Sodium in PDB 6k8g: H/D Exchanged Hen Egg-White Lysozyme

All present enzymatic activity of H/D Exchanged Hen Egg-White Lysozyme:
3.2.1.17;

The structure of H/D Exchanged Hen Egg-White Lysozyme, PDB code: 6k8g was solved by A.Kita, Y.Morimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.094, 79.094, 37.828, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 25.5

The structure of H/D Exchanged Hen Egg-White Lysozyme also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the H/D Exchanged Hen Egg-White Lysozyme (pdb code 6k8g). 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 H/D Exchanged Hen Egg-White Lysozyme, PDB code: 6k8g:

Sodium binding site 1 out of 1 in the H/D Exchanged Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of H/D Exchanged Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:32.8 occ:1.00 OG A:SER72 2.3 37.2 1.0 HB2 A:SER72 2.3 41.3 1.0 O A:SER60 2.3 21.9 1.0 O A:CYS64 2.5 15.6 1.0 O A:ARG73 2.6 34.2 1.0 D1 A:HOH352 2.6 26.8 1.0 O A:HOH352 2.6 22.4 1.0 O A:HOH316 2.6 39.3 1.0 CB A:SER72 2.7 34.4 1.0 D2 A:HOH316 2.8 47.1 1.0 D2 A:HOH352 3.1 26.8 1.0 HA A:ASN65 3.2 20.5 1.0 HB3 A:SER72 3.3 41.3 1.0 D1 A:HOH316 3.3 47.1 1.0 C A:SER60 3.5 18.8 1.0 C A:ARG73 3.5 29.2 1.0 C A:CYS64 3.5 15.4 1.0 C A:SER72 3.8 32.4 1.0 N A:ARG73 3.9 27.7 1.0 H A:CYS64 3.9 17.1 0.9 D A:CYS64 3.9 17.1 0.1 CA A:SER72 3.9 35.2 1.0 HB2 A:SER60 3.9 17.5 1.0 HB A:THR69 3.9 24.7 1.0 HB2 A:ASN74 3.9 24.0 1.0 HA A:ASN74 3.9 22.6 1.0 D A:ARG73 4.0 33.2 0.8 H A:ARG73 4.0 33.2 0.2 HA A:SER60 4.0 15.6 1.0 CA A:ASN65 4.0 17.1 1.0 HA A:ARG61 4.1 25.5 1.0 O A:ARG61 4.1 26.5 1.0 N A:ASN65 4.2 15.3 1.0 D1 A:HOH371 4.2 31.4 1.0 CA A:SER60 4.3 13.0 1.0 D A:ASP66 4.3 17.2 0.9 C A:ARG61 4.3 21.3 1.0 H A:ASP66 4.3 17.2 0.1 N A:ASN74 4.4 30.1 1.0 O A:SER72 4.4 27.6 1.0 CA A:ARG73 4.4 24.4 1.0 HA A:SER72 4.4 42.3 1.0 N A:CYS64 4.4 14.3 1.0 CA A:ASN74 4.5 18.8 1.0 N A:ARG61 4.5 19.5 1.0 CA A:ARG61 4.5 21.3 1.0 CB A:SER60 4.6 14.6 1.0 CA A:CYS64 4.6 16.2 1.0 N A:TRP62 4.6 19.5 1.0 CB A:ASN74 4.7 20.0 1.0 HB2 A:ASN65 4.7 20.9 1.0 D A:TRP63 4.7 22.6 1.0 H A:TRP63 4.7 22.6 0.0 H A:SER72 4.7 47.5 0.3 D A:SER72 4.7 47.5 0.7 CB A:THR69 4.8 20.6 1.0 HA A:ARG73 4.8 29.3 1.0 OD1 A:ASN65 4.9 30.0 1.0 N A:SER72 4.9 39.5 1.0 C A:TRP62 4.9 14.3 1.0 N A:TRP63 4.9 18.8 1.0 CB A:ASN65 4.9 17.4 1.0 D2 A:HOH371 4.9 31.4 1.0 N A:ASP66 4.9 14.4 1.0 D A:TRP62 4.9 23.4 1.0 H A:TRP62 4.9 23.4 0.0 O A:THR69 5.0 26.0 1.0 HG A:SER60 5.0 18.4 0.3 DG A:SER60 5.0 18.4 0.7 O A:HOH371 5.0 26.2 1.0

A.Kita, Y.Morimoto. H/D Exchanged Hen Egg-White Lysozyme To Be Published.