Sodium in PDB 5kxm: Hen Egg White Lysozyme at 100K, Data Set 3

All present enzymatic activity of Hen Egg White Lysozyme at 100K, Data Set 3:
3.2.1.17;

The structure of Hen Egg White Lysozyme at 100K, Data Set 3, PDB code: 5kxm 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)	37.20 / 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 (%)	15.2 / 18

The structure of Hen Egg White Lysozyme at 100K, Data Set 3 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Hen Egg White Lysozyme at 100K, Data Set 3 (pdb code 5kxm). 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 3, PDB code: 5kxm:
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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:10.1 occ:1.00 O A:SER60 2.3 10.4 0.4 O A:ARG73 2.3 13.2 0.3 O A:SER60 2.3 8.8 0.6 O A:CYS64 2.3 8.6 0.2 O A:CYS64 2.4 8.0 0.8 O A:HOH384 2.4 11.1 1.0 O A:HOH339 2.5 8.8 1.0 O A:ARG73 2.5 9.1 0.4 O A:ARG73 2.5 14.2 0.2 OG A:SER72 2.6 11.4 1.0 CB A:SER72 3.3 11.6 1.0 C A:ARG73 3.4 12.8 0.3 C A:SER60 3.4 9.7 0.4 C A:CYS64 3.5 6.8 0.8 C A:SER60 3.5 8.5 0.6 C A:CYS64 3.5 8.2 0.2 C A:ARG73 3.5 9.1 0.4 C A:ARG73 3.5 13.9 0.2 CA A:ASN65 3.9 7.1 0.8 N A:ARG73 3.9 13.5 0.3 N A:ARG73 3.9 11.8 0.4 N A:ARG73 3.9 13.0 0.2 CA A:ASN65 4.0 8.2 0.2 CA A:SER60 4.1 8.4 0.4 N A:ASN65 4.1 7.0 0.8 CA A:SER60 4.1 7.5 0.6 C A:SER72 4.1 12.5 1.0 N A:ASN65 4.2 8.2 0.2 CA A:ARG73 4.2 14.2 0.3 CB A:SER60 4.2 7.9 0.4 CB A:SER60 4.3 7.7 0.6 N A:ASN74 4.3 11.7 0.3 CA A:ARG73 4.3 10.6 0.4 CA A:ARG73 4.3 13.3 0.2 CA A:SER72 4.4 11.9 1.0 N A:CYS64 4.4 7.9 0.8 N A:CYS64 4.4 8.0 0.2 N A:ASN74 4.4 9.0 0.4 N A:ARG61 4.5 10.1 0.4 N A:ASN74 4.5 14.7 0.2 O A:ARG61 4.5 12.2 0.6 C A:ARG61 4.5 10.9 0.6 N A:ARG61 4.6 9.3 0.6 C A:ARG61 4.6 10.2 0.4 CA A:ASN74 4.6 10.6 0.3 CA A:CYS64 4.6 8.1 0.2 O A:ARG61 4.6 11.2 0.4 N A:ASP66 4.6 6.9 0.8 CA A:CYS64 4.6 7.6 0.8 OD1 A:ASN65 4.6 8.4 0.8 CA A:ASN74 4.6 8.4 0.4 N A:ASP66 4.6 8.2 0.2 O A:SER72 4.7 13.2 1.0 CA A:ASN74 4.7 15.2 0.2 CB A:THR69 4.7 8.8 0.5 CB A:ASN74 4.7 10.2 0.3 CL A:CL204 4.7 11.3 1.0 CB A:ASN65 4.7 8.5 0.8 CA A:ARG61 4.8 11.7 0.4 C A:ASN65 4.8 6.3 0.8 CB A:THR69 4.8 10.8 0.3 CA A:ARG61 4.8 11.5 0.6 CB A:THR69 4.8 11.4 0.2 CB A:ASN74 4.8 7.8 0.4 C A:ASN65 4.8 8.2 0.2 N A:TRP62 4.9 10.9 0.6 N A:TRP62 4.9 10.0 0.4 O A:HOH331 4.9 22.9 1.0 CB A:ASN74 4.9 15.2 0.2 OD1 A:ASP66 5.0 7.7 0.2 N A:TRP63 5.0 8.9 1.0

Sodium binding site 2 out of 2 in the Hen Egg White Lysozyme at 100K, Data Set 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:35.7 occ:1.00 O A:HOH432 2.3 24.0 1.0 O A:HOH342 2.4 14.4 1.0 OE1 A:GLU35 2.5 6.8 0.4 OE1 A:GLU35 2.5 11.7 0.6 O A:HOH370 2.6 19.4 1.0 O A:HOH310 3.0 11.9 1.0 OD2 A:ASP52 3.2 10.2 0.6 OD2 A:ASP52 3.3 8.3 0.2 CD A:GLU35 3.5 6.3 0.4 CD A:GLU35 3.5 11.2 0.6 OD2 A:ASP52 3.7 8.1 0.2 OE2 A:GLU35 3.7 6.2 0.4 OE2 A:GLU35 3.8 12.0 0.6 CB A:GLN57 3.9 8.1 0.3 CB A:GLN57 3.9 7.5 0.7 CG A:ASP52 4.1 8.2 0.2 O A:HOH408 4.1 15.8 1.0 CG A:ASP52 4.2 8.3 0.6 CG A:ASP52 4.3 8.2 0.2 CG A:GLN57 4.4 8.4 0.3 O A:HOH372 4.4 11.6 1.0 CG A:GLN57 4.4 7.8 0.7 OD1 A:ASN44 4.5 9.1 0.2 O A:HOH327 4.5 25.6 1.0 O A:GLN57 4.7 8.8 0.3 O A:GLN57 4.7 7.8 0.7 OE1 A:GLN57 4.7 7.9 0.7 CB A:ASP52 4.8 8.3 0.2 OE1 A:GLN57 4.8 8.4 0.3 CB A:ASP52 4.8 8.0 0.2 CB A:ASP52 4.8 7.0 0.6 OD1 A:ASP52 4.8 7.8 0.2 CG A:GLU35 4.8 6.4 0.4 CG A:GLU35 4.9 9.8 0.6 OD1 A:ASP52 4.9 8.3 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