Sodium in PDB 8ezu: Lysozyme Anomalous Dataset at 273 K and 7.1 Kev

All present enzymatic activity of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev:
3.2.1.17;

The structure of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev, PDB code: 8ezu was solved by T.Doukov, F.Yabukarski, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.66 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.322, 77.322, 37.082, 90, 90, 90
R / Rfree (%)	13.3 / 17.1

The structure of Lysozyme Anomalous Dataset at 273 K and 7.1 Kev also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

The binding sites of Sodium atom in the Lysozyme Anomalous Dataset at 273 K and 7.1 Kev (pdb code 8ezu). 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 273 K and 7.1 Kev, PDB code: 8ezu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:29.9 occ:0.88 O A:HOH362 2.3 27.0 1.0 O A:SER60 2.3 20.6 1.0 O A:ARG73 2.4 29.2 1.0 OG A:SER72 2.5 37.6 1.0 O A:HOH349 2.5 22.1 1.0 O A:CYS64 2.6 17.4 1.0 CB A:SER72 3.2 36.4 1.0 C A:ARG73 3.4 36.8 1.0 C A:SER60 3.5 19.8 1.0 C A:CYS64 3.6 19.1 1.0 N A:ARG73 3.9 29.6 1.0 CA A:ASN65 3.9 20.3 1.0 C A:SER72 4.0 36.1 1.0 CA A:SER60 4.1 17.0 1.0 N A:ASN65 4.2 18.7 1.0 CA A:SER72 4.2 40.1 1.0 CA A:ARG73 4.3 30.5 1.0 N A:ASN74 4.3 29.1 1.0 CB A:SER60 4.4 17.5 1.0 O A:ARG61 4.5 25.1 1.0 C A:ARG61 4.5 21.6 1.0 CA A:ASN74 4.5 22.8 1.0 N A:ARG61 4.5 19.5 1.0 N A:CYS64 4.6 19.4 1.0 O A:SER72 4.6 34.4 1.0 OD1 A:ASN65 4.6 29.9 1.0 CL A:CL203 4.6 21.9 0.5 CB A:ASN74 4.7 23.1 1.0 CA A:CYS64 4.7 16.8 1.0 N A:ASP66 4.8 19.9 1.0 CA A:ARG61 4.8 21.5 0.5 CB A:THR69 4.8 22.5 1.0 CA A:ARG61 4.8 22.4 0.5 CB A:ASN65 4.8 22.1 1.0 N A:TRP62 4.8 20.4 1.0 C A:ASN65 4.9 20.1 1.0

Sodium binding site 2 out of 2 in the Lysozyme Anomalous Dataset at 273 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 273 K and 7.1 Kev within 5.0Å range: probe atom residue distance (Å) B Occ A:Na214 b:37.3 occ:0.66 O A:HOH352 2.1 41.5 1.0 O A:HOH327 2.3 26.4 1.0 O A:HOH371 2.4 42.3 1.0 O A:HOH331 2.5 25.9 1.0 OE1 A:GLU35 2.6 18.8 1.0 CD A:GLU35 3.8 17.5 1.0 O A:GLU35 4.0 15.7 1.0 O A:HOH302 4.2 31.9 1.0 CA A:GLU35 4.2 14.9 1.0 OE1 A:GLN57 4.4 15.8 1.0 CG A:GLN57 4.4 16.0 1.0 OE2 A:GLU35 4.4 20.1 1.0 O A:PHE34 4.6 20.2 1.0 C A:GLU35 4.6 17.2 1.0 OD2 A:ASP52 4.7 24.0 1.0 CB A:GLU35 4.7 16.3 1.0 CB A:GLN57 4.7 17.2 1.0 CG A:GLU35 4.8 17.2 1.0 CD A:GLN57 4.9 15.5 1.0 CB A:ALA110 4.9 22.8 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