Sodium in PDB 5kxl: Hen Egg White Lysozyme at 100K, Data Set 2

All present enzymatic activity of Hen Egg White Lysozyme at 100K, Data Set 2:
3.2.1.17;

The structure of Hen Egg White Lysozyme at 100K, Data Set 2, PDB code: 5kxl 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 (°)	77.312, 77.312, 37.213, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 16.4

The structure of Hen Egg White Lysozyme at 100K, Data Set 2 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 2 (pdb code 5kxl). 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 2, PDB code: 5kxl:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:9.8 occ:1.00 O A:SER60 2.3 8.3 0.4 O A:SER60 2.3 9.6 0.3 O A:SER60 2.4 8.9 0.3 O A:HOH351 2.4 11.6 1.0 O A:CYS64 2.4 8.6 1.0 O A:ARG73 2.4 12.3 0.4 O A:HOH354 2.4 8.9 1.0 O A:ARG73 2.5 12.4 0.6 OG A:SER72 2.5 12.1 0.4 OG A:SER72 2.5 12.6 0.6 CB A:SER72 3.2 12.1 0.4 CB A:SER72 3.3 12.6 0.6 C A:SER60 3.5 8.7 0.3 C A:SER60 3.5 8.3 0.4 C A:SER60 3.5 9.9 0.3 C A:ARG73 3.5 12.3 0.4 C A:CYS64 3.5 7.5 1.0 C A:ARG73 3.5 12.2 0.6 N A:ARG73 3.8 13.4 0.6 CA A:ASN65 3.9 7.5 0.5 CA A:ASN65 3.9 8.5 0.1 N A:ARG73 3.9 13.1 0.4 CA A:ASN65 3.9 8.1 0.4 C A:SER72 4.0 13.0 0.6 CA A:SER60 4.1 9.4 0.3 N A:ASN65 4.1 7.6 0.5 CA A:SER60 4.1 8.1 0.3 CA A:SER60 4.1 7.0 0.4 N A:ASN65 4.1 8.0 0.1 N A:ASN65 4.1 8.0 0.4 C A:SER72 4.2 12.3 0.4 CB A:SER60 4.2 8.0 0.3 CB A:SER60 4.2 9.1 0.3 CA A:ARG73 4.3 13.3 0.6 CA A:SER72 4.3 12.8 0.6 CA A:ARG73 4.3 13.4 0.4 CB A:SER60 4.3 7.5 0.4 O A:ARG61 4.3 9.9 0.3 CA A:SER72 4.3 12.4 0.4 N A:CYS64 4.4 8.5 1.0 N A:ASN74 4.4 11.9 1.0 C A:ARG61 4.5 9.4 0.3 N A:ARG61 4.5 8.7 0.3 C A:ARG61 4.5 10.4 0.4 O A:SER72 4.5 13.4 0.6 OD1 A:ASN65 4.5 7.8 0.5 N A:ARG61 4.5 9.0 0.4 N A:ASP66 4.5 6.9 0.5 O A:ARG61 4.6 10.5 0.4 N A:ARG61 4.6 10.4 0.3 C A:ARG61 4.6 11.3 0.3 CA A:ASN74 4.6 10.9 1.0 CA A:CYS64 4.6 8.0 1.0 CL A:CL201 4.6 11.5 1.0 N A:ASP66 4.6 7.4 0.4 N A:ASP66 4.6 8.6 0.1 OD1 A:ASN65 4.7 8.5 0.1 O A:ARG61 4.7 11.8 0.3 CB A:THR69 4.7 9.1 0.4 CB A:ASN65 4.7 8.8 0.1 CB A:THR69 4.7 10.3 0.4 CA A:ARG61 4.7 11.0 0.4 CA A:ARG61 4.7 9.8 0.3 C A:ASN65 4.7 6.8 0.5 CB A:ASN65 4.7 8.8 0.5 CB A:ASN74 4.8 10.6 1.0 O A:SER72 4.8 12.7 0.4 C A:ASN65 4.8 8.5 0.1 CA A:ARG61 4.8 11.7 0.3 CB A:THR69 4.8 11.8 0.2 C A:ASN65 4.8 7.4 0.4 N A:TRP62 4.8 10.5 0.4 N A:TRP62 4.9 10.9 0.3 CB A:ASN65 4.9 8.8 0.4 O A:HOH434 4.9 23.1 1.0 OD1 A:ASN65 4.9 9.7 0.4 N A:TRP62 5.0 8.7 0.3 N A:TRP63 5.0 8.3 0.4 N A:TRP63 5.0 9.8 0.3

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:49.7 occ:1.00 O A:HOH410 2.4 26.9 1.0 O A:HOH360 2.4 15.3 1.0 OE1 A:GLU35 2.5 9.4 0.5 OE1 A:GLU35 2.5 9.1 0.2 O A:HOH327 2.6 22.2 1.0 OE1 A:GLU35 2.6 8.6 0.4 O A:HOH302 2.9 13.5 1.0 OD2 A:ASP52 3.3 10.6 0.4 CD A:GLU35 3.4 8.5 0.2 CD A:GLU35 3.4 9.2 0.5 OD2 A:ASP52 3.4 17.6 0.6 OE2 A:GLU35 3.5 7.9 0.2 CD A:GLU35 3.6 8.1 0.4 OE2 A:GLU35 3.6 9.6 0.5 CB A:GLN57 3.8 8.2 0.3 CB A:GLN57 3.9 6.6 0.3 OE2 A:GLU35 3.9 7.7 0.4 CB A:GLN57 4.1 7.9 0.4 O A:HOH398 4.1 17.0 1.0 CG A:ASP52 4.2 7.4 0.4 CG A:ASP52 4.2 15.1 0.6 CG A:GLN57 4.2 8.7 0.3 CG A:GLN57 4.4 7.0 0.3 O A:HOH317 4.4 12.4 1.0 O A:GLN57 4.5 6.6 0.3 CG A:GLN57 4.5 8.3 0.4 O A:HOH326 4.6 27.0 1.0 O A:GLN57 4.6 8.5 0.3 OE1 A:GLN57 4.7 9.0 0.4 OE1 A:GLN57 4.7 7.1 0.3 OE1 A:GLN57 4.7 8.9 0.3 CB A:ASP52 4.8 6.1 0.4 CG A:GLU35 4.8 8.7 0.5 CB A:ASP52 4.8 11.5 0.6 CG A:GLU35 4.8 8.8 0.2 O A:GLN57 4.9 8.0 0.4 OD1 A:ASP52 4.9 16.3 0.6 OD1 A:ASP52 4.9 7.6 0.4 CG A:GLU35 5.0 8.2 0.4 CD A:GLN57 5.0 8.5 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