Sodium in PDB 5b5j: Hen Egg White Lysozyme with Boron Tracedrug Utx-97

All present enzymatic activity of Hen Egg White Lysozyme with Boron Tracedrug Utx-97:
3.2.1.17;

The structure of Hen Egg White Lysozyme with Boron Tracedrug Utx-97, PDB code: 5b5j was solved by Y.Morimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.76 / 1.26
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.440, 78.440, 37.353, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.3

The binding sites of Sodium atom in the Hen Egg White Lysozyme with Boron Tracedrug Utx-97 (pdb code 5b5j). 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 White Lysozyme with Boron Tracedrug Utx-97, PDB code: 5b5j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hen Egg White Lysozyme with Boron Tracedrug Utx-97


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg White Lysozyme with Boron Tracedrug Utx-97 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:10.3 occ:1.00 O A:SER60 2.3 10.2 1.0 O A:HOH406 2.4 12.4 1.0 O A:CYS64 2.4 6.9 1.0 O A:ARG73 2.4 11.8 1.0 O A:HOH380 2.5 9.4 1.0 OG A:SER72 2.5 11.4 1.0 CB A:SER72 3.2 14.0 1.0 C A:SER60 3.4 9.1 1.0 C A:CYS64 3.5 7.1 1.0 C A:ARG73 3.5 13.0 1.0 CA A:ASN65 3.9 8.2 1.0 N A:ARG73 4.0 13.2 1.0 CA A:SER60 4.0 7.7 1.0 N A:ASN65 4.1 7.2 1.0 C A:SER72 4.1 13.9 1.0 CB A:SER60 4.2 7.4 1.0 CA A:SER72 4.3 14.3 1.0 N A:ASN74 4.4 11.4 1.0 CA A:ARG73 4.4 14.3 1.0 N A:CYS64 4.4 7.7 1.0 N A:ARG61 4.5 9.9 1.0 CA A:ASN74 4.5 10.2 1.0 CA A:CYS64 4.6 8.2 1.0 C A:ARG61 4.6 10.9 1.0 O A:HOH432 4.6 23.5 1.0 O A:ARG61 4.6 12.7 1.0 CB A:ASN74 4.6 10.3 1.0 O A:SER72 4.7 15.4 1.0 N A:ASP66 4.7 7.2 1.0 OD1 A:ASN65 4.7 9.9 1.0 O A:HOH457 4.7 4.0 1.0 CB A:THR69 4.7 10.1 1.0 CB A:ASN65 4.8 8.8 1.0 N A:TRP62 4.8 9.8 1.0 C A:ASN65 4.9 6.5 1.0 CA A:ARG61 4.9 11.4 1.0 O A:HOH456 5.0 23.4 1.0

Sodium binding site 2 out of 2 in the Hen Egg White Lysozyme with Boron Tracedrug Utx-97


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hen Egg White Lysozyme with Boron Tracedrug Utx-97 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:24.6 occ:1.00 O A:HOH467 2.2 34.5 1.0 O A:HOH460 2.6 29.3 1.0 O A:ASN19 2.8 10.4 1.0 C A:ASN19 3.8 10.0 1.0 CB A:ASN19 4.0 14.8 1.0 N A:GLY22 4.2 7.8 1.0 O A:HOH390 4.4 17.7 1.0 CA A:ASN19 4.5 11.2 1.0 CA A:GLY22 4.5 8.2 1.0 O A:HOH511 4.6 25.1 1.0 O A:HOH485 4.7 19.4 1.0 O A:HOH354 4.7 26.9 1.0 N A:TYR20 4.8 9.3 1.0 N A:ARG21 4.8 8.0 1.0 CA A:TYR20 4.9 8.6 1.0

Y.Morimoto, H.Nagasawa, Y.Uto, T.Chatake, H.Hori. Structural Insight Into Protein Binding of Boron Tracedrug Utx-97 Revealed By the Co-Crystal Structure with Lysozyme at 1.26 Angstrom Resolution. J Pharm Sci V. 105 2298 2016.
ISSN: ISSN 1520-6017
PubMed: 27422088
DOI: 10.1016/J.XPHS.2016.06.005