Sodium in PDB 6qy0: Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged

All present enzymatic activity of Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged:
3.2.1.17;

The structure of Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged, PDB code: 6qy0 was solved by J.Lieske, A.Tolstikova, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.54 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.860, 79.860, 38.020, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.5

The structure of Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged (pdb code 6qy0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged, PDB code: 6qy0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:33.4 occ:1.00 H A:GLU7 2.4 21.1 1.0 O A:HOH370 2.4 30.6 1.0 HA3 A:GLY4 2.8 23.6 1.0 H A:CYS6 2.8 23.9 1.0 HB2 A:CYS6 3.0 27.3 1.0 HB2 A:GLU7 3.2 27.8 1.0 N A:GLU7 3.2 17.6 1.0 N A:CYS6 3.4 19.9 1.0 CA A:GLY4 3.6 19.6 1.0 C A:GLY4 3.6 14.8 1.0 CB A:CYS6 3.8 22.8 1.0 HB3 A:GLU7 3.8 27.8 1.0 CB A:GLU7 3.8 23.2 1.0 N A:ARG5 3.8 19.4 1.0 H A:ARG5 3.8 23.3 1.0 CA A:CYS6 3.9 18.3 1.0 C A:CYS6 4.0 14.8 1.0 CA A:GLU7 4.1 15.7 1.0 O A:GLY4 4.1 16.8 1.0 HA2 A:GLY4 4.2 23.6 1.0 C A:ARG5 4.3 24.8 1.0 H A:GLY4 4.4 23.8 1.0 HB3 A:CYS6 4.4 27.3 1.0 HA A:GLU7 4.5 18.8 1.0 N A:GLY4 4.6 19.8 1.0 CA A:ARG5 4.6 25.4 1.0 HB3 A:ARG5 4.8 31.9 1.0 HA A:CYS6 4.8 22.0 1.0 SG A:CYS6 4.9 20.6 1.0 H A:LEU8 5.0 21.4 1.0

Sodium binding site 2 out of 2 in the Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 3000 Patterns Merged within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:21.9 occ:0.67 HB2 A:SER72 2.1 38.3 1.0 OG A:SER72 2.3 45.8 1.0 O A:HOH310 2.3 26.6 0.7 O A:SER60 2.3 20.5 1.0 O A:CYS64 2.5 14.2 1.0 O A:HOH350 2.6 23.9 1.0 O A:ARG73 2.6 27.6 0.6 CB A:SER72 2.6 31.9 1.0 HA A:ASN65 3.0 18.5 1.0 H A:ASN74 3.2 23.1 0.5 HB3 A:SER72 3.2 38.3 1.0 C A:SER60 3.5 14.3 1.0 C A:CYS64 3.5 14.0 1.0 H A:ARG73 3.5 31.3 0.5 C A:ARG73 3.6 29.0 0.6 HB2 A:ASN74 3.7 22.5 0.5 CA A:SER72 3.8 42.2 1.0 N A:ARG73 3.8 26.1 0.5 C A:SER72 3.8 40.8 1.0 N A:ASN74 3.8 19.2 0.5 HB A:THR69 3.9 20.5 1.0 H A:CYS64 3.9 17.5 1.0 HB2 A:SER60 3.9 19.9 1.0 CA A:ASN65 3.9 15.4 1.0 HA A:SER60 4.0 14.6 1.0 N A:ARG73 4.0 26.2 0.6 HA A:ASN74 4.0 22.2 0.6 HA A:ASN74 4.1 20.2 0.5 N A:ASN65 4.2 14.6 1.0 HA A:ARG61 4.2 26.6 1.0 CA A:SER60 4.2 12.2 1.0 H A:ASP66 4.2 17.3 1.0 O A:ARG61 4.2 23.2 1.0 H A:ARG73 4.3 31.4 0.6 HB2 A:ASN74 4.3 16.9 0.6 HA A:SER72 4.3 50.7 1.0 C A:ARG61 4.4 20.6 1.0 CA A:ASN74 4.4 16.9 0.5 O A:SER72 4.4 28.1 1.0 HB2 A:ASN65 4.4 20.3 1.0 N A:ASN74 4.4 23.4 0.6 N A:CYS64 4.4 14.6 1.0 CB A:ASN74 4.4 18.7 0.5 CA A:ARG73 4.5 27.1 0.6 N A:ARG61 4.5 16.0 1.0 CB A:SER60 4.5 16.6 1.0 CA A:ARG61 4.6 22.2 1.0 CA A:ASN74 4.6 18.6 0.6 OD1 A:ASN65 4.6 28.9 1.0 CA A:CYS64 4.6 16.1 1.0 CB A:ASN65 4.7 16.9 1.0 C A:ARG73 4.7 23.7 0.5 H A:SER72 4.7 37.7 1.0 CB A:THR69 4.8 17.1 1.0 O A:HOH354 4.8 24.3 1.0 HG21 A:THR69 4.8 24.3 1.0 H A:TRP63 4.8 17.3 1.0 CA A:ARG73 4.8 27.3 0.5 N A:SER72 4.8 31.4 1.0 N A:TRP62 4.8 19.0 1.0 N A:ASP66 4.9 14.4 1.0 O A:THR69 4.9 23.4 1.0 HA A:ARG73 4.9 32.5 0.6 CB A:ASN74 4.9 14.1 0.6 C A:ASN65 4.9 12.8 1.0 H A:ASN65 5.0 17.6 1.0

A.Tolstikova, M.Levantino, O.Yefanov, V.Hennicke, P.Fischer, J.Meyer, A.Mozzanica, S.Redford, E.Crosas, N.L.Opara, M.Barthelmess, J.Lieske, D.Oberthuer, E.Wator, I.Mohacsi, M.Wulff, B.Schmitt, H.N.Chapman, A.Meents. 1 Khz Fixed-Target Serial Crystallography Using A Multilayer Monochromator and An Integrating Pixel Detector. Iucrj V. 6 927 2019.
ISSN: ESSN 2052-2525
PubMed: 31576225
DOI: 10.1107/S205225251900914X