Sodium in PDB 8rnv: Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2

All present enzymatic activity of Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2:
3.2.1.17;

The structure of Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2, PDB code: 8rnv was solved by M.Oszajca, M.Flejszar, A.Szura, P.Drozdz, M.Brindell, K.Kurpiewska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.06 / 1.08
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.542, 78.542, 37.106, 90, 90, 90
R / Rfree (%)	15.4 / 16.7

The structure of Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2 also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2 (pdb code 8rnv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2, PDB code: 8rnv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:14.9 occ:0.63 O A:SER60 2.3 19.4 1.0 O A:HOH384 2.4 22.7 1.0 O A:HOH369 2.4 16.6 1.0 O A:ARG73 2.5 26.9 1.0 OG A:SER72 2.5 24.2 1.0 O A:CYS64 2.5 15.3 1.0 CB A:SER72 3.2 24.1 1.0 C A:SER60 3.4 18.4 1.0 C A:ARG73 3.5 23.8 1.0 C A:CYS64 3.6 15.1 1.0 N A:ARG73 3.9 23.3 1.0 CA A:ASN65 4.0 15.4 1.0 CA A:SER60 4.0 14.8 1.0 C A:SER72 4.2 24.1 1.0 N A:ASN65 4.2 14.8 1.0 CB A:SER60 4.3 14.7 1.0 CA A:SER72 4.3 24.2 1.0 CA A:ARG73 4.3 23.7 1.0 N A:ASN74 4.4 21.6 1.0 O A:ARG61 4.5 21.3 0.6 C A:ARG61 4.5 20.4 0.6 N A:ARG61 4.5 18.5 0.6 N A:ARG61 4.5 19.3 0.5 N A:CYS64 4.5 15.2 1.0 C A:ARG61 4.5 20.6 0.5 O A:ARG61 4.6 21.5 0.5 CA A:ASN74 4.6 19.4 1.0 CB A:THR69 4.7 16.7 1.0 N A:ASP66 4.7 13.9 1.0 OD1 A:ASN65 4.7 19.0 1.0 CA A:CYS64 4.7 14.8 1.0 CA A:ARG61 4.7 21.0 0.6 NA A:NA207 4.7 18.4 1.0 CB A:ASN74 4.7 19.7 1.0 CA A:ARG61 4.8 21.7 0.5 O A:SER72 4.8 25.0 1.0 N A:TRP62 4.8 19.6 1.0 CB A:ASN65 4.9 16.2 1.0 C A:ASN65 4.9 13.9 1.0 O A:THR69 5.0 19.5 1.0

Sodium binding site 2 out of 3 in the Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:36.9 occ:1.00 NZ A:LYS33 3.6 24.6 1.0 CE2 A:PHE38 3.7 16.5 1.0 CZ3 A:TRP123 4.0 22.2 1.0 CE A:LYS33 4.0 22.9 1.0 CD A:LYS33 4.2 20.2 1.0 CZ A:PHE38 4.4 16.3 1.0 CD A:ARG5 4.4 23.8 1.0 CB A:ARG5 4.5 22.9 1.0 CD2 A:PHE38 4.6 16.3 1.0 CE3 A:TRP123 4.8 20.4 1.0 CH2 A:TRP123 4.8 23.2 1.0 CG A:ARG5 4.9 23.4 1.0

Sodium binding site 3 out of 3 in the Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hen Egg White Lysozyme Soaked with Cis-Ru(Dmso)4CL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:18.4 occ:1.00 N A:THR69 3.1 16.5 1.0 O A:THR69 3.1 19.5 1.0 O A:HOH416 3.2 34.5 1.0 O A:HOH369 3.2 16.6 1.0 N A:ARG68 3.5 16.9 1.0 O A:HOH353 3.5 42.4 1.0 C A:GLY67 3.5 16.9 1.0 C A:THR69 3.6 18.7 1.0 CA A:GLY67 3.7 17.1 1.0 OG A:SER72 3.7 24.2 1.0 N A:GLY67 3.7 15.7 1.0 OD1 A:ASN65 3.7 19.0 1.0 CA A:THR69 3.8 16.8 1.0 O A:HOH384 4.0 22.7 1.0 C A:ARG68 4.1 18.3 1.0 CB A:THR69 4.1 16.7 1.0 O A:GLY67 4.1 18.9 1.0 CA A:ARG68 4.2 17.2 1.0 OD1 A:ASP66 4.3 14.1 1.0 N A:PRO70 4.5 20.3 1.0 NA A:NA205 4.7 14.9 0.6 OG1 A:THR69 4.8 16.1 1.0 C A:ASP66 4.8 14.8 1.0 O A:HOH349 4.9 31.1 0.7 N A:ASP66 4.9 13.9 1.0 CB A:SER72 4.9 24.1 1.0 CG A:ASN65 4.9 18.4 1.0 CA A:PRO70 5.0 22.1 1.0

M.Oszajca, M.Flejszar, A.Szura, P.Drozdz, M.Brindell, K.Kurpiewska. Exploring the Coordination Chemistry of Ruthenium Complexes with Lysozymes: Structural and in Solution Studies To Be Published.