Sodium in PDB 6kcb: Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography

All present enzymatic activity of Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography:
3.2.1.17;

The structure of Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography, PDB code: 6kcb was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.18 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.450, 79.450, 38.470, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.5

The structure of Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography (pdb code 6kcb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography, PDB code: 6kcb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:38.7 occ:1.00 O A:SER78 2.3 33.5 1.0 O A:CYS82 2.4 33.3 1.0 O A:HOH356 2.5 38.8 1.0 O A:ARG91 2.6 41.4 1.0 OG A:SER90 2.6 40.4 1.0 O A:HOH333 2.7 34.5 1.0 CB A:SER90 3.2 39.1 1.0 C A:CYS82 3.5 31.4 1.0 C A:SER78 3.5 31.3 1.0 C A:ARG91 3.6 42.7 1.0 CA A:ASN83 4.0 33.8 1.0 N A:ARG91 4.0 41.5 1.0 C A:SER90 4.1 45.0 1.0 N A:ASN83 4.1 32.3 1.0 CA A:SER78 4.2 31.0 1.0 CA A:SER90 4.3 43.9 1.0 C A:ARG79 4.4 39.5 1.0 N A:CYS82 4.4 28.8 1.0 CA A:ARG91 4.4 40.5 1.0 O A:ARG79 4.4 40.4 1.0 N A:ASN92 4.5 40.0 1.0 CB A:SER78 4.5 31.0 1.0 N A:ARG79 4.5 30.8 1.0 O A:SER90 4.5 44.1 1.0 CA A:ARG79 4.6 38.0 1.0 CA A:CYS82 4.6 30.0 1.0 CA A:ASN92 4.6 35.2 1.0 N A:TRP80 4.7 35.7 1.0 N A:ASP84 4.8 31.4 1.0 O A:HOH358 4.8 37.5 1.0 CB A:ASN92 4.8 36.1 1.0 CB A:THR87 4.8 35.6 1.0 CB A:ASN83 4.9 31.1 1.0 OD1 A:ASN83 4.9 41.6 1.0 C A:ASN83 4.9 32.3 1.0 N A:TRP81 4.9 30.1 1.0 O A:THR87 5.0 42.4 1.0

Sodium binding site 2 out of 2 in the Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Room Temperature Structure of Lysozyme Delivered in Shortening A By Serial Millisecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:43.3 occ:1.00 O A:ARG39 3.0 37.1 1.0 CL A:CL202 3.4 37.3 1.0 CE2 A:TYR41 3.7 29.3 1.0 CA A:GLY40 3.9 34.8 1.0 CZ A:TYR41 3.9 29.4 1.0 C A:GLY40 4.0 32.8 1.0 CD2 A:TYR41 4.1 29.9 1.0 C A:ARG39 4.1 35.4 1.0 O A:GLY40 4.1 33.8 1.0 OH A:TYR41 4.2 30.0 1.0 N A:GLY40 4.5 32.5 1.0 CE1 A:TYR41 4.6 29.8 1.0 N A:TYR41 4.6 31.9 1.0 CG A:TYR41 4.7 26.7 1.0 CD1 A:TYR41 4.9 29.5 1.0

K.H.Nam, K.H.Nam. N/A N/A.
ISSN: ESSN 2045-2322
PubMed: 31919476
DOI: 10.1038/S41598-019-56135-1