Sodium in PDB 6syc: Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5

All present enzymatic activity of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5:
3.2.1.17;

The structure of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5, PDB code: 6syc was solved by A.Camara-Artigas, M.Plaza-Garrido, M.C.Salinas-Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.39 / 1.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.719, 76.559, 84.076, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.6

The structure of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5 also contains other interesting chemical elements:

Bromine	(Br)	32 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5 (pdb code 6syc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5, PDB code: 6syc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:23.0 occ:1.00 H A:ASP66 2.1 14.4 1.0 HG A:SER72 2.1 40.3 1.0 HA A:ASN65 2.5 15.9 1.0 HB A:THR69 2.8 18.9 1.0 HB2 A:SER72 2.9 35.3 1.0 OG A:SER72 2.9 33.5 1.0 N A:ASP66 2.9 12.0 1.0 HB2 A:SER60 2.9 16.8 1.0 O A:HOH360 3.0 20.9 1.0 O A:SER60 3.1 16.2 1.0 OD1 A:ASP66 3.2 13.7 1.0 CB A:SER72 3.2 29.4 1.0 OD1 A:ASN65 3.3 20.4 1.0 HB3 A:SER72 3.3 35.3 1.0 H A:GLY67 3.3 18.6 1.0 O A:CYS64 3.3 12.6 1.0 CA A:ASN65 3.3 13.3 1.0 C A:ASN65 3.6 11.9 1.0 HG1 A:THR69 3.6 19.3 1.0 H A:THR69 3.6 19.4 1.0 CB A:THR69 3.6 15.7 1.0 OG1 A:THR69 3.8 16.1 1.0 CB A:SER60 3.9 14.0 1.0 N A:GLY67 3.9 15.5 1.0 CG A:ASP66 3.9 13.5 1.0 CA A:ASP66 4.0 12.9 1.0 C A:SER60 4.1 14.8 1.0 HG A:SER60 4.1 15.6 1.0 CG A:ASN65 4.1 20.6 1.0 H A:ARG68 4.1 19.5 1.0 C A:CYS64 4.2 12.2 1.0 N A:ASN65 4.2 13.0 1.0 CB A:ASN65 4.3 16.4 1.0 HA A:SER60 4.3 15.4 1.0 N A:THR69 4.3 16.2 1.0 C A:ASP66 4.3 13.9 1.0 CB A:ASP66 4.4 12.7 1.0 CA A:SER60 4.4 12.9 1.0 O A:THR69 4.4 17.6 1.0 HB3 A:ASP66 4.4 15.2 1.0 HB3 A:SER60 4.5 16.8 1.0 HG21 A:THR69 4.5 19.4 1.0 CA A:THR69 4.5 15.9 1.0 OG A:SER60 4.5 13.0 1.0 HB2 A:ASN65 4.6 19.7 1.0 CG2 A:THR69 4.7 16.1 1.0 CA A:SER72 4.7 26.4 1.0 HA A:ASP66 4.8 15.5 1.0 N A:ARG68 4.8 16.3 1.0 O A:ASN65 4.8 13.0 1.0 OD2 A:ASP66 4.9 15.5 1.0 HA A:SER72 4.9 31.6 1.0 CA A:GLY67 5.0 16.2 1.0 HA A:ARG61 5.0 19.2 1.0 C A:THR69 5.0 18.8 1.0 HA2 A:GLY67 5.0 19.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:19.0 occ:1.00 HG B:SER72 2.4 37.0 1.0 O B:CYS64 2.4 13.9 1.0 O B:HOH335 2.4 23.2 1.0 O B:SER60 2.4 15.1 1.0 O B:HOH346 2.5 21.6 1.0 OG B:SER72 2.5 30.9 1.0 O B:ARG73 2.6 22.7 1.0 HB2 B:SER72 2.6 34.2 1.0 HA B:ASN65 2.9 17.9 1.0 CB B:SER72 3.1 28.5 1.0 C B:CYS64 3.4 13.0 1.0 HB2 B:SER60 3.6 15.6 1.0 C B:SER60 3.6 13.6 1.0 HB3 B:SER72 3.6 34.2 1.0 C B:ARG73 3.6 22.7 1.0 HB B:THR69 3.7 21.8 1.0 H B:ARG73 3.8 27.8 1.0 CA B:ASN65 3.8 14.9 1.0 H B:CYS64 3.9 16.2 1.0 N B:ARG73 3.9 23.2 1.0 HB2 B:ASN74 4.0 20.0 1.0 H B:ASP66 4.0 15.9 1.0 HA B:SER60 4.0 16.1 1.0 N B:ASN65 4.0 15.0 1.0 HA B:ASN74 4.1 22.7 1.0 CA B:SER60 4.2 13.4 1.0 C B:SER72 4.3 24.9 1.0 O B:HOH306 4.3 28.6 1.0 CA B:SER72 4.3 28.8 1.0 CB B:SER60 4.3 13.0 1.0 HB2 B:ASN65 4.4 20.0 1.0 O B:ARG61 4.4 17.3 1.0 OD1 B:ASN65 4.4 20.1 1.0 N B:CYS64 4.4 13.5 1.0 HA B:ARG61 4.5 19.8 1.0 CA B:ARG73 4.5 22.8 1.0 N B:ASN74 4.5 21.7 1.0 C B:ARG61 4.5 16.0 1.0 O B:HOH368 4.6 20.2 1.0 CA B:CYS64 4.6 13.5 1.0 CB B:THR69 4.6 18.1 1.0 CB B:ASN65 4.6 16.6 1.0 CA B:ASN74 4.6 18.9 1.0 N B:ARG61 4.6 15.2 1.0 N B:ASP66 4.7 13.3 1.0 CB B:ASN74 4.7 16.7 1.0 HG22 B:THR69 4.8 22.2 1.0 CA B:ARG61 4.8 16.5 1.0 C B:ASN65 4.8 13.3 1.0 HG21 B:THR69 4.8 22.2 1.0 HA B:SER72 4.8 34.6 1.0 H B:ASN65 4.9 18.0 1.0 H B:TRP63 4.9 17.2 1.0 HA B:ARG73 4.9 27.3 1.0 O B:SER72 4.9 23.7 1.0 CG2 B:THR69 5.0 18.5 1.0 N B:TRP62 5.0 16.5 1.0

M.Plaza-Garrido, M.C.Salinas-Garcia, D.Alba-Elena, J.C.Martinez, A.Camara-Artigas. Lysozyme Crystals Dyed with Bromophenol Blue: Where Has the Dye Gone? Acta Crystallogr D Struct V. 76 845 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32876060
DOI: 10.1107/S2059798320008803