Sodium in PDB 8dcw: Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)

All present enzymatic activity of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands):
3.2.1.17;

The structure of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands), PDB code: 8dcw was solved by A.S.Soares, Y.Yamada, J.Jakoncic, D.K.Schneider, H.J.Bernstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.42 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.78, 78.78, 37.57, 90, 90, 90
R / Rfree (%)	18.7 / 23.7

The structure of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) (pdb code 8dcw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands), PDB code: 8dcw:

Sodium binding site 1 out of 1 in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:17.8 occ:1.00 O A:SER60 2.2 17.1 1.0 O A:HOH436 2.3 19.4 1.0 O A:HOH389 2.4 12.9 1.0 O A:CYS64 2.4 16.4 1.0 OG A:SER72 2.4 22.8 1.0 O A:ARG73 2.6 18.4 1.0 CB A:SER72 3.3 22.5 1.0 C A:SER60 3.4 17.0 1.0 C A:CYS64 3.5 16.0 1.0 C A:ARG73 3.7 22.2 1.0 CA A:ASN65 3.9 15.3 1.0 CA A:SER60 4.0 15.7 1.0 N A:ASN65 4.1 15.1 1.0 N A:ARG73 4.2 23.8 1.0 CB A:SER60 4.2 14.4 1.0 C A:SER72 4.2 23.9 1.0 CA A:SER72 4.3 22.9 1.0 O A:ARG61 4.4 18.8 0.5 O A:HOH418 4.4 54.1 1.0 N A:ARG61 4.4 17.9 0.5 C A:ARG61 4.5 19.2 0.5 N A:ARG61 4.5 18.1 0.5 N A:CYS64 4.5 16.2 1.0 N A:ASP66 4.6 13.6 1.0 N A:ASN74 4.6 19.8 1.0 CA A:CYS64 4.6 16.6 1.0 CA A:ARG73 4.6 25.8 1.0 CL A:CL206 4.6 24.0 1.0 N A:TRP62 4.7 20.2 0.5 CB A:THR69 4.7 17.5 1.0 OD1 A:ASN65 4.7 15.9 1.0 O A:SER72 4.7 20.1 1.0 CA A:ARG61 4.7 18.9 0.5 C A:ASN65 4.7 13.7 1.0 CA A:ASN74 4.7 19.3 1.0 C A:ARG61 4.8 19.7 0.5 CA A:ARG61 4.8 19.3 0.5 CB A:ASN74 4.8 18.8 1.0 CB A:ASN65 4.9 15.6 1.0 N A:TRP62 4.9 19.4 0.5 OG A:SER60 4.9 15.3 1.0 O A:THR69 5.0 19.7 1.0

A.S.Soares, Y.Yamada, J.Jakoncic, S.Mcsweeney, R.M.Sweet, J.Skinner, J.Foadi, M.R.Fuchs, D.K.Schneider, W.Shi, B.Andi, L.C.Andrews, H.J.Bernstein. Serial Crystallography with Multi-Stage Merging of Thousands of Images. Acta Crystallogr.,Sect.F V. 78 281 2022.
ISSN: ESSN 2053-230X
PubMed: 35787556
DOI: 10.1107/S2053230X22006422