Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401 b:8.3 occ:1.00 OE2 A:GLU217 2.1 13.6 1.0 O A:HOH653 2.2 16.9 1.0 OD1 A:ASP257 2.2 14.7 1.0 OD2 A:ASP255 2.3 16.6 1.0 OD1 A:ASP255 2.3 14.6 1.0 NE2 A:HIS220 2.4 13.8 1.0 CG A:ASP255 2.6 15.2 1.0 CD A:GLU217 3.0 13.8 1.0 CD2 A:HIS220 3.1 13.4 1.0 CG A:ASP257 3.1 15.0 1.0 OE1 A:GLU217 3.4 15.2 1.0 OD2 A:ASP257 3.4 19.9 1.0 CE1 A:HIS220 3.4 14.1 1.0 O A:HOH702 3.8 27.4 1.0 ND2 A:ASN247 4.0 13.9 1.0 O A:HOH591 4.1 14.8 1.0 CB A:ASP255 4.1 13.9 1.0 CG A:HIS220 4.3 12.0 1.0 CG A:GLU217 4.4 13.3 1.0 ND1 A:HIS220 4.4 13.6 1.0 O A:HOH595 4.5 40.6 1.0 CB A:ASP257 4.6 14.8 1.0 O A:HOH576 4.6 30.0 1.0 OD2 A:ASP287 4.7 19.1 1.0 CE A:LYS183 4.8 15.1 1.0 NZ A:LYS183 4.8 19.6 1.0 CA A:ASP257 4.9 13.1 1.0 MG A:MG402 5.0 26.7 1.0 N A:ASP257 5.0 12.7 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg402 b:26.7 occ:1.00 OD2 A:ASP245 2.0 17.2 1.0 OE2 A:GLU181 2.1 24.7 1.0 OD2 A:ASP287 2.1 19.1 1.0 OE1 A:GLU217 2.1 15.2 1.0 O A:HOH576 2.3 30.0 1.0 O A:HOH510 2.4 32.9 1.0 CD A:GLU181 2.9 19.3 1.0 OE1 A:GLU181 3.1 23.7 1.0 CG A:ASP287 3.2 15.3 1.0 CG A:ASP245 3.3 14.6 1.0 CD A:GLU217 3.4 13.8 1.0 CB A:ASP287 3.7 14.9 1.0 O A:HOH720 3.9 30.6 1.0 O A:HOH653 4.0 16.9 1.0 CB A:ASP245 4.0 14.3 1.0 CE1 A:HIS220 4.2 14.1 1.0 CG A:GLU217 4.2 13.3 1.0 OD1 A:ASP245 4.2 16.1 1.0 CB A:GLU217 4.2 12.4 1.0 CG A:GLU181 4.3 17.0 1.0 OD1 A:ASP287 4.3 15.9 1.0 OE2 A:GLU217 4.3 13.6 1.0 ND2 A:ASN215 4.8 17.3 1.0 NE2 A:HIS220 4.8 13.8 1.0 ND1 A:HIS220 4.8 13.6 1.0 MG A:MG401 5.0 8.3 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