Sodium in PDB 6ybr: Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip.

All present enzymatic activity of Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip.:
5.3.1.5;

The structure of Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip., PDB code: 6ybr was solved by J.A.Gavira, S.Martinez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.99 / 1.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.990, 99.380, 103.100, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 13.1

The structure of Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip. also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip. (pdb code 6ybr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip., PDB code: 6ybr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:28.7 occ:1.00 OD1 A:ASP163 2.7 19.7 1.0 O A:HOH526 2.8 31.6 1.0 OH A:TYR212 2.9 21.5 1.0 N A:ARG208 3.0 21.3 1.0 N A:GLU207 3.4 19.0 0.3 N A:GLU207 3.4 19.1 0.7 CE1 A:TYR212 3.4 19.4 1.0 CZ A:TYR212 3.6 19.1 1.0 CB A:GLU207 3.6 21.3 0.3 CA A:ASP163 3.6 17.0 1.0 CG A:ASP163 3.7 18.2 1.0 CB A:ARG208 3.7 25.1 1.0 CA A:GLU207 3.8 20.7 0.3 CB A:GLU207 3.8 24.5 0.7 CA A:GLU207 3.8 21.3 0.7 C A:GLU207 3.8 22.1 0.7 C A:GLU207 3.8 21.7 0.3 CA A:ARG208 3.8 22.4 1.0 CB A:LEU206 4.0 17.0 1.0 CG A:ARG208 4.1 30.4 1.0 CB A:ASP163 4.1 17.9 1.0 C A:LEU206 4.2 19.2 1.0 C A:ARG208 4.2 20.4 1.0 O A:ARG208 4.3 21.2 1.0 O A:PHE162 4.3 17.5 1.0 O A:ASP163 4.4 19.9 1.0 N A:ASP163 4.4 16.3 1.0 C A:ASP163 4.5 17.9 1.0 CA A:LEU206 4.6 17.7 1.0 CD1 A:TYR212 4.6 18.4 1.0 C A:PHE162 4.6 16.2 1.0 CD A:ARG208 4.7 39.0 1.0 CG A:GLU207 4.7 25.1 0.3 OD2 A:ASP163 4.8 20.2 1.0 CG A:GLU207 4.8 27.2 0.7 CA A:GLY166 4.8 19.3 1.0 CE2 A:TYR212 4.8 18.4 1.0 O A:HOH511 4.9 50.1 1.0 O A:GLU207 5.0 24.3 0.7 CG A:LEU206 5.0 17.1 1.0 O A:GLU207 5.0 24.7 0.3

Sodium binding site 2 out of 2 in the Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rt Structure of Glucose Isomerase Obtained at 1.20 A Resolution From Crystal Grown in A Mylar Microchip. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:18.5 occ:1.00 OE1 A:GLN222 2.7 16.1 1.0 O A:HOH645 2.9 16.7 1.0 N A:ASP264 2.9 12.8 1.0 N A:GLN249 3.0 11.9 1.0 O A:GLN249 3.1 13.9 1.0 CA A:GLY248 3.5 12.9 1.0 CD A:GLN222 3.6 14.7 1.0 O A:ALA262 3.6 15.7 1.0 NE2 A:GLN222 3.7 16.4 1.0 CA A:GLY263 3.7 14.9 1.0 CB A:ASP264 3.7 14.0 1.0 O A:HOH627 3.8 15.6 1.0 C A:GLY248 3.8 12.1 1.0 C A:GLY263 3.8 13.7 1.0 CA A:ASP264 3.8 12.3 1.0 C A:GLN249 3.9 12.2 1.0 CA A:GLN249 3.9 11.7 1.0 CG1 A:VAL218 3.9 14.5 1.0 O A:ASP264 4.2 12.9 1.0 CB A:GLN249 4.2 12.0 1.0 C A:ASP264 4.4 12.4 1.0 O A:HOH648 4.4 25.5 1.0 O A:ASN247 4.5 13.1 1.0 C A:ALA262 4.5 14.2 1.0 N A:GLY263 4.6 14.9 1.0 N A:GLY248 4.8 12.0 1.0 O A:GLY263 5.0 15.9 1.0 O A:GLY248 5.0 13.6 1.0

J.A.Gavira, I.Rodriguez-Ruiz, S.Martinez-Rodriguez, S.Basu, S.Teychene, A.A.Mccarthy, C.Mueller-Dieckman. Attaining Atomic Resolution From in Situ Data Collection at Room Temperature Using Counter-Diffusion-Based Low-Cost Microchips. Acta Crystallogr D Struct V. 76 751 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32744257
DOI: 10.1107/S2059798320008475