Sodium in PDB 7deq: Lysozyme-Sugar Complex in D2O

All present enzymatic activity of Lysozyme-Sugar Complex in D2O:
3.2.1.17;

The structure of Lysozyme-Sugar Complex in D2O, PDB code: 7deq 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)	34.45 / 1.03
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.029, 77.029, 38.285, 90, 90, 90
R / Rfree (%)	13.3 / 14.9

The structure of Lysozyme-Sugar Complex in D2O also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Lysozyme-Sugar Complex in D2O (pdb code 7deq). 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-Sugar Complex in D2O, PDB code: 7deq:

Sodium binding site 1 out of 1 in the Lysozyme-Sugar Complex in D2O


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme-Sugar Complex in D2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:11.5 occ:0.55 O A:SER60 2.3 13.8 1.0 O A:DOD391 2.4 13.1 1.0 O A:ARG73 2.5 19.1 1.0 O A:DOD395 2.5 19.6 1.0 OG A:SER72 2.5 21.1 1.0 O A:CYS64 2.5 11.5 1.0 CB A:SER72 3.3 21.9 1.0 C A:SER60 3.4 11.4 1.0 C A:ARG73 3.5 18.8 1.0 C A:CYS64 3.5 10.9 1.0 CA A:ASN65 3.9 11.6 1.0 N A:ARG73 4.0 20.9 1.0 CA A:SER60 4.1 9.8 1.0 C A:SER72 4.1 21.9 1.0 N A:ASN65 4.2 11.1 1.0 CB A:SER60 4.3 10.6 1.0 CA A:SER72 4.3 23.1 1.0 N A:ASN74 4.4 16.9 1.0 CA A:ARG73 4.4 20.1 1.0 O A:DOD423 4.5 36.5 1.0 N A:ARG61 4.5 12.0 1.0 N A:CYS64 4.5 11.2 1.0 C A:ARG61 4.5 13.3 1.0 CA A:ASN74 4.5 13.8 1.0 O A:ARG61 4.6 15.6 1.0 CB A:ASN74 4.6 13.2 1.0 O A:SER72 4.7 22.5 1.0 OD1 A:ASN65 4.7 15.3 1.0 CA A:CYS64 4.7 10.6 1.0 CA A:ARG61 4.7 14.3 1.0 CB A:THR69 4.7 12.1 1.0 CL A:CL203 4.7 16.4 0.6 N A:ASP66 4.7 10.7 1.0 CB A:ASN65 4.8 13.3 1.0 N A:TRP62 4.8 11.2 1.0 O A:THR69 4.9 17.8 1.0 C A:ASN65 4.9 10.4 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