Sodium in PDB 7der: Lysozyme Alone in H2O

All present enzymatic activity of Lysozyme Alone in H2O:
3.2.1.17;

The structure of Lysozyme Alone in H2O, PDB code: 7der was solved by I.Tanaka, T.Chatake, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.56 / 1.03
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.777, 78.777, 37.093, 90, 90, 90
R / Rfree (%)	14.9 / 17.3

The structure of Lysozyme Alone in H2O also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Lysozyme Alone in H2O (pdb code 7der). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Lysozyme Alone in H2O, PDB code: 7der:

Sodium binding site 1 out of 1 in the Lysozyme Alone in H2O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Alone in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:15.3 occ:1.00 O A:SER60 2.2 16.8 1.0 O A:HOH438 2.3 18.7 1.0 O A:HOH391 2.4 13.9 1.0 O A:ARG73 2.5 19.8 1.0 OG A:SER72 2.5 18.1 1.0 O A:CYS64 2.6 12.0 1.0 CB A:SER72 3.3 18.4 1.0 C A:SER60 3.3 15.2 1.0 C A:ARG73 3.5 18.4 1.0 C A:CYS64 3.7 11.3 1.0 N A:ARG73 3.9 19.9 1.0 CA A:SER60 4.0 11.7 1.0 CA A:ASN65 4.1 11.9 1.0 C A:SER72 4.2 18.9 1.0 CB A:SER60 4.2 11.6 1.0 CA A:ARG73 4.3 18.8 1.0 N A:ASN65 4.3 11.6 1.0 CA A:SER72 4.3 18.3 1.0 N A:ARG61 4.4 17.8 1.0 N A:ASN74 4.4 17.0 1.0 C A:ARG61 4.5 18.3 1.0 CB A:THR69 4.5 13.7 1.0 O A:ARG61 4.6 18.4 1.0 N A:CYS64 4.7 12.8 1.0 N A:ASP66 4.7 10.5 1.0 CA A:ARG61 4.7 19.9 1.0 CA A:ASN74 4.7 16.4 1.0 OD1 A:ASN65 4.7 16.6 1.0 CL A:CL204 4.7 16.4 1.0 N A:TRP62 4.8 16.1 1.0 O A:SER72 4.8 20.6 1.0 O A:THR69 4.8 16.3 1.0 CA A:CYS64 4.8 11.8 1.0 CB A:ASN74 4.9 16.4 1.0 CB A:ASN65 4.9 14.2 1.0 C A:ASN65 4.9 10.6 1.0 OG1 A:THR69 5.0 12.7 1.0 OG A:SER60 5.0 10.6 1.0 CG2 A:THR69 5.0 14.9 1.0

I.Tanaka, R.Nishinomiya, R.Goto, S.Shimazaki, T.Chatake. Recent Structural Insights Into the Mechanism of Lysozyme Hydrolysis. Acta Crystallogr D Struct V. 77 288 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 33645532
DOI: 10.1107/S2059798321000346