Sodium in PDB 6qy1: Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 1500 Patterns Merged

All present enzymatic activity of Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 1500 Patterns Merged:
3.2.1.17;

The structure of Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 1500 Patterns Merged, PDB code: 6qy1 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 (%)	18.6 / 20.6

The structure of Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 1500 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, 1500 Patterns Merged (pdb code 6qy1). 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, 1500 Patterns Merged, PDB code: 6qy1:
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, 1500 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, 1500 Patterns Merged within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:30.6 occ:1.00 H A:GLU7 2.4 24.1 1.0 O A:HOH371 2.5 32.7 1.0 HA3 A:GLY4 2.8 23.9 1.0 H A:CYS6 2.9 24.6 1.0 HB2 A:CYS6 3.0 29.5 1.0 HB2 A:GLU7 3.1 25.9 1.0 N A:GLU7 3.2 20.1 1.0 N A:CYS6 3.5 20.5 1.0 CA A:GLY4 3.6 19.9 1.0 C A:GLY4 3.6 15.6 1.0 HB3 A:GLU7 3.7 25.9 1.0 CB A:GLU7 3.8 21.6 1.0 H A:ARG5 3.8 25.2 1.0 N A:ARG5 3.8 21.0 1.0 CB A:CYS6 3.8 24.6 1.0 CA A:CYS6 3.9 15.8 1.0 C A:CYS6 4.0 16.4 1.0 CA A:GLU7 4.0 16.4 1.0 HA2 A:GLY4 4.2 23.9 1.0 O A:GLY4 4.2 16.9 1.0 H A:GLY4 4.4 29.1 1.0 C A:ARG5 4.4 18.5 1.0 HA A:GLU7 4.4 19.7 1.0 HB3 A:CYS6 4.4 29.5 1.0 N A:GLY4 4.5 24.3 1.0 CA A:ARG5 4.7 23.8 1.0 HB3 A:ARG5 4.8 27.2 1.0 HA A:CYS6 4.9 18.9 1.0 SG A:CYS6 4.9 21.9 1.0 H A:LEU8 5.0 20.8 1.0

Sodium binding site 2 out of 2 in the Pink Beam Serial Crystallography: Lysozyme, 5 Us Exposure, 1500 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, 1500 Patterns Merged within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:20.1 occ:0.60 HB2 A:SER72 2.1 43.3 1.0 OG A:SER72 2.2 41.4 1.0 O A:SER60 2.3 21.2 1.0 O A:HOH310 2.3 24.8 0.6 O A:CYS64 2.5 16.8 1.0 O A:HOH353 2.6 24.7 1.0 CB A:SER72 2.6 36.0 1.0 O A:ARG73 2.7 25.5 0.5 HA A:ASN65 3.0 25.4 1.0 HB3 A:SER72 3.2 43.3 1.0 H A:ASN74 3.2 26.4 0.5 C A:CYS64 3.5 15.6 1.0 C A:SER60 3.5 18.0 1.0 H A:ARG73 3.6 30.6 0.5 HB2 A:ASN74 3.6 24.1 0.5 C A:ARG73 3.7 26.3 0.5 CA A:SER72 3.8 38.1 1.0 N A:ARG73 3.8 25.5 0.5 C A:SER72 3.8 37.1 1.0 N A:ASN74 3.8 22.0 0.5 HB A:THR69 3.8 23.4 1.0 HB2 A:SER60 3.9 19.0 1.0 CA A:ASN65 3.9 21.2 1.0 H A:CYS64 3.9 15.6 1.0 HA A:SER60 4.0 16.3 1.0 N A:ARG73 4.0 25.6 0.5 HA A:ASN74 4.0 24.9 0.5 HA A:ASN74 4.1 23.4 0.5 N A:ASN65 4.1 14.7 1.0 HA A:ARG61 4.1 28.1 1.0 H A:ASP66 4.2 17.9 1.0 H A:ARG73 4.3 30.7 0.5 CA A:SER60 4.3 13.6 1.0 HA A:SER72 4.3 45.8 1.0 HB2 A:ASN74 4.3 23.6 0.5 O A:ARG61 4.3 25.3 1.0 CA A:ASN74 4.3 19.5 0.5 HB2 A:ASN65 4.4 24.2 1.0 C A:ARG61 4.4 21.1 1.0 O A:SER72 4.4 25.6 1.0 CB A:ASN74 4.4 20.1 0.5 N A:CYS64 4.4 13.0 1.0 N A:ASN74 4.5 20.8 0.5 CA A:ARG73 4.5 23.7 0.5 N A:ARG61 4.5 17.8 1.0 CB A:SER60 4.5 15.8 1.0 CA A:ARG61 4.6 23.4 1.0 CA A:CYS64 4.6 16.6 1.0 CA A:ASN74 4.6 20.7 0.5 CB A:ASN65 4.7 20.2 1.0 C A:ARG73 4.7 22.5 0.5 OD1 A:ASN65 4.7 32.1 1.0 H A:SER72 4.7 31.0 1.0 O A:HOH360 4.7 24.6 1.0 CB A:THR69 4.7 19.5 1.0 HG21 A:THR69 4.8 24.7 1.0 N A:TRP62 4.8 19.7 1.0 CA A:ARG73 4.8 23.8 0.5 N A:SER72 4.8 25.9 1.0 O A:THR69 4.9 25.3 1.0 N A:ASP66 4.9 14.9 1.0 H A:TRP63 4.9 17.1 1.0 H A:ASN65 4.9 17.6 1.0 CB A:ASN74 4.9 19.7 0.5 C A:ASN65 5.0 17.0 1.0 HA A:ARG73 5.0 28.5 0.5

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