Sodium in PDB 8rny: Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]

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

The structure of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)], PDB code: 8rny 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)	19.13 / 1.02
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.883, 78.883, 37.026, 90, 90, 90
R / Rfree (%)	12.9 / 14.4

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

Chlorine	(Cl)	8 atoms
Ruthenium	(Ru)	2 atoms

The binding sites of Sodium atom in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] (pdb code 8rny). 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 with [H2IND][Trans-RUCL4(Dmso) (Hind)], PDB code: 8rny:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Hen Egg White Lysozyme Soaked with 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 Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:12.6 occ:1.00 O A:SER60 2.4 12.3 1.0 O A:CYS64 2.4 11.5 1.0 O A:HOH385 2.4 15.3 1.0 O A:ARG73 2.4 15.0 1.0 O A:HOH361 2.5 12.3 1.0 OG A:SER72 2.5 15.7 1.0 CB A:SER72 3.2 15.6 1.0 C A:ARG73 3.5 15.1 1.0 C A:CYS64 3.5 11.1 1.0 C A:SER60 3.5 11.1 1.0 CA A:ASN65 3.9 11.3 1.0 N A:ARG73 3.9 16.1 1.0 CA A:SER60 4.1 10.5 1.0 N A:ASN65 4.1 11.0 1.0 C A:SER72 4.2 16.6 1.0 CB A:SER60 4.2 11.1 1.0 CA A:ARG73 4.3 16.2 1.0 CA A:SER72 4.3 16.4 1.0 N A:ASN74 4.4 15.9 1.0 N A:CYS64 4.4 11.1 1.0 O A:HOH406 4.6 35.8 1.0 CA A:ASN74 4.6 14.7 1.0 O A:ARG61 4.6 16.5 1.0 C A:ARG61 4.6 15.0 1.0 N A:ARG61 4.6 11.9 1.0 N A:ASP66 4.6 10.6 1.0 CA A:CYS64 4.6 11.3 1.0 OD1 A:ASN65 4.7 13.7 1.0 CB A:ASN74 4.7 14.5 1.0 CL A:CL205 4.7 14.8 1.0 CB A:THR69 4.7 12.1 1.0 O A:SER72 4.8 18.4 1.0 CB A:ASN65 4.8 13.3 1.0 C A:ASN65 4.8 10.4 1.0 CA A:ARG61 4.8 14.4 1.0 N A:TRP62 4.9 13.0 1.0

Sodium binding site 2 out of 3 in the Hen Egg White Lysozyme Soaked with 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 Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range: probe atom residue distance (Å) B Occ A:Na212 b:85.3 occ:1.00 O A:HOH373 2.4 54.5 1.0 O A:HOH335 2.7 41.1 1.0 OD2 A:ASP87 2.9 27.1 1.0 OG1 A:THR89 3.2 17.8 1.0 NH2 A:ARG14 3.4 30.6 0.6 OD1 A:ASP87 3.4 20.5 1.0 CG A:ASP87 3.5 21.5 1.0 NE2 A:HIS15 3.8 26.0 1.0 CE1 A:HIS15 4.4 24.0 1.0 CZ A:ARG14 4.6 28.6 0.6 CB A:THR89 4.6 16.6 1.0 NH1 A:ARG14 4.9 25.3 0.6 CB A:ASP87 4.9 17.8 1.0 CD2 A:HIS15 5.0 25.3 1.0

Sodium binding site 3 out of 3 in the Hen Egg White Lysozyme Soaked with 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 Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range: probe atom residue distance (Å) B Occ A:Na213 b:64.0 occ:1.00 O A:HOH396 2.6 45.9 1.0 O A:HOH343 2.7 28.2 1.0 CL A:CL207 2.8 25.5 1.0 O A:HOH390 3.3 34.7 1.0 CE2 A:PHE3 3.9 14.2 1.0 NZ A:LYS1 3.9 19.8 0.7 CZ A:PHE3 4.0 14.9 1.0 O A:HOH356 4.1 24.4 1.0 CB A:ALA11 4.2 14.5 1.0 O A:HOH373 4.7 54.5 1.0 O A:HOH435 4.8 38.8 1.0 O A:SER86 4.9 16.7 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.