Sodium in PDB 8b3u: Hen Egg White Lysozyme 6S in Situ Crystallization

The structure of Hen Egg White Lysozyme 6S in Situ Crystallization, PDB code: 8b3u was solved by A.Henkel, M.Galchenkova, O.Yefanov, J.Hakanpaeae, H.N.Chapman, D.Oberthuer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.60 / 1.71
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.2, 79.2, 37.8, 90, 90, 90
R / Rfree (%)	16.6 / 19.4

The structure of Hen Egg White Lysozyme 6S in Situ Crystallization also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Hen Egg White Lysozyme 6S in Situ Crystallization (pdb code 8b3u). 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 Hen Egg White Lysozyme 6S in Situ Crystallization, PDB code: 8b3u:

Sodium binding site 1 out of 1 in the Hen Egg White Lysozyme 6S in Situ Crystallization


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 6S in Situ Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:47.8 occ:1.00 H A:ILE88 2.4 30.0 1.0 HG12 A:ILE88 2.6 29.0 1.0 HA A:ASP87 3.0 37.4 1.0 HE1 A:HIS15 3.3 46.0 1.0 N A:ILE88 3.3 25.0 1.0 CG1 A:ILE88 3.6 24.2 1.0 HG23 A:ILE88 3.6 30.3 1.0 HZ A:PHE3 3.6 43.5 1.0 O A:HOH341 3.7 43.4 1.0 HB1 A:ALA11 3.7 26.4 1.0 CA A:ASP87 3.8 31.1 1.0 HG13 A:ILE88 3.8 29.0 1.0 OD1 A:ASP87 3.8 41.1 1.0 HH12 A:ARG14 3.9 61.7 0.6 CE1 A:HIS15 4.0 38.3 1.0 C A:ASP87 4.0 27.6 1.0 O A:SER86 4.1 32.5 1.0 CB A:ILE88 4.3 26.4 1.0 CA A:ILE88 4.3 23.1 1.0 CG2 A:ILE88 4.4 25.3 1.0 HB2 A:ALA11 4.4 26.4 1.0 HD11 A:ILE88 4.4 30.8 1.0 H A:THR89 4.5 26.8 1.0 CB A:ALA11 4.5 22.0 1.0 CZ A:PHE3 4.5 36.3 1.0 CG A:ASP87 4.5 42.6 1.0 CD1 A:ILE88 4.5 25.7 1.0 HH11 A:ARG14 4.6 61.7 0.6 NH1 A:ARG14 4.6 51.4 0.6 CB A:ASP87 4.6 30.2 1.0 HE2 A:PHE3 4.6 40.8 1.0 HD13 A:ILE88 4.6 30.8 1.0 HB2 A:ASP87 4.7 36.2 1.0 HD1 A:HIS15 4.8 50.2 1.0 ND1 A:HIS15 4.8 41.9 1.0 HG21 A:ILE88 4.8 30.3 1.0 N A:ASP87 4.8 25.1 1.0 N A:THR89 4.9 22.3 1.0 NE2 A:HIS15 4.9 41.7 1.0 C A:SER86 4.9 31.5 1.0 HE2 A:HIS15 4.9 50.0 1.0 HB3 A:ALA11 5.0 26.4 1.0 CE2 A:PHE3 5.0 34.0 1.0

A.Henkel, M.Galchenkova, J.Maracke, O.Yefanov, J.Hakanpaa, J.R.Mesters, H.N.Chapman, D.Oberthur. Jinxed: Just in Time Crystallization For Easy Structure Determination of Biological Macromolecules Biorxiv 2022.
ISSN: ISSN 2692-8205
DOI: 10.1101/2022.10.26.513656