Ruthenium in PDB 5v4g: Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

All present enzymatic activity of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites:
3.2.1.17;

The structure of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites, PDB code: 5v4g was solved by M.P.Sullivan, C.G.Hartinger, D.C.Goldstone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.77 / 1.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.282, 80.282, 36.928, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.6

The structure of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Ruthenium atom in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites (pdb code 5v4g). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites, PDB code: 5v4g:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru202 b:23.7 occ:0.90 RU1 A:RU7202 0.0 23.7 0.9 C6 A:RU7202 2.2 26.2 0.9 NE2 A:HIS15 2.2 19.0 1.0 C5 A:RU7202 2.2 24.2 0.9 C3 A:RU7202 2.2 24.8 0.9 C2 A:RU7202 2.2 25.1 0.9 C1 A:RU7202 2.2 25.3 0.9 C4 A:RU7202 2.2 25.4 0.9 CL1 A:RU7202 2.4 27.1 0.9 CL2 A:RU7202 2.5 26.7 0.9 CE1 A:HIS15 3.1 20.6 1.0 CD2 A:HIS15 3.2 19.4 1.0 C7 A:RU7202 3.4 29.5 0.9 C8 A:RU7202 3.4 27.6 0.9 C10 A:RU7202 3.9 28.4 0.9 ND1 A:HIS15 4.2 19.9 1.0 CG A:HIS15 4.3 17.8 1.0 OD1 A:ASP87 4.6 22.6 1.0 C9 A:RU7202 4.7 30.4 0.9 OG1 A:THR89 4.9 19.0 1.0

Ruthenium binding site 2 out of 3 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru203 b:40.2 occ:0.50 RU1 A:RU7203 0.0 40.2 0.5 C6 A:RU7203 2.2 30.1 0.5 C3 A:RU7203 2.2 35.4 0.5 C2 A:RU7203 2.2 33.0 0.5 C5 A:RU7203 2.2 29.6 0.5 C1 A:RU7203 2.2 32.3 0.5 C4 A:RU7203 2.2 32.9 0.5 CL1 A:RU7203 2.4 41.0 0.5 CL1 A:RU7204 2.4 42.4 0.5 OD2 A:ASP101 2.6 33.3 1.0 RU1 A:RU7204 3.2 42.1 0.5 C7 A:RU7203 3.3 31.6 0.5 C8 A:RU7203 3.4 29.0 0.5 CG A:ASP101 3.5 34.5 1.0 OD1 A:ASP101 3.7 34.3 1.0 C10 A:RU7203 3.9 25.6 0.5 C9 A:RU7203 4.7 28.4 0.5 CB A:ASP101 4.9 30.0 1.0

Ruthenium binding site 3 out of 3 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru204 b:42.1 occ:0.50 RU1 A:RU7204 0.0 42.1 0.5 OD1 A:ASP101 2.2 34.3 1.0 CL1 A:RU7204 2.2 42.4 0.5 CL1 A:RU7203 2.6 41.0 0.5 CG A:ASP101 3.2 34.5 1.0 RU1 A:RU7203 3.2 40.2 0.5 OD2 A:ASP101 3.4 33.3 1.0 N A:GLY102 4.1 27.5 1.0 CB A:ASP101 4.5 30.0 1.0 C3 A:RU7203 4.5 35.4 0.5 C2 A:RU7203 4.6 33.0 0.5 CA A:GLY102 4.8 26.8 1.0 C4 A:RU7203 4.9 32.9 0.5 CA A:ASP101 5.0 27.8 1.0

M.P.Sullivan, M.Groessl, S.M.Meier, R.L.Kingston, D.C.Goldstone, C.G.Hartinger. The Metalation of Hen Egg White Lysozyme Impacts Protein Stability As Shown By Ion Mobility Mass Spectrometry, Differential Scanning Calorimetry, and X-Ray Crystallography. Chem. Commun. (Camb.) V. 53 4246 2017.
ISSN: ESSN 1364-548X
PubMed: 28361137
DOI: 10.1039/C6CC10150J