Ruthenium in PDB 3mnn: A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core

The structure of A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core, PDB code: 3mnn was solved by M.S.Ong, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.13 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.350, 109.860, 182.590, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 27.7

The structure of A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Ruthenium atom in the A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core (pdb code 3mnn). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core, PDB code: 3mnn:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ F:Ru2001 b:0.5 occ:1.00 C10 F:MML2002 2.2 0.5 1.0 C9 F:MML2002 2.2 0.6 1.0 C5 F:MML2002 2.2 0.5 1.0 C2 F:MML2002 2.2 0.6 1.0 C3 F:MML2002 2.2 0.8 1.0 C4 F:MML2002 2.3 0.6 1.0 P1 F:PTW2003 2.3 0.5 1.0 NZ F:LYS59 2.5 52.5 1.0 OE2 F:GLU63 2.9 58.1 1.0 CE F:LYS59 3.2 53.2 1.0 C1 F:MML2002 3.3 0.4 1.0 C6 F:MML2002 3.4 0.3 1.0 CD F:GLU63 3.5 54.5 1.0 C16 F:PTW2003 3.5 0.3 1.0 C20 F:PTW2003 3.5 0.2 1.0 C18 F:PTW2003 3.6 0.5 1.0 OE1 F:GLU63 3.8 56.2 1.0 C7 F:MML2002 3.8 0.6 1.0 CD F:LYS59 4.5 51.0 1.0 CG F:LYS59 4.7 45.3 1.0 C8 F:MML2002 4.7 0.2 1.0 CG F:GLU63 4.7 50.4 1.0 N1 F:PTW2003 4.8 0.5 1.0 N2 F:PTW2003 4.8 0.3 1.0 N3 F:PTW2003 4.8 0.8 1.0

Ruthenium binding site 2 out of 3 in the A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ G:Ru2001 b:0.6 occ:1.00 C10 G:MML2002 2.2 0.2 1.0 C9 G:MML2002 2.2 0.9 1.0 C5 G:MML2002 2.2 0.3 1.0 C2 G:MML2002 2.2 0.3 1.0 C3 G:MML2002 2.3 0.7 1.0 C4 G:MML2002 2.3 0.4 1.0 P1 G:PTW2003 2.3 0.2 1.0 OE1 G:GLU64 2.6 72.6 1.0 OE2 G:GLU61 2.6 70.4 1.0 C1 G:MML2002 3.3 0.3 1.0 C6 G:MML2002 3.4 0.1 1.0 C18 G:PTW2003 3.5 0.8 1.0 C20 G:PTW2003 3.5 0.6 1.0 C16 G:PTW2003 3.5 0.4 1.0 CD G:GLU61 3.6 67.8 1.0 CD G:GLU64 3.7 68.7 1.0 OE1 G:GLU61 4.1 67.6 1.0 C8 G:MML2002 4.1 0.7 1.0 OE2 G:GLU64 4.5 71.8 1.0 C7 G:MML2002 4.6 0.9 1.0 CG G:GLU64 4.7 67.8 1.0 N3 G:PTW2003 4.7 0.1 1.0 CG G:GLU61 4.7 64.6 1.0 N2 G:PTW2003 4.8 0.2 1.0 N1 G:PTW2003 4.8 0.8 1.0 CB G:GLU64 4.9 65.8 1.0

Ruthenium binding site 3 out of 3 in the A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ H:Ru2001 b:0.9 occ:1.00 C10 H:MML2002 2.2 0.8 1.0 C9 H:MML2002 2.2 0.0 1.0 C5 H:MML2002 2.2 0.1 1.0 C2 H:MML2002 2.2 0.8 1.0 C3 H:MML2002 2.3 0.9 1.0 C4 H:MML2002 2.3 0.0 1.0 P1 H:PTW2003 2.3 0.2 1.0 NE2 H:HIS106 2.4 67.7 1.0 CE1 H:HIS106 3.1 67.4 1.0 C1 H:MML2002 3.3 0.7 1.0 C6 H:MML2002 3.4 0.0 1.0 CD2 H:HIS106 3.5 65.5 1.0 C20 H:PTW2003 3.5 0.4 1.0 C18 H:PTW2003 3.5 0.2 1.0 C16 H:PTW2003 3.5 0.2 1.0 C8 H:MML2002 3.8 0.1 1.0 OE1 H:GLU102 4.0 71.4 1.0 ND1 H:HIS106 4.3 66.4 1.0 CG H:HIS106 4.5 64.5 1.0 C7 H:MML2002 4.7 0.9 1.0 N2 H:PTW2003 4.8 0.5 1.0 N3 H:PTW2003 4.8 0.4 1.0 N1 H:PTW2003 4.8 0.4 1.0

B.Wu, M.S.Ong, M.Groessl, Z.Adhireksan, C.G.Hartinger, P.J.Dyson, C.A.Davey. A Ruthenium Antimetastasis Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Chemistry V. 17 3562 2011.
ISSN: ISSN 0947-6539
PubMed: 21344528
DOI: 10.1002/CHEM.201100298