Sodium in PDB 5fel: Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method

All present enzymatic activity of Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method:
3.2.1.17;

The structure of Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method, PDB code: 5fel was solved by S.Tsujino, T.Tomizaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.01 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.020, 80.020, 37.690, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 19.9

The structure of Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method (pdb code 5fel). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method, PDB code: 5fel:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:24.7 occ:1.00 OG A:SER91 2.9 17.6 1.0 O A:TYR53 2.9 13.6 1.0 N A:LEU56 3.1 15.2 1.0 N A:ILE55 3.4 13.2 1.0 C A:GLY54 3.5 13.3 1.0 CA A:GLY54 3.6 13.7 1.0 CB A:SER91 3.6 17.8 1.0 N A:GLN57 3.6 13.8 1.0 CA A:LEU56 3.7 14.7 1.0 CB A:LEU56 3.8 18.5 1.0 CD1 A:ILE58 3.8 19.0 1.0 C A:LEU56 3.8 16.2 1.0 CG1 A:ILE58 3.9 15.8 1.0 C A:TYR53 3.9 13.8 1.0 O A:GLY54 4.1 12.9 1.0 O A:HOH302 4.1 27.4 1.0 CG2 A:ILE55 4.1 20.2 1.0 C A:ILE55 4.1 14.7 1.0 N A:GLY54 4.2 13.0 1.0 O A:LEU83 4.2 20.6 1.0 N A:ILE58 4.2 13.7 1.0 CA A:ILE55 4.2 15.3 1.0 CB A:LEU83 4.3 18.6 1.0 CB A:ILE58 4.3 15.8 1.0 CA A:SER91 4.4 16.2 1.0 CD2 A:LEU83 4.6 22.2 1.0 CA A:GLN57 4.7 12.5 1.0 O A:LEU56 4.7 14.6 1.0 CB A:ILE55 4.8 19.2 1.0 CG A:LEU83 4.8 20.1 1.0 CG A:LEU56 4.8 19.6 1.0 CD1 A:LEU83 4.9 21.4 1.0 CA A:ILE58 4.9 15.0 1.0 C A:GLN57 4.9 14.2 1.0 CA A:LEU83 5.0 18.3 1.0

Sodium binding site 2 out of 2 in the Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hen Egg Lysozyme at Room Temperature Solved From Dataset Acquired By Oscillation Method within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:19.9 occ:1.00 O A:SER60 2.4 18.9 1.0 O A:CYS64 2.4 16.9 1.0 O A:ARG73 2.5 22.3 1.0 O A:HOH330 2.5 19.5 1.0 O A:HOH331 2.5 24.2 1.0 OG A:SER72 2.6 22.6 1.0 CB A:SER72 3.3 23.5 1.0 C A:CYS64 3.4 15.4 1.0 C A:SER60 3.5 16.4 1.0 C A:ARG73 3.6 23.4 1.0 CA A:ASN65 3.9 17.5 1.0 N A:ARG73 4.0 22.3 1.0 N A:ASN65 4.1 15.9 1.0 CA A:SER60 4.1 13.3 1.0 C A:SER72 4.2 27.9 1.0 CA A:SER72 4.3 24.9 1.0 CB A:SER60 4.4 13.9 1.0 CA A:ARG73 4.4 24.1 1.0 N A:ASN74 4.4 22.1 1.0 N A:CYS64 4.4 14.2 1.0 C A:ARG61 4.5 21.8 1.0 O A:ARG61 4.5 24.0 1.0 CA A:ASN74 4.6 20.5 1.0 CA A:CYS64 4.6 14.2 1.0 N A:ARG61 4.6 15.8 1.0 CB A:ASN74 4.7 21.6 1.0 N A:ASP66 4.7 15.3 1.0 OD1 A:ASN65 4.7 26.7 1.0 O A:SER72 4.7 27.4 1.0 CB A:THR69 4.7 17.6 1.0 CL A:CL202 4.7 34.0 1.0 CA A:ARG61 4.8 20.3 1.0 CB A:ASN65 4.8 19.6 1.0 C A:ASN65 4.9 15.5 1.0 N A:TRP62 4.9 19.4 1.0

S.Tsujino, T.Tomizaki. Ultrasonic Acoustic Levitation For Fast Frame Rate X-Ray Protein Crystallography at Room Temperature. Sci Rep V. 6 25558 2016.
ISSN: ESSN 2045-2322
PubMed: 27150272
DOI: 10.1038/SREP25558