Ruthenium in PDB 4uwv: Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8)

All present enzymatic activity of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8):
3.2.1.17;

The structure of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8), PDB code: 4uwv was solved by M.F.A.Santos, A.Mukhopadhyay, M.J.Romao, C.C.Romao, T.Santos-Silva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.26 / 1.77
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.220, 80.220, 37.160, 90.00, 90.00, 90.00
R / Rfree (%)	18.099 / 22.198

The structure of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8) also contains other interesting chemical elements:

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

The binding sites of Ruthenium atom in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8) (pdb code 4uwv). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8), PDB code: 4uwv:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru1132 b:49.5 occ:0.70 C A:CMO1135 2.3 29.3 0.7 NE2 A:HIS15 2.4 39.3 1.0 O A:HOH2124 2.4 31.0 0.7 O A:HOH2020 2.5 35.6 0.7 O A:HOH2018 2.6 29.7 0.7 O A:HOH2019 3.0 45.0 0.7 O A:CMO1135 3.0 32.3 0.7 CE1 A:HIS15 3.3 36.9 1.0 CD2 A:HIS15 3.4 35.5 1.0 OD1 A:ASP87 4.2 32.9 1.0 ND1 A:HIS15 4.4 34.6 1.0 CG A:HIS15 4.5 30.5 1.0 OG1 A:THR89 4.8 24.3 1.0

Ruthenium binding site 2 out of 3 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru1133 b:56.9 occ:0.65 OD1 A:ASP101 2.4 45.6 1.0 O A:HOH2102 2.6 45.3 1.0 O A:HOH2125 2.6 45.8 0.7 O A:HOH2099 2.6 30.6 0.7 OD2 A:ASP101 2.7 40.1 1.0 RU A:RU1134 2.8 81.0 0.7 CG A:ASP101 2.9 41.7 1.0 O A:HOH2100 3.0 33.5 0.7 O A:HOH2101 4.2 51.5 0.7 CB A:ASP101 4.4 34.9 1.0 CD1 A:LEU75 4.4 28.1 1.0 CH2 A:TRP63 4.7 22.1 1.0 O A:ASP101 4.8 34.2 1.0

Ruthenium binding site 3 out of 3 in the Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Lysozyme Soaked with A Ruthenium Based Corm with A Pyridine Ligand (Complex 8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru1134 b:81.0 occ:0.65 O A:HOH2101 1.6 51.5 0.7 OD2 A:ASP101 2.6 40.1 1.0 RU A:RU1133 2.8 56.9 0.7 O A:HOH2102 3.2 45.3 1.0 O A:HOH2125 3.6 45.8 0.7 CG A:ASP101 3.7 41.7 1.0 OD1 A:ASP101 4.2 45.6 1.0 CH2 A:TRP63 4.4 22.1 1.0 CD1 A:LEU75 4.4 28.1 1.0 O A:HOH2044 4.4 44.3 1.0 CZ2 A:TRP63 4.4 22.2 1.0 CE3 A:TRP62 4.6 42.5 1.0 CD2 A:TRP62 4.8 37.6 1.0 O A:HOH2100 4.9 33.5 0.7 CZ3 A:TRP62 4.9 48.5 1.0 CB A:ASP101 5.0 34.9 1.0

J.Seixas, M.F.A.Santos, A.Mukhopadhyay, A.C.Coelho, P.M.Reis, L.F.Veiros, A.R.Marques, N.Penacho, A.M.L.Goncalves, M.J Romao, G.J.L.Bernardes, T.Santos-Silva, C.C.Romao. A Contribution to the Rational Design of Ru(Co) 3CI2L Complexes For in Vivo Delivery of Co Dalton Trans 2014.
ISSN: ESSN 1477-9234
PubMed: 25427784
DOI: 10.1039/C4DT02966F