Sodium in PDB 4xjf: X-Ray Structure of Lysozyme B1

All present enzymatic activity of X-Ray Structure of Lysozyme B1:
3.2.1.17;

The structure of X-Ray Structure of Lysozyme B1, PDB code: 4xjf was solved by C.Y.Huang, V.Olieric, K.Diederichs, M.Wang, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.55 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.100, 79.100, 38.470, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.7

The structure of X-Ray Structure of Lysozyme B1 also contains other interesting chemical elements:

Bromine

(Br)

5 atoms

The binding sites of Sodium atom in the X-Ray Structure of Lysozyme B1 (pdb code 4xjf). 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 X-Ray Structure of Lysozyme B1, PDB code: 4xjf:

Sodium binding site 1 out of 1 in the X-Ray Structure of Lysozyme B1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Lysozyme B1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:28.2 occ:1.00 O A:SER60 2.3 23.9 1.0 O A:CYS64 2.4 19.3 1.0 O A:ARG73 2.5 31.0 0.9 O A:HOH351 2.5 26.4 0.8 OG A:SER72 2.6 35.3 1.0 O A:HOH330 2.7 24.9 0.9 CB A:SER72 3.2 34.7 1.0 C A:CYS64 3.4 19.4 1.0 C A:SER60 3.5 18.1 1.0 C A:ARG73 3.5 30.9 0.9 CA A:ASN65 3.9 21.8 1.0 N A:ARG73 4.0 25.5 0.9 C A:SER72 4.1 39.8 1.0 N A:ASN65 4.1 19.4 1.0 CA A:SER60 4.3 17.6 1.0 CA A:SER72 4.3 34.8 1.0 N A:CYS64 4.3 17.1 1.0 C A:ARG61 4.3 27.8 0.9 O A:ARG61 4.4 27.4 0.9 N A:ASN74 4.4 30.5 1.0 CA A:ARG73 4.4 24.9 0.9 O A:SER72 4.5 36.3 1.0 CA A:ASN74 4.5 22.5 1.0 CA A:CYS64 4.5 18.8 1.0 N A:ARG61 4.5 15.7 0.9 CB A:SER60 4.5 21.5 1.0 CA A:ARG61 4.6 23.0 0.9 N A:TRP62 4.7 24.6 1.0 CB A:ASN74 4.7 24.6 1.0 BR A:BR205 4.7 45.5 0.5 CB A:ASN65 4.7 21.5 1.0 OD1 A:ASN65 4.8 35.4 1.0 N A:ASP66 4.8 19.8 1.0 CB A:THR69 4.8 24.0 1.0 C A:ASN65 4.9 18.7 1.0 O A:THR69 4.9 31.3 1.0 N A:TRP63 4.9 18.7 1.0 C A:TRP62 5.0 21.9 1.0

C.Y.Huang, V.Olieric, P.Ma, E.Panepucci, K.Diederichs, M.Wang, M.Caffrey. In Meso in Situ Serial X-Ray Crystallography of Soluble and Membrane Proteins. Acta Crystallogr.,Sect.D V. 71 1238 2015.
ISSN: ESSN 1399-0047
PubMed: 26057665
DOI: 10.1107/S1399004715005210