Calcium 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:

Potassium	(K)	2 atoms
Cobalt	(Co)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Diol Dehydratase Complexed with Adomecbl and 1,2-Propanediol, PDB code: 7xrl:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca602 b:7.2 occ:1.00 OE1 A:GLU221 2.3 8.3 1.0 OE1 A:GLU170 2.4 8.7 1.0 OE1 A:GLN141 2.4 11.1 1.0 OE1 A:GLN296 2.4 10.1 1.0 O A:SER362 2.4 9.4 1.0 O2 A:PGO601 2.5 10.5 1.0 O1 A:PGO601 2.5 9.7 1.0 C2 A:PGO601 3.3 16.4 1.0 CD A:GLU170 3.3 12.8 1.0 C1 A:PGO601 3.3 11.8 1.0 CD A:GLU221 3.3 10.4 1.0 C A:SER362 3.4 8.4 1.0 CD A:GLN296 3.4 8.3 1.0 CD A:GLN141 3.5 12.3 1.0 OE2 A:GLU170 3.6 8.1 1.0 OE2 A:GLU221 3.7 10.5 1.0 NE2 A:GLN296 3.8 7.2 1.0 CB A:SER362 4.0 9.6 1.0 NE2 A:HIS143 4.1 8.0 1.0 NE2 A:GLN141 4.1 9.8 1.0 OG A:SER362 4.2 7.5 1.0 OD2 A:ASP335 4.2 9.0 1.0 CA A:SER362 4.2 10.8 1.0 NE2 A:GLN200 4.2 9.9 1.0 N A:GLY363 4.3 10.4 1.0 CA A:GLY363 4.5 10.5 1.0 CD2 A:HIS143 4.5 10.3 1.0 CG A:GLU221 4.6 6.5 1.0 CG A:GLU170 4.6 7.8 1.0 C3 A:PGO601 4.7 12.4 1.0 CG A:GLN296 4.7 5.7 1.0 CG A:GLN141 4.7 9.0 1.0 CB A:GLU170 4.8 10.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca602 b:13.2 occ:1.00 OE1 D:GLU170 2.3 13.6 1.0 O D:SER362 2.3 11.6 1.0 OE1 D:GLN296 2.4 16.5 1.0 OE1 D:GLU221 2.4 16.9 1.0 OE1 D:GLN141 2.4 17.3 1.0 O2 D:PGO601 2.5 16.2 1.0 O1 D:PGO601 2.5 17.6 1.0 CD D:GLU170 3.3 18.3 1.0 CD D:GLU221 3.3 16.2 1.0 C1 D:PGO601 3.3 17.0 1.0 C2 D:PGO601 3.3 20.3 1.0 CD D:GLN296 3.4 17.6 1.0 C D:SER362 3.4 15.1 1.0 CD D:GLN141 3.6 18.2 1.0 OE2 D:GLU170 3.6 16.6 1.0 OE2 D:GLU221 3.7 16.1 1.0 NE2 D:GLN296 3.7 11.8 1.0 CB D:SER362 4.0 11.9 1.0 NE2 D:HIS143 4.1 15.2 1.0 OD2 D:ASP335 4.1 13.2 1.0 NE2 D:GLN200 4.1 13.8 1.0 NE2 D:GLN141 4.1 13.0 1.0 OG D:SER362 4.2 10.6 1.0 CA D:SER362 4.2 14.3 1.0 N D:GLY363 4.3 12.7 1.0 CA D:GLY363 4.5 12.0 1.0 CD2 D:HIS143 4.5 16.4 1.0 CG D:GLU221 4.5 11.8 1.0 CG D:GLU170 4.6 17.7 1.0 C3 D:PGO601 4.7 20.3 1.0 CG D:GLN296 4.7 12.7 1.0 CG D:GLN141 4.8 13.9 1.0 CB D:GLU170 4.8 14.9 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