Sodium in PDB 5kxn: Hen Egg White Lysozyme at 100K, Data Set 4

All present enzymatic activity of Hen Egg White Lysozyme at 100K, Data Set 4:
3.2.1.17;

The structure of Hen Egg White Lysozyme at 100K, Data Set 4, PDB code: 5kxn was solved by S.Russi, A.Gonzalez, L.R.Kenner, D.A.Keedy, J.S.Fraser, H.Van Den Bedem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.66 / 1.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.311, 77.311, 37.212, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 17.8

The structure of Hen Egg White Lysozyme at 100K, Data Set 4 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Hen Egg White Lysozyme at 100K, Data Set 4 (pdb code 5kxn). 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 Hen Egg White Lysozyme at 100K, Data Set 4, PDB code: 5kxn:

Sodium binding site 1 out of 1 in the Hen Egg White Lysozyme at 100K, Data Set 4


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 at 100K, Data Set 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:11.9 occ:1.00 O A:SER60 2.3 16.7 0.3 O A:SER60 2.3 9.5 0.2 O A:SER60 2.3 10.2 0.4 O A:CYS64 2.4 9.8 0.3 O A:HOH376 2.4 14.1 1.0 O A:ARG73 2.4 15.4 0.5 O A:ARG73 2.4 14.3 0.6 O A:CYS64 2.4 11.4 0.4 O A:HOH331 2.5 11.2 1.0 O A:CYS64 2.5 12.6 0.2 OG A:SER72 2.5 15.6 0.6 OG A:SER72 2.5 16.1 0.5 CB A:SER72 3.2 14.9 0.6 CB A:SER72 3.3 15.7 0.5 C A:CYS64 3.4 9.1 0.3 C A:SER60 3.4 8.6 0.2 C A:SER60 3.4 12.3 0.3 C A:ARG73 3.5 14.6 0.5 C A:SER60 3.5 11.9 0.4 C A:ARG73 3.5 13.5 0.6 C A:CYS64 3.5 11.1 0.2 C A:CYS64 3.5 10.2 0.4 N A:ARG73 3.8 15.6 0.5 CA A:ASN65 3.9 9.9 0.3 N A:ARG73 3.9 15.6 0.6 CA A:ASN65 3.9 9.7 0.4 CA A:ASN65 4.0 10.8 0.2 C A:SER72 4.0 13.8 0.6 N A:ASN65 4.1 9.9 0.3 CA A:SER60 4.1 9.7 0.4 CA A:SER60 4.1 9.1 0.2 CA A:SER60 4.1 10.9 0.3 N A:ASN65 4.2 10.7 0.2 N A:ASN65 4.2 10.1 0.4 C A:SER72 4.2 15.1 0.5 CB A:SER60 4.2 10.3 0.3 CA A:ARG73 4.2 16.1 0.5 CA A:SER72 4.3 14.2 0.6 CB A:SER60 4.3 10.3 0.4 CB A:SER60 4.3 9.8 0.2 CA A:ARG73 4.3 15.1 0.6 N A:CYS64 4.3 7.4 0.3 CA A:SER72 4.4 15.0 0.5 N A:ASN74 4.4 13.5 0.6 N A:ASN74 4.4 14.6 0.5 N A:CYS64 4.5 11.6 0.2 O A:ARG61 4.5 9.8 0.2 C A:ARG61 4.5 9.7 0.2 N A:ARG61 4.5 9.1 0.3 N A:ARG61 4.5 8.3 0.2 C A:ARG61 4.5 9.8 0.3 O A:SER72 4.5 13.5 0.6 N A:CYS64 4.5 13.5 0.4 CA A:CYS64 4.5 8.4 0.3 N A:ARG61 4.6 16.4 0.4 CA A:ASN74 4.6 13.5 0.5 OD1 A:ASN65 4.6 8.8 0.4 N A:ASP66 4.6 9.0 0.4 CB A:THR69 4.6 12.6 0.4 CA A:CYS64 4.6 11.0 0.2 N A:ASP66 4.6 11.1 0.2 CA A:ASN74 4.6 11.5 0.6 O A:HOH392 4.6 6.1 1.0 O A:ARG61 4.6 12.2 0.3 N A:ASP66 4.6 9.8 0.3 OD1 A:ASN65 4.7 10.8 0.3 CA A:CYS64 4.7 12.1 0.4 CB A:ASN65 4.7 11.0 0.3 CB A:ASN74 4.7 12.9 0.5 O A:HOH411 4.7 26.7 1.0 CB A:THR69 4.7 10.5 0.3 CA A:ARG61 4.7 9.8 0.2 O A:SER72 4.7 16.3 0.5 CA A:ARG61 4.8 11.3 0.3 C A:ARG61 4.8 20.2 0.4 N A:TRP62 4.8 9.8 0.3 C A:ASN65 4.8 8.4 0.4 C A:ASN65 4.8 9.1 0.3 N A:TRP62 4.8 17.1 0.4 CB A:ASN65 4.8 10.9 0.4 N A:TRP62 4.8 11.6 0.2 CB A:ASN74 4.9 11.8 0.6 C A:ASN65 4.9 10.6 0.2 CB A:THR69 4.9 14.6 0.3 OD1 A:ASP66 4.9 12.7 0.2 CA A:ARG61 4.9 19.2 0.4 N A:TRP63 4.9 7.8 0.3 CB A:ASN65 5.0 10.6 0.2

S.Russi, A.Gonzalez, L.R.Kenner, D.A.Keedy, J.S.Fraser, H.Van Den Bedem. Conformational Variation of Proteins at Room Temperature Is Not Dominated By Radiation Damage. J Synchrotron Radiat V. 24 73 2017.
ISSN: ESSN 1600-5775
PubMed: 28009548
DOI: 10.1107/S1600577516017343