Sodium in PDB 8ezo: Lysozyme Anomalous Dataset at 220 K and 7.1 Kev

All present enzymatic activity of Lysozyme Anomalous Dataset at 220 K and 7.1 Kev:
3.2.1.17;

The structure of Lysozyme Anomalous Dataset at 220 K and 7.1 Kev, PDB code: 8ezo was solved by T.Doukov, F.Yabukarski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.48 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	76.909, 76.909, 36.961, 90, 90, 90
R / Rfree (%)	15.6 / 19.1

The structure of Lysozyme Anomalous Dataset at 220 K and 7.1 Kev also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Sodium atom in the Lysozyme Anomalous Dataset at 220 K and 7.1 Kev (pdb code 8ezo). 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 Anomalous Dataset at 220 K and 7.1 Kev, PDB code: 8ezo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Lysozyme Anomalous Dataset at 220 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Anomalous Dataset at 220 K and 7.1 Kev within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:34.2 occ:0.78 O A:HOH340 2.1 30.7 1.0 O A:SER60 2.3 30.3 1.0 O A:HOH338 2.4 28.1 1.0 O A:ARG73 2.4 40.9 1.0 OG A:SER72 2.5 48.4 1.0 O A:CYS64 2.6 29.4 1.0 CB A:SER72 3.2 48.6 1.0 C A:SER60 3.5 28.1 1.0 C A:ARG73 3.5 41.1 1.0 C A:CYS64 3.7 24.4 1.0 N A:ARG73 3.8 41.5 1.0 CA A:ASN65 4.0 27.1 1.0 C A:SER72 4.1 46.4 1.0 CA A:SER60 4.1 25.7 1.0 CA A:ARG73 4.2 34.4 1.0 O A:ARG61 4.3 36.4 1.0 CA A:SER72 4.3 46.7 1.0 N A:ASN65 4.3 24.3 1.0 CB A:SER60 4.3 23.1 1.0 N A:ASN74 4.4 34.9 1.0 C A:ARG61 4.4 27.7 1.0 N A:ARG61 4.5 26.6 1.0 CL A:CL203 4.5 31.8 0.7 OD1 A:ASN65 4.6 34.9 1.0 CA A:ASN74 4.6 29.2 1.0 CA A:ARG61 4.7 26.9 0.5 CA A:ARG61 4.7 28.1 0.5 N A:CYS64 4.7 27.4 1.0 CB A:THR69 4.7 27.7 1.0 O A:SER72 4.7 45.5 1.0 N A:ASP66 4.8 26.0 1.0 CB A:ASN74 4.8 31.5 1.0 CB A:ASN65 4.8 27.9 1.0 O A:THR69 4.9 30.2 1.0 CA A:CYS64 4.9 25.3 1.0 N A:TRP62 4.9 26.4 1.0 C A:ASN65 4.9 30.3 1.0

Sodium binding site 2 out of 2 in the Lysozyme Anomalous Dataset at 220 K and 7.1 Kev


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme Anomalous Dataset at 220 K and 7.1 Kev within 5.0Å range: probe atom residue distance (Å) B Occ A:Na212 b:27.0 occ:0.74 O A:HOH324 2.4 25.7 1.0 O A:HOH376 2.4 29.0 1.0 O A:HOH319 2.4 23.3 1.0 OE1 A:GLU35 2.4 21.1 1.0 O A:HOH327 2.5 24.5 1.0 CD A:GLU35 3.6 19.4 1.0 O A:HOH304 4.1 24.4 1.0 OE2 A:GLU35 4.2 20.6 1.0 CA A:GLU35 4.2 18.9 1.0 O A:GLU35 4.3 23.3 1.0 CG A:GLN57 4.4 14.9 1.0 O A:PHE34 4.5 23.0 1.0 OE1 A:GLN57 4.5 18.5 1.0 OD2 A:ASP52 4.6 24.8 1.0 CG A:GLU35 4.6 19.1 1.0 CB A:GLU35 4.7 21.4 1.0 CB A:ALA110 4.7 22.3 1.0 C A:GLU35 4.7 17.5 1.0 CB A:GLN57 4.8 17.0 1.0 CD A:GLN57 5.0 17.3 1.0

T.Doukov, D.Herschlag, F.Yabukarski. Obtaining Anomalous and Ensemble Information From Protein Crystals From 220 K Up to Physiological Temperatures Acta Crystallogr.,Sect.D V. D79 212 2023.
ISSN: ESSN 1399-0047
DOI: 10.1107/S205979832300089X