Sodium in PDB 7o2o: Lysozyme Structure From Microfluidic-Based in Situ Data Collection

All present enzymatic activity of Lysozyme Structure From Microfluidic-Based in Situ Data Collection:
3.2.1.17;

The structure of Lysozyme Structure From Microfluidic-Based in Situ Data Collection, PDB code: 7o2o was solved by A.Gardais, L.Chavas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.28 / 1.83
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.599, 79.599, 37.867, 90, 90, 90
R / Rfree (%)	17.6 / 19.6

The binding sites of Sodium atom in the Lysozyme Structure From Microfluidic-Based in Situ Data Collection (pdb code 7o2o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Lysozyme Structure From Microfluidic-Based in Situ Data Collection, PDB code: 7o2o:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Lysozyme Structure From Microfluidic-Based in Situ Data Collection


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Structure From Microfluidic-Based in Situ Data Collection within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:55.0 occ:1.00 O A:GLY49 3.1 28.9 1.0 NH2 A:ARG45 3.1 54.3 1.0 CD A:ARG45 3.3 41.1 1.0 CZ A:ARG45 3.5 52.7 1.0 NE A:ARG45 3.6 48.4 1.0 NE A:ARG68 3.6 31.5 1.0 CZ A:ARG68 3.8 31.6 1.0 C A:GLY49 3.9 28.6 1.0 O A:HOH415 3.9 24.3 1.0 CD A:ARG68 4.0 30.2 1.0 CA A:GLY49 4.1 30.3 1.0 NH2 A:ARG68 4.2 28.9 1.0 NH1 A:ARG68 4.4 30.8 1.0 NH1 A:ARG45 4.5 52.8 1.0 O A:ARG68 4.5 28.4 1.0 CG A:ARG45 4.6 34.7 1.0 CG A:ARG68 4.8 26.9 1.0 OG1 A:THR51 4.8 21.0 1.0

Sodium binding site 2 out of 3 in the Lysozyme Structure From Microfluidic-Based in Situ Data Collection


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme Structure From Microfluidic-Based in Situ Data Collection within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:20.9 occ:1.00 ND2 A:ASN113 3.2 23.6 1.0 CB A:ASN113 3.6 21.9 1.0 CG A:ASN113 3.9 24.8 1.0 CA A:ALA110 4.0 23.1 1.0 O A:VAL109 4.1 23.4 1.0 CG1 A:VAL109 4.1 28.7 1.0 C A:VAL109 4.3 22.9 1.0 N A:ALA110 4.4 22.7 1.0 CD A:ARG114 4.4 26.7 1.0 CG A:ARG114 4.6 26.3 1.0 CB A:ALA110 4.6 24.0 1.0 CA A:ASN113 4.9 22.0 1.0

Sodium binding site 3 out of 3 in the Lysozyme Structure From Microfluidic-Based in Situ Data Collection


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lysozyme Structure From Microfluidic-Based in Situ Data Collection within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:31.6 occ:1.00 OG A:SER24 3.0 28.2 1.0 N A:GLY26 3.1 21.4 1.0 CA A:GLY26 3.4 21.3 1.0 CB A:SER24 3.5 24.2 1.0 CA A:GLN121 3.6 28.8 0.5 CA A:GLN121 3.6 28.8 0.5 O A:HOH407 3.7 64.5 1.0 CB A:GLN121 3.8 31.4 0.5 CG A:GLN121 3.9 36.6 0.5 CD1 A:ILE124 3.9 33.1 1.0 N A:GLN121 3.9 28.1 1.0 CG A:GLN121 4.0 37.0 0.5 N A:LEU25 4.2 22.6 1.0 CB A:GLN121 4.2 31.6 0.5 C A:SER24 4.3 22.2 1.0 C A:LEU25 4.3 22.8 1.0 CG1 A:ILE124 4.3 30.3 1.0 CD A:GLN121 4.3 43.8 0.5 C A:VAL120 4.3 28.1 1.0 O A:VAL120 4.3 27.3 1.0 CG2 A:VAL120 4.3 29.7 1.0 CA A:SER24 4.5 22.5 1.0 OE1 A:GLN121 4.5 46.3 0.5 C A:GLY26 4.5 20.9 1.0 CA A:LEU25 4.6 23.2 1.0 N A:ASN27 4.7 20.0 1.0 O A:SER24 4.7 21.2 1.0 C A:GLN121 4.8 28.7 1.0 NE2 A:GLN121 4.9 44.6 0.5 CB A:LEU25 4.9 24.4 1.0

R.Vasireddi, A.Gardais, L.M.G.Chavas. Manufacturing of Ultra-Thin X-Ray-Compatible Coc Microfluidic Devices For Optimal in Situ Macromolecular Crystallography Experiments. Micromachines (Basel) V. 13 2022.
ISSN: ISSN 2072-666X
PubMed: 36014287
DOI: 10.3390/MI13081365