Sodium in PDB 4d9z: Lysozyme at 318K

All present enzymatic activity of Lysozyme at 318K:
3.2.1.17;

The structure of Lysozyme at 318K, PDB code: 4d9z was solved by P.Sharma, Ashish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.36 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.010, 55.954, 72.484, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.8

The structure of Lysozyme at 318K also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Lysozyme at 318K (pdb code 4d9z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Lysozyme at 318K, PDB code: 4d9z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Lysozyme at 318K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme at 318K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:25.2 occ:1.00 O A:HOH412 3.5 36.4 1.0 ND2 A:ASN113 3.5 20.4 1.0 NH1 A:ARG114 3.5 19.8 0.5 NE A:ARG114 3.7 18.5 0.5 CA A:ALA110 3.8 14.0 1.0 CG1 A:VAL109 4.0 23.2 1.0 CZ A:ARG114 4.1 18.0 0.5 CB A:ASN113 4.1 17.0 1.0 N A:ALA110 4.2 14.5 1.0 O A:VAL109 4.2 15.6 1.0 CB A:ALA110 4.2 15.2 1.0 CD A:ARG114 4.3 17.1 0.5 CG A:ASN113 4.3 18.5 1.0 C A:VAL109 4.3 13.9 1.0 CG A:ARG114 4.7 16.5 0.5 O A:HOH410 4.7 29.9 1.0 CD A:ARG114 4.9 18.8 0.5 C A:ALA110 4.9 16.0 1.0 CB A:VAL109 5.0 23.3 1.0

Sodium binding site 2 out of 2 in the Lysozyme at 318K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme at 318K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:34.6 occ:1.00 NZ A:LYS96 3.4 17.5 1.0 O A:HIS15 3.5 16.1 1.0 C A:HIS15 3.8 17.4 1.0 O A:HOH352 3.8 31.6 1.0 CA A:GLY16 3.9 15.3 1.0 O A:HOH409 3.9 31.6 1.0 N A:GLY16 4.1 12.7 1.0 CA A:HIS15 4.6 12.9 1.0 CE A:LYS96 4.8 12.0 1.0 O A:ARG14 4.8 17.7 1.0 C A:GLY16 4.9 16.7 1.0

P.Sharma, N.Verma, P.K.Singh, S.Korpole, Ashish. Characterization of Heat Induced Spherulites of Lysozyme Reveals New Insight on Amyloid Initiation Sci Rep V. 6 22475 2016.
ISSN: ESSN 2045-2322
PubMed: 26926993
DOI: 10.1038/SREP22475