Sodium in PDB 5lvk: Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]

All present enzymatic activity of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]:
3.2.1.17;

The structure of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)], PDB code: 5lvk was solved by K.Kurpiewska, A.Szura, K.Lewinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.37 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.039, 64.100, 111.311, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 28.1

The structure of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] also contains other interesting chemical elements:

Ruthenium	(Ru)	2 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Sodium atom in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] (pdb code 5lvk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)], PDB code: 5lvk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:18.1 occ:1.00 O B:HOH403 2.6 12.9 1.0 O A:HOH332 2.8 14.3 1.0 O B:HOH323 2.9 5.7 1.0 ND2 A:ASN66 3.2 12.3 1.0 N B:TYR45 3.2 11.0 1.0 CG A:ASN66 3.6 8.2 1.0 O2 A:SO4201 3.6 9.4 1.0 CB B:TYR45 3.7 13.6 1.0 CB A:ASN66 3.7 7.5 1.0 ND2 A:ASN75 3.7 9.2 1.0 CA B:ASN44 3.8 9.6 1.0 C B:ASN44 4.0 11.7 1.0 CA B:TYR45 4.0 12.8 1.0 O3 A:SO4201 4.1 13.1 1.0 N B:ASN44 4.3 7.4 1.0 O B:THR43 4.4 5.4 1.0 S A:SO4201 4.4 16.8 1.0 OD1 A:ASN66 4.4 8.9 1.0 C B:THR43 4.5 7.0 1.0 OD1 B:ASN44 4.6 12.2 1.0 OG1 B:THR43 4.6 4.4 1.0 CG A:ASN75 4.7 11.8 1.0 O A:HOH307 4.7 22.5 1.0 O1 A:SO4201 4.8 9.0 1.0

Sodium binding site 2 out of 3 in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:26.4 occ:1.00 O B:HOH330 2.4 5.3 1.0 O A:HOH335 2.8 2.7 1.0 O B:HOH351 3.1 13.4 1.0 N B:GLY37 3.7 6.0 1.0 CB A:ARG98 3.8 2.9 1.0 O A:CYS77 3.8 4.1 1.0 C B:SER36 3.9 6.7 1.0 CA A:CYS77 3.9 7.1 1.0 CA B:GLY37 4.0 5.9 1.0 CG A:ARG98 4.0 1.7 1.0 O B:SER36 4.1 4.0 1.0 C A:CYS77 4.2 6.3 1.0 O B:LYS33 4.2 5.5 1.0 CD A:ARG98 4.3 7.7 1.0 CB A:CYS77 4.4 4.5 1.0 O A:ALA76 4.5 9.9 1.0 CA B:SER36 4.5 6.3 1.0 O A:ALA94 4.6 11.6 1.0 O B:TRP34 4.6 11.4 1.0 SG A:CYS77 4.6 3.2 1.0 O A:HOH345 4.6 6.6 1.0 N B:SER36 4.7 9.2 1.0 NH2 A:ARG101 5.0 11.2 1.0

Sodium binding site 3 out of 3 in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:14.2 occ:1.00 O B:HOH345 2.7 5.0 1.0 ND2 B:ASN88 2.8 8.9 1.0 N B:ASP91 2.8 3.7 1.0 O B:HOH356 3.0 12.1 1.0 O B:ASN88 3.1 8.0 1.0 CG B:ASP91 3.2 12.5 1.0 O B:HOH335 3.2 7.0 1.0 CB B:ASP91 3.3 9.1 1.0 N B:ALA90 3.4 7.6 1.0 OD1 B:ASP91 3.5 6.1 1.0 OD2 B:ASP91 3.6 13.8 1.0 CA B:ASP91 3.6 7.4 1.0 C B:ASN88 3.7 6.5 1.0 C B:ALA90 3.8 5.2 1.0 CB B:ALA90 3.8 7.1 1.0 CA B:ALA90 3.8 6.9 1.0 CG B:ASN88 3.9 11.6 1.0 C B:ILE89 4.1 7.8 1.0 CB B:ASN88 4.1 8.9 1.0 N B:ILE89 4.2 9.1 1.0 CA B:ILE89 4.4 7.0 1.0 CA B:ASN88 4.6 5.9 1.0 C B:ASP91 4.7 5.8 1.0 N B:ALA92 4.7 9.0 1.0 O B:ALA83 4.8 9.9 1.0 O B:ILE89 4.9 10.2 1.0 O B:ALA90 4.9 6.2 1.0 OD1 B:ASN88 5.0 12.7 1.0

M.Oszajca, K.Kurpiewska, P.Halajko, A.Szura, K.Lewinski, M.Brindell. Ligand-Dependent Interaction of Anticancer Ruthenium Complexes with Hen Egg White Lysozyme and Human Lysozyme To Be Published.