Ruthenium in PDB 6txg: Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound

All present enzymatic activity of Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound:
3.4.21.64;

The structure of Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound, PDB code: 6txg was solved by L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.26 / 1.37
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.708, 67.708, 107.314, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 16.8

The structure of Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Ruthenium atom in the Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound (pdb code 6txg). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound, PDB code: 6txg:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in the Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru307 b:15.4 occ:0.54 RU A:NYN307 0.0 15.4 0.5 OD1 A:ASP200 2.1 13.0 1.0 N1 A:NYN307 2.1 14.6 0.5 N2 A:NYN307 2.1 20.4 0.5 S2 A:NYN307 2.3 18.2 0.5 S3 A:NYN307 2.3 16.0 0.5 S1 A:NYN307 2.3 18.6 0.5 H032 A:NYN307 2.6 17.5 0.5 H031 A:NYN307 2.6 17.5 0.5 H041 A:NYN307 2.6 24.5 0.5 H042 A:NYN307 2.6 24.5 0.5 CA A:CA306 2.7 11.2 0.5 C2 A:NYN307 3.0 20.0 0.5 C1 A:NYN307 3.0 18.9 0.5 O A:HOH607 3.0 19.9 0.5 CG A:ASP200 3.1 9.5 1.0 C3 A:NYN307 3.2 21.7 0.5 C7 A:NYN307 3.2 19.2 0.5 C4 A:NYN307 3.2 23.9 0.5 C6 A:NYN307 3.2 15.1 0.5 C5 A:NYN307 3.3 19.4 0.5 C8 A:NYN307 3.3 16.3 0.5 H14 A:NYN307 3.5 24.0 0.5 OD2 A:ASP200 3.6 9.9 1.0 H12 A:NYN307 3.6 22.6 0.5 H13 A:NYN307 3.6 22.6 0.5 H8 A:NYN307 3.7 23.0 0.5 H15 A:NYN307 3.7 24.0 0.5 H4 A:NYN307 3.8 23.3 0.5 H2 A:NYN307 3.8 28.6 0.5 H6 A:NYN307 3.8 18.1 0.5 H17 A:NYN307 3.8 26.1 0.5 H11 A:NYN307 3.9 19.5 0.5 H16 A:NYN307 3.9 26.1 0.5 H10 A:NYN307 3.9 19.5 0.5 O A:HOH605 3.9 23.8 1.0 H3 A:NYN307 3.9 28.6 0.5 H7 A:NYN307 4.0 18.1 0.5 H5 A:NYN307 4.0 23.3 0.5 H9 A:NYN307 4.0 23.0 0.5 O A:PRO175 4.2 17.1 1.0 O A:HOH447 4.2 16.0 0.5 CB A:ASP200 4.4 10.5 1.0 O A:HOH493 4.8 14.8 1.0 CA A:ASP200 4.9 9.1 1.0 O A:VAL177 5.0 14.5 1.0

Ruthenium binding site 2 out of 2 in the Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Proteinase K in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru309 b:19.1 occ:0.39 RU A:NYN309 0.0 19.1 0.4 O A:HOH619 2.0 19.3 0.6 NA A:NA308 2.1 8.5 0.6 N2 A:NYN309 2.1 23.3 0.4 N1 A:NYN309 2.1 16.8 0.4 OD1 A:ASP260 2.3 38.4 1.0 S2 A:NYN309 2.3 25.1 0.4 S1 A:NYN309 2.3 20.4 0.4 S3 A:NYN309 2.3 19.6 0.4 H042 A:NYN309 2.6 28.0 0.4 H041 A:NYN309 2.6 28.0 0.4 H032 A:NYN309 2.6 20.1 0.4 H031 A:NYN309 2.6 20.1 0.4 CG A:ASP260 2.8 37.6 1.0 C2 A:NYN309 3.0 20.3 0.4 C1 A:NYN309 3.0 15.8 0.4 OD2 A:ASP260 3.1 42.4 1.0 C8 A:NYN309 3.2 23.7 0.4 C7 A:NYN309 3.2 22.9 0.4 C6 A:NYN309 3.2 23.9 0.4 C3 A:NYN309 3.3 23.1 0.4 C4 A:NYN309 3.3 24.6 0.4 C5 A:NYN309 3.3 24.5 0.4 H15 A:NYN309 3.5 24.4 0.4 H13 A:NYN309 3.6 18.9 0.4 H12 A:NYN309 3.6 18.9 0.4 H7 A:NYN309 3.7 28.6 0.4 O A:HOH656 3.7 17.9 0.6 H14 A:NYN309 3.7 24.4 0.4 H10 A:NYN309 3.7 28.4 0.4 H9 A:NYN309 3.8 27.4 0.4 H2 A:NYN309 3.8 29.5 0.4 H17 A:NYN309 3.9 27.7 0.4 H5 A:NYN309 3.9 29.4 0.4 H16 A:NYN309 3.9 27.7 0.4 H8 A:NYN309 3.9 27.4 0.4 H4 A:NYN309 3.9 29.4 0.4 CB A:ASP260 4.0 21.2 1.0 H11 A:NYN309 4.0 28.4 0.4 H3 A:NYN309 4.0 29.5 0.4 H6 A:NYN309 4.0 28.6 0.4 O A:HOH615 4.1 12.5 0.6 O A:HOH401 4.2 30.2 1.0 O A:THR16 4.3 26.3 1.0 CA A:ASP260 4.4 19.0 1.0 O A:HOH419 4.9 18.9 1.0 N A:ASP260 5.0 17.2 1.0

L.Chiniadis, I.Bratsos, K.Bethanis, M.Karpusas, P.Giastas, A.Papakyriakou. High-Resolution Crystal Structures of A "Half Sandwich"-Type Ru(II) Coordination Compound Bound to Hen Egg-White Lysozyme and Proteinase K. J.Biol.Inorg.Chem. 2020.
ISSN: ESSN 1432-1327
PubMed: 32266561
DOI: 10.1007/S00775-020-01786-Z