45.8 1.0
C E:LYS122 4.7 52.0 1.0
N A:HIS113 4.7 59.7 1.0
C A:HIS113 4.9 58.4 1.0
O A:HIS113 4.9 57.9 1.0

Gold binding site 2 out of 2 in 5dnn

Go back to Gold Binding Sites List in 5dnn
Gold binding site 2 out of 2 in the Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Au1002

b:68.5
occ:0.70
AU1 E:AUF1002 0.0 68.5 0.7
P1 E:AUF1002 1.9 74.1 0.7
ND1 E:HIS113 2.1 52.2 1.0
C3 E:AUF1002 3.0 65.0 0.7
C4 E:AUF1002 3.0 58.3 0.7
C1 E:AUF1002 3.0 69.4 0.7
C5 E:AUF1002 3.1 71.2 0.7
CE1 E:HIS113 3.1 57.0 1.0
CG E:HIS113 3.1 53.7 1.0
C2 E:AUF1002 3.4 71.3 0.7
CB E:HIS113 3.4 55.1 1.0
CA E:HIS113 3.7 57.7 1.0
CB A:LYS122 4.2 62.8 1.0
CB A:LEU126 4.2 50.1 1.0
NE2 E:HIS113 4.3 58.7 1.0
CD2 E:HIS113 4.3 56.0 1.0
O A:LYS122 4.4 66.0 1.0
C6 E:AUF1002 4.4 81.1 0.7
CD2 A:LEU126 4.5 53.5 1.0
CD1 A:LEU126 4.6 53.3 1.0
N E:HIS113 4.6 54.0 1.0
CG A:LEU126 4.7 53.0 1.0
CD A:LYS122 4.7 64.7 1.0
C A:LYS122 4.7 60.1 1.0
C E:HIS113 4.8 58.8 1.0
CG A:LYS122 4.9 61.0 1.0
O E:HIS113 4.9 58.8 1.0
CA A:LYS122 5.0 58.9 1.0

Reference:

Z.Adhireksan, G.Palermo, T.Riedel, Z.Ma, R.Muhammad, U.Rothlisberger, P.J.Dyson, C.A.Davey. Allosteric Cross-Talk in Chromatin Can Mediate Drug-Drug Synergy Nat Commun V. 8 14860 2017.
ISSN: ESSN 2041-1723
PubMed: 28358030
DOI: 10.1038/NCOMMS14860
Page generated: Mon Jul 7 01:33:32 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy