Sodium in PDB 5kxk: Hen Egg White Lysozyme at 100K, Data Set 1

All present enzymatic activity of Hen Egg White Lysozyme at 100K, Data Set 1:
3.2.1.17;

The structure of Hen Egg White Lysozyme at 100K, Data Set 1, PDB code: 5kxk 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)	38.65 / 1.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.289, 77.289, 37.205, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.1

The structure of Hen Egg White Lysozyme at 100K, Data Set 1 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 1 (pdb code 5kxk). 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 at 100K, Data Set 1, PDB code: 5kxk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hen Egg White Lysozyme at 100K, Data Set 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:10.0 occ:1.00 O A:SER60 2.3 8.4 0.4 O A:SER60 2.3 9.1 0.4 O A:SER60 2.3 9.9 0.2 O A:CYS64 2.4 8.1 1.0 O A:HOH339 2.4 10.9 1.0 O A:HOH341 2.4 8.6 1.0 OG A:SER72 2.5 11.3 1.0 O A:ARG73 2.7 16.2 1.0 CB A:SER72 3.2 11.5 1.0 C A:ARG73 3.4 13.1 1.0 C A:SER60 3.5 7.8 0.4 C A:CYS64 3.5 7.1 1.0 C A:SER60 3.5 8.7 0.4 C A:SER60 3.5 9.8 0.2 N A:ARG73 3.8 13.2 1.0 CA A:ASN65 3.8 7.9 0.1 CA A:ASN65 3.9 7.3 0.9 CA A:SER60 4.1 7.1 0.4 CA A:SER60 4.1 9.4 0.2 N A:ASN65 4.1 7.5 0.1 N A:ASN65 4.1 7.2 0.9 CA A:SER60 4.1 7.9 0.4 C A:SER72 4.1 12.4 1.0 CB A:SER60 4.2 9.2 0.2 CB A:SER60 4.2 6.7 0.4 CA A:ARG73 4.3 14.1 1.0 CA A:SER72 4.3 11.9 1.0 CB A:SER60 4.3 8.0 0.4 N A:ASN74 4.4 11.2 0.8 N A:ASN74 4.4 12.9 0.1 N A:ASN74 4.4 12.8 0.2 N A:CYS64 4.4 8.0 1.0 O A:ARG61 4.5 9.3 0.4 C A:ARG61 4.5 9.1 0.4 OD1 A:ASN65 4.5 7.5 0.1 N A:ARG61 4.5 8.0 0.4 C A:ARG61 4.6 10.7 0.4 C A:ARG61 4.6 11.3 0.2 N A:ARG61 4.6 9.5 0.4 N A:ASP66 4.6 6.8 0.9 CA A:ASN74 4.6 10.0 0.8 N A:ARG61 4.6 10.1 0.2 CA A:CYS64 4.6 7.7 1.0 CA A:ASN74 4.6 12.8 0.1 CA A:ASN74 4.6 12.6 0.2 O A:SER72 4.6 13.1 1.0 CL A:CL204 4.6 11.1 1.0 O A:ARG61 4.6 10.9 0.4 CB A:ASN65 4.6 8.1 0.1 OD1 A:ASN65 4.6 9.1 0.9 O A:ARG61 4.6 11.9 0.2 N A:ASP66 4.7 8.2 0.1 CB A:THR69 4.7 9.3 0.6 CA A:ARG61 4.7 9.2 0.4 CA A:ARG61 4.7 11.4 0.4 CB A:ASN74 4.8 9.8 0.8 C A:ASN65 4.8 6.6 0.9 CB A:ASN74 4.8 13.0 0.1 CB A:THR69 4.8 10.5 0.4 N A:TRP62 4.8 10.9 0.2 C A:ASN65 4.8 8.0 0.1 CB A:ASN65 4.8 8.8 0.9 CB A:ASN74 4.8 12.7 0.2 O A:HOH444 4.8 21.4 1.0 CA A:ARG61 4.8 11.3 0.2 N A:TRP62 4.8 10.3 0.4 OD1 A:ASP66 4.9 7.9 0.1 N A:TRP62 4.9 8.3 0.4 C A:TRP62 5.0 10.4 0.2 N A:TRP63 5.0 8.3 0.4

Sodium binding site 2 out of 2 in the Hen Egg White Lysozyme at 100K, Data Set 1


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 at 100K, Data Set 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:35.5 occ:1.00 O A:HOH344 2.4 13.7 1.0 OE1 A:GLU35 2.5 9.7 1.0 O A:HOH434 2.6 27.8 1.0 O A:HOH373 2.6 19.4 1.0 O A:HOH308 3.0 11.6 1.0 OD2 A:ASP52 3.1 8.9 0.3 OD2 A:ASP52 3.2 7.3 0.3 CD A:GLU35 3.5 8.6 1.0 OD2 A:ASP52 3.7 9.7 0.4 OE2 A:GLU35 3.7 9.3 1.0 CB A:GLN57 3.9 7.5 1.0 CG A:ASP52 4.1 7.1 0.3 O A:HOH403 4.2 15.6 1.0 CG A:ASP52 4.2 8.3 0.3 CG A:ASP52 4.2 8.6 0.4 CG A:GLN57 4.4 8.0 1.0 O A:HOH372 4.4 11.2 1.0 O A:HOH329 4.6 25.0 1.0 O A:GLN57 4.7 8.3 1.0 OE1 A:GLN57 4.7 8.5 1.0 ND2 A:ASN44 4.7 10.4 0.4 CB A:ASP52 4.8 7.6 0.3 CB A:ASP52 4.8 6.9 0.3 CB A:ASP52 4.8 7.6 0.4 OD1 A:ASP52 4.8 8.5 0.4 CG A:GLU35 4.8 8.2 1.0 O A:HOH432 4.9 46.9 1.0 OD1 A:ASP52 4.9 6.9 0.3

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