Sodium in PDB 4rds: Lysozyme Crystallized with Red Food Coloring Dye

All present enzymatic activity of Lysozyme Crystallized with Red Food Coloring Dye:
3.2.1.17;

The structure of Lysozyme Crystallized with Red Food Coloring Dye, PDB code: 4rds was solved by E.M.Irimpan, I.I.Mathews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.28 / 1.23
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.890, 78.890, 36.840, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.3

The structure of Lysozyme Crystallized with Red Food Coloring Dye also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Lysozyme Crystallized with Red Food Coloring Dye (pdb code 4rds). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Lysozyme Crystallized with Red Food Coloring Dye, PDB code: 4rds:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Lysozyme Crystallized with Red Food Coloring Dye


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Crystallized with Red Food Coloring Dye within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:15.1 occ:1.00 O A:SER60 2.3 14.2 1.0 O A:HOH328 2.4 17.0 1.0 O A:ARG73 2.4 16.9 1.0 O A:CYS64 2.4 12.5 1.0 O A:HOH316 2.4 13.5 1.0 OG A:SER72 2.5 17.8 1.0 CB A:SER72 3.3 17.3 1.0 C A:SER60 3.4 11.9 1.0 C A:ARG73 3.5 16.0 1.0 C A:CYS64 3.5 11.2 1.0 N A:ARG73 3.9 17.3 1.0 CA A:ASN65 3.9 12.0 1.0 CA A:SER60 4.1 11.7 1.0 N A:ASN65 4.2 11.9 1.0 C A:SER72 4.2 17.6 1.0 CB A:SER60 4.3 11.9 1.0 CA A:ARG73 4.3 17.5 1.0 CA A:SER72 4.4 17.9 1.0 N A:ASN74 4.4 15.5 1.0 O A:ARG61 4.4 18.1 1.0 N A:ARG61 4.5 13.5 1.0 C A:ARG61 4.5 14.5 1.0 N A:CYS64 4.5 11.4 1.0 CA A:ASN74 4.6 15.1 1.0 N A:ASP66 4.6 11.1 1.0 OD1 A:ASN65 4.6 15.3 1.0 CA A:CYS64 4.7 11.8 1.0 CB A:THR69 4.7 12.7 1.0 NA A:NA205 4.7 14.3 1.0 CA A:ARG61 4.7 15.5 1.0 CB A:ASN74 4.7 15.2 1.0 CB A:ASN65 4.8 13.2 1.0 O A:SER72 4.8 21.1 1.0 C A:ASN65 4.8 10.3 1.0 N A:TRP62 4.9 13.4 1.0 O A:HOH313 5.0 28.8 1.0

Sodium binding site 2 out of 3 in the Lysozyme Crystallized with Red Food Coloring Dye


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme Crystallized with Red Food Coloring Dye within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:17.2 occ:1.00 OG1 A:THR51 2.6 11.4 1.0 OD2 A:ASP66 2.7 11.3 1.0 O A:GLY49 2.9 19.6 1.0 NE A:ARG68 3.0 20.5 1.0 OG1 A:THR69 3.0 12.2 1.0 N A:THR51 3.4 10.6 1.0 CB A:THR51 3.4 10.3 1.0 C A:SER50 3.5 12.3 1.0 CG A:ARG68 3.6 14.9 1.0 CG A:ASP66 3.6 10.3 1.0 NE A:ARG45 3.6 26.3 1.0 CA A:SER50 3.7 13.9 1.0 OG A:SER60 3.7 12.1 1.0 CD A:ARG68 3.8 15.8 1.0 OD1 A:ASP66 3.8 11.4 1.0 O A:ARG68 3.9 18.6 1.0 CZ A:ARG68 3.9 18.1 1.0 C A:GLY49 3.9 18.9 1.0 NH2 A:ARG68 3.9 19.7 1.0 NH2 A:ARG45 3.9 19.4 1.0 CA A:THR51 4.0 10.1 1.0 CZ A:ARG45 4.0 24.6 1.0 O A:SER50 4.1 13.2 1.0 C A:ARG68 4.3 14.6 1.0 N A:SER50 4.3 15.0 1.0 OH A:TYR53 4.3 10.6 1.0 CB A:THR69 4.3 12.7 1.0 CD A:ARG45 4.3 20.7 1.0 N A:THR69 4.6 13.7 1.0 CB A:ARG68 4.7 13.8 1.0 CB A:SER60 4.7 11.9 1.0 CA A:THR69 4.7 13.2 1.0 CG2 A:THR51 4.7 10.9 1.0 CG2 A:THR69 4.9 13.9 1.0 CB A:ASP66 4.9 10.8 1.0 CB A:SER50 4.9 14.6 1.0

Sodium binding site 3 out of 3 in the Lysozyme Crystallized with Red Food Coloring Dye


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lysozyme Crystallized with Red Food Coloring Dye within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:14.3 occ:1.00 O A:HOH313 3.1 28.8 1.0 O A:HOH316 3.2 13.5 1.0 N A:THR69 3.2 13.7 1.0 O A:THR69 3.3 14.9 1.0 O A:HOH402 3.3 31.8 1.0 N A:ARG68 3.5 12.1 1.0 C A:GLY67 3.5 12.9 1.0 CA A:GLY67 3.6 13.3 1.0 OG A:SER72 3.6 17.8 1.0 C A:THR69 3.6 13.7 1.0 N A:GLY67 3.7 12.4 1.0 OD1 A:ASN65 3.7 15.3 1.0 CA A:THR69 3.8 13.2 1.0 O A:HOH328 4.0 17.0 1.0 O A:GLY67 4.2 16.4 1.0 C A:ARG68 4.2 14.6 1.0 CB A:THR69 4.2 12.7 1.0 OD1 A:ASP66 4.2 11.4 1.0 CA A:ARG68 4.3 13.3 1.0 N A:PRO70 4.5 15.5 1.0 NA A:NA203 4.7 15.1 1.0 C A:ASP66 4.8 11.3 1.0 O A:HOH329 4.8 18.9 0.5 OG1 A:THR69 4.8 12.2 1.0 CB A:SER72 4.8 17.3 1.0 N A:ASP66 4.9 11.1 1.0 CG A:ASN65 4.9 14.8 1.0

E.M.Irimpan, I.I.Mathews. Lysozyme Crystallized with Red Food Coloring Dye. To Be Published.