Potassium in PDB 7xrl: Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol

All present enzymatic activity of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol:
4.2.1.28;

The structure of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol, PDB code: 7xrl was solved by N.Shibata, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.72 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.718, 117.246, 201.55, 90, 90, 90
R / Rfree (%)	16.7 / 20.6

The structure of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Potassium atom in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol (pdb code 7xrl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol, PDB code: 7xrl:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol within 5.0Å range: probe atom residue distance (Å) B Occ A:K603 b:12.8 occ:1.00 OE2 A:GLU265 2.7 10.5 1.0 OE1 A:GLU280 2.7 10.2 1.0 O A:GLY261 2.8 11.5 1.0 O A:HOH895 2.8 9.4 1.0 O A:HOH767 2.9 8.2 1.0 SG A:CYS283 3.0 13.8 1.0 OG A:SER264 3.0 14.1 1.0 OE1 A:GLU265 3.4 12.3 1.0 CD A:GLU265 3.4 8.9 1.0 C A:GLY261 3.6 12.1 1.0 N A:GLY261 3.9 8.8 1.0 CA A:GLU280 3.9 10.7 1.0 CD A:GLU280 4.0 8.8 1.0 CB A:SER264 4.1 11.1 1.0 CB A:GLU280 4.2 10.3 1.0 N A:GLU280 4.3 10.0 1.0 CB A:CYS283 4.3 7.8 1.0 N A:SER262 4.3 10.7 1.0 CA A:GLY261 4.3 6.8 1.0 CA A:SER262 4.4 11.5 1.0 O A:LEU279 4.5 8.9 1.0 N A:SER264 4.5 10.7 1.0 C A:LEU279 4.6 11.4 1.0 N A:GLY227 4.7 9.8 1.0 N A:GLY263 4.7 8.9 1.0 CG A:GLU280 4.7 12.3 1.0 CB A:SER260 4.7 10.8 1.0 C A:SER262 4.8 11.3 1.0 CG A:GLU265 4.8 9.4 1.0 CA A:SER264 4.9 11.9 1.0 OE2 A:GLU280 4.9 7.7 1.0 C A:SER260 4.9 10.0 1.0

Potassium binding site 2 out of 2 in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol within 5.0Å range: probe atom residue distance (Å) B Occ D:K603 b:15.6 occ:1.00 OE2 D:GLU265 2.7 12.3 1.0 OE1 D:GLU280 2.8 12.8 1.0 O D:HOH780 2.8 10.8 1.0 O D:GLY261 2.9 11.6 1.0 O D:HOH757 3.0 10.7 1.0 SG D:CYS283 3.0 15.7 1.0 OG D:SER264 3.1 14.2 1.0 OE1 D:GLU265 3.2 13.6 1.0 CD D:GLU265 3.3 12.0 1.0 C D:GLY261 3.5 11.7 1.0 N D:GLY261 3.9 10.1 1.0 CA D:GLU280 3.9 9.2 1.0 CD D:GLU280 4.0 12.5 1.0 CB D:GLU280 4.2 10.2 1.0 N D:SER262 4.2 11.0 1.0 CB D:SER264 4.2 15.3 1.0 N D:GLU280 4.3 10.4 1.0 CB D:CYS283 4.3 9.7 1.0 CA D:GLY261 4.3 13.2 1.0 CA D:SER262 4.4 11.6 1.0 O D:LEU279 4.4 12.7 1.0 C D:LEU279 4.5 12.7 1.0 N D:SER264 4.5 12.4 1.0 CB D:SER260 4.6 12.4 1.0 N D:GLY227 4.7 13.7 1.0 N D:GLY263 4.7 15.5 1.0 CG D:GLU280 4.7 11.0 1.0 C D:SER262 4.8 13.6 1.0 CG D:GLU265 4.8 14.1 1.0 OE2 D:GLU280 4.9 12.8 1.0 C D:SER260 4.9 15.0 1.0 CA D:SER264 5.0 12.6 1.0

N.Shibata, Y.Higuchi, B.Krautler, T.Toraya. Structural Insights Into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase. Chemistry V. 28 02196 2022.
ISSN: ISSN 0947-6539
PubMed: 35974426
DOI: 10.1002/CHEM.202202196