Sodium in PDB 8cvv: 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme

All present enzymatic activity of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme:
3.2.1.17;

The structure of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme, PDB code: 8cvv was solved by A.M.Wolff, M.C.Thompson, J.S.Fraser, E.Nango, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.09 / 1.57
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.439, 79.439, 38.192, 90, 90, 90
R / Rfree (%)	14.5 / 17

The structure of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme (pdb code 8cvv). 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 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme, PDB code: 8cvv:

Sodium binding site 1 out of 1 in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:17.7 occ:1.00 O A:SER60 2.3 16.3 1.0 O A:CYS64 2.4 13.5 1.0 OG A:SER72 2.5 22.5 1.0 O A:HOH356 2.5 16.1 1.0 O A:ARG73 2.5 20.2 1.0 O A:HOH357 2.5 22.9 1.0 HB2 A:SER72 2.9 26.0 1.0 HA A:ASN65 3.1 17.6 1.0 CB A:SER72 3.2 21.7 1.0 C A:SER60 3.5 14.3 1.0 C A:CYS64 3.5 13.3 1.0 C A:ARG73 3.5 20.4 1.0 HB2 A:SER60 3.5 14.5 1.0 HB A:THR69 3.8 19.4 1.0 HA A:SER60 3.9 14.3 1.0 HB3 A:SER72 3.9 26.0 1.0 HD22 A:ASN65 3.9 29.5 1.0 H A:CYS64 3.9 15.3 1.0 HB2 A:ASN74 4.0 22.6 1.0 N A:ARG73 4.0 22.1 1.0 CA A:ASN65 4.0 14.6 1.0 H A:ARG73 4.0 26.5 1.0 HA A:ASN74 4.1 22.9 1.0 CA A:SER60 4.1 12.0 1.0 H A:ASP66 4.1 17.6 1.0 C A:SER72 4.1 22.6 1.0 N A:ASN65 4.2 13.8 1.0 CB A:SER60 4.3 12.1 1.0 CA A:SER72 4.3 22.5 1.0 CA A:ARG73 4.4 21.7 1.0 N A:ASN74 4.4 19.4 1.0 N A:CYS64 4.5 12.8 1.0 HA A:ARG61 4.5 20.5 1.0 N A:ARG61 4.6 14.4 1.0 C A:ARG61 4.6 15.5 1.0 CA A:ASN74 4.6 19.0 1.0 HB2 A:ASN65 4.6 20.8 1.0 CA A:CYS64 4.7 12.3 1.0 O A:SER72 4.7 23.6 1.0 O A:ARG61 4.7 17.1 1.0 CB A:THR69 4.7 16.2 1.0 ND2 A:ASN65 4.7 24.6 1.0 CB A:ASN74 4.7 18.9 1.0 HG21 A:THR69 4.8 20.6 1.0 N A:ASP66 4.8 14.6 1.0 CL A:CL204 4.8 36.0 1.0 CA A:ARG61 4.8 17.1 1.0 HA A:ARG73 4.8 26.0 1.0 N A:TRP62 4.8 15.2 1.0 H A:TRP63 4.8 15.3 1.0 CB A:ASN65 4.9 17.3 1.0 O A:THR69 4.9 19.2 1.0 HA A:SER72 4.9 27.0 1.0 C A:ASN65 4.9 14.2 1.0 HB3 A:SER60 5.0 14.5 1.0 H A:SER72 5.0 26.4 1.0

A.M.Wolff, E.Nango, I.D.Young, A.S.Brewster, M.Kubo, T.Nomura, M.Sugahara, S.Owada, B.A.Barad, K.Ito, A.Bhowmick, S.Carbajo, T.Hino, J.M.Holton, D.Im, L.J.O'riordan, T.Tanaka, R.Tanaka, R.G.Sierra, F.Yumoto, K.Tono, S.Iwata, N.K.Sauter, J.S.Fraser, M.C.Thompson. Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-Ray Crystallography Biorxiv 2022.
DOI: 10.1101/2022.06.10.495662