Sodium in PDB 8f0b: Lysozyme Anomalous Dataset at 240 K and 7.1 Kev

All present enzymatic activity of Lysozyme Anomalous Dataset at 240 K and 7.1 Kev:
3.2.1.17;

The structure of Lysozyme Anomalous Dataset at 240 K and 7.1 Kev, PDB code: 8f0b 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)	34.51 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.106, 77.106, 37.042, 90, 90, 90
R / Rfree (%)	13.7 / 19.8

The structure of Lysozyme Anomalous Dataset at 240 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 240 K and 7.1 Kev (pdb code 8f0b). 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 240 K and 7.1 Kev, PDB code: 8f0b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Lysozyme Anomalous Dataset at 240 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 240 K and 7.1 Kev within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:30.0 occ:0.78 O A:HOH354 2.2 25.8 1.0 O A:SER60 2.2 24.4 1.0 OG A:SER72 2.4 40.7 1.0 O A:ARG73 2.5 32.1 1.0 O A:HOH345 2.5 21.1 1.0 O A:CYS64 2.6 16.8 1.0 CB A:SER72 3.3 50.4 1.0 C A:SER60 3.4 22.1 1.0 C A:ARG73 3.4 34.1 1.0 C A:CYS64 3.7 17.1 1.0 N A:ARG73 3.8 33.0 1.0 C A:SER72 4.0 46.8 1.0 CA A:ASN65 4.0 18.5 1.0 CA A:SER60 4.1 18.0 1.0 CA A:ARG73 4.2 28.3 1.0 CA A:SER72 4.3 47.6 1.0 O A:ARG61 4.3 30.8 1.0 N A:ASN65 4.3 17.7 1.0 CB A:SER60 4.3 14.8 1.0 N A:ASN74 4.4 22.4 1.0 C A:ARG61 4.4 27.4 1.0 N A:ARG61 4.4 22.7 1.0 CL A:CL203 4.6 28.1 0.7 O A:SER72 4.6 38.2 1.0 CA A:ARG61 4.6 25.9 0.5 CA A:ASN74 4.6 21.2 1.0 N A:CYS64 4.6 20.2 1.0 OD1 A:ASN65 4.7 25.3 1.0 CA A:ARG61 4.7 26.3 0.5 CB A:THR69 4.7 19.0 1.0 N A:ASP66 4.7 17.4 1.0 CA A:CYS64 4.8 17.7 1.0 CB A:ASN74 4.8 22.2 1.0 N A:TRP62 4.9 24.6 1.0 CB A:ASN65 4.9 21.9 1.0 O A:THR69 4.9 22.1 1.0 C A:ASN65 5.0 17.3 1.0

Sodium binding site 2 out of 2 in the Lysozyme Anomalous Dataset at 240 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 240 K and 7.1 Kev within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:18.6 occ:0.41 O A:HOH340 2.2 37.2 1.0 O A:HOH392 2.2 46.5 1.0 O A:HOH338 2.4 23.1 1.0 O A:HOH341 2.5 24.1 1.0 OE1 A:GLU35 2.6 21.3 1.0 CD A:GLU35 3.7 17.4 1.0 O A:HOH301 4.0 26.4 1.0 O A:GLU35 4.1 18.2 1.0 CA A:GLU35 4.3 17.3 1.0 OE2 A:GLU35 4.4 18.0 1.0 O A:HOH332 4.4 36.5 1.0 CG A:GLN57 4.4 14.5 1.0 OE1 A:GLN57 4.5 17.4 1.0 O A:PHE34 4.6 22.8 1.0 OD2 A:ASP52 4.7 21.5 1.0 C A:GLU35 4.7 18.6 1.0 CB A:GLN57 4.8 17.3 1.0 CG A:GLU35 4.8 17.1 1.0 CB A:GLU35 4.8 18.1 1.0 CB A:ALA110 4.8 22.8 1.0 CD A:GLN57 5.0 15.3 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