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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: Sat Dec 12 01:54:16 2020

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