Ruthenium in PDB 2xjw: Lysozyme-Co Releasing Molecule Adduct

All present enzymatic activity of Lysozyme-Co Releasing Molecule Adduct:
3.2.1.17;

The structure of Lysozyme-Co Releasing Molecule Adduct, PDB code: 2xjw was solved by T.Santos-Silva, A.Mukhopadhyay, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.76 / 1.67
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.400, 78.400, 36.970, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.8

The structure of Lysozyme-Co Releasing Molecule Adduct also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Ruthenium atom in the Lysozyme-Co Releasing Molecule Adduct (pdb code 2xjw). 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-Co Releasing Molecule Adduct, PDB code: 2xjw:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the Lysozyme-Co Releasing Molecule Adduct


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Lysozyme-Co Releasing Molecule Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru1130 b:29.6 occ:0.80 C A:CMO1135 1.8 19.3 0.8 C A:CMO1134 1.9 29.7 0.8 O A:HOH2019 2.1 30.1 0.8 NE2 A:HIS15 2.2 33.4 1.0 O A:HOH2020 2.3 20.6 0.8 O A:HOH2007 2.3 33.4 0.8 O A:CMO1134 2.9 28.4 0.8 O A:CMO1135 3.0 19.5 0.8 CE1 A:HIS15 3.1 36.9 1.0 CD2 A:HIS15 3.3 26.5 1.0 ND1 A:HIS15 4.3 35.4 1.0 CG A:HIS15 4.4 29.4 1.0 OD2 A:ASP87 4.5 39.2 1.0 OD1 A:ASP87 4.8 32.5 1.0 CG A:ASP87 4.9 34.7 1.0 CG A:ARG14 4.9 33.3 1.0

Ruthenium binding site 2 out of 3 in the Lysozyme-Co Releasing Molecule Adduct


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Lysozyme-Co Releasing Molecule Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru1131 b:41.7 occ:0.50 C A:CMO1136 1.9 42.2 0.5 C A:CMO1141 1.9 36.5 0.5 O A:HOH2024 2.1 21.7 0.5 OD2 A:ASP18 2.1 36.6 1.0 O A:HOH2025 2.1 63.1 0.5 O A:HOH2148 2.2 32.2 0.5 CG A:ASP18 2.9 31.3 1.0 OD1 A:ASP18 3.0 34.5 1.0 O A:CMO1136 3.1 38.4 0.5 O A:CMO1141 3.2 36.1 0.5 ND2 A:ASN19 4.3 32.5 0.5 CB A:ASP18 4.4 27.7 1.0 CE A:LYS13 4.8 43.2 1.0

Ruthenium binding site 3 out of 3 in the Lysozyme-Co Releasing Molecule Adduct


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Lysozyme-Co Releasing Molecule Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru1132 b:32.7 occ:0.40 C A:CMO1137 1.9 19.9 0.4 C A:CMO1142 2.0 22.3 0.4 O A:HOH2149 2.2 28.1 0.4 OD2 A:ASP52 2.2 28.0 1.0 O A:HOH2047 2.2 28.7 1.0 O A:HOH2075 2.3 20.9 1.0 O A:CMO1142 3.1 24.5 0.4 CG A:ASP52 3.1 20.8 1.0 O A:CMO1137 3.1 15.3 0.4 O A:HOH2126 3.2 29.0 1.0 OD1 A:ASP52 3.5 17.7 1.0 O A:HOH2048 4.0 29.3 1.0 O A:GLN57 4.0 14.5 1.0 O A:HOH2077 4.2 17.7 1.0 O A:HOH2067 4.3 36.2 1.0 CB A:ASP52 4.3 12.6 1.0 OD1 A:ASN46 4.5 25.8 1.0 OE1 A:GLU35 4.5 17.2 1.0 O A:HOH2018 4.7 34.2 1.0 CB A:GLN57 4.8 11.7 1.0 ND2 A:ASN59 4.8 26.7 0.6 ND2 A:ASN46 4.9 19.2 1.0 CG1 A:VAL109 5.0 19.3 0.5

T.Santos-Silva, A.Mukhopadhyay, J.D.Seixas, G.J.Bernardes, C.C.Romao, M.J.Romao. Corm-3 Reactivity Toward Proteins: the Crystal Structure of A Ru(II) Dicarbonyl-Lysozyme Complex. J.Am.Chem.Soc. V. 133 1192 2011.
ISSN: ISSN 0002-7863
PubMed: 21204537
DOI: 10.1021/JA108820S