Calcium in PDB 4aq0: Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin

All present enzymatic activity of Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin:
3.2.1.24;

The structure of Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin, PDB code: 4aq0 was solved by E.Baranova, P.Tiels, N.Callewaert, H.Remaut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.50 / 2.09
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.620, 91.790, 224.210, 90.00, 90.00, 90.00
R / Rfree (%)	17.027 / 20.349

The binding sites of Calcium atom in the Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin (pdb code 4aq0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin, PDB code: 4aq0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1772 b:40.9 occ:1.00 O A:HOH2418 2.4 14.7 1.0 OD1 A:ASN588 2.4 17.3 1.0 OD2 A:ASP662 2.5 15.1 1.0 OE1 A:GLU589 2.6 15.5 1.0 CD A:GLU589 3.4 15.8 1.0 CG A:ASP662 3.5 12.8 1.0 OE2 A:GLU589 3.6 16.6 1.0 CG A:ASN588 3.7 16.3 1.0 O A:HOH2460 3.8 30.8 1.0 O A:HOH2272 3.8 22.9 1.0 OD1 A:ASP662 3.9 12.7 1.0 NE2 A:GLN536 4.1 20.2 1.0 O A:HOH2273 4.3 21.7 1.0 CA A:ASN588 4.4 14.3 1.0 O A:ASP660 4.4 12.5 1.0 OD1 A:ASP355 4.4 13.7 1.0 O A:ALA587 4.5 12.7 1.0 N A:GLU589 4.5 14.2 1.0 CB A:ASN588 4.5 14.7 1.0 ND2 A:ASN588 4.6 18.1 1.0 CB A:ASP660 4.7 12.7 1.0 CB A:ASP662 4.8 12.1 1.0 CG A:GLU589 4.8 14.8 1.0 OE1 A:GLN536 4.9 22.3 1.0 CD A:GLN536 4.9 20.9 1.0 CB A:ALA625 4.9 12.6 1.0 N A:ASP660 4.9 12.4 1.0 C A:ASN588 5.0 14.5 1.0

Calcium binding site 2 out of 2 in the Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the GH92 Family Glycosyl Hydrolase CCMAN5 in Complex with Deoxymannojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1772 b:30.7 occ:1.00 OD1 B:ASN588 2.4 21.8 1.0 OE1 B:GLU589 2.5 20.0 1.0 OD2 B:ASP662 2.6 12.1 1.0 O3 B:DMJ1773 2.6 24.4 1.0 O2 B:DMJ1773 2.6 26.3 1.0 O B:HOH2439 2.7 15.1 1.0 O B:HOH2440 2.9 31.6 1.0 CD B:GLU589 3.5 21.3 1.0 CG B:ASN588 3.6 20.1 1.0 CG B:ASP662 3.6 12.5 1.0 C2 B:DMJ1773 3.6 25.6 1.0 C3 B:DMJ1773 3.7 24.8 1.0 O B:HOH2408 3.7 23.2 1.0 OE2 B:GLU589 3.7 22.8 1.0 OD1 B:ASP355 3.8 16.0 1.0 O B:HOH2057 3.8 12.7 1.0 OD1 B:ASP662 4.0 13.2 1.0 ND2 B:ASN588 4.3 21.9 1.0 CA B:ASN588 4.4 18.4 1.0 C4 B:DMJ1773 4.5 24.4 1.0 OE1 B:GLN536 4.5 23.8 1.0 N B:GLU589 4.6 19.1 1.0 CB B:ASN588 4.6 18.6 1.0 CB B:ASP660 4.7 13.0 1.0 O B:ASP660 4.7 12.7 1.0 CG B:ASP355 4.8 15.7 1.0 O B:ALA587 4.8 16.1 1.0 CB B:ASP662 4.8 12.1 1.0 CG B:GLU589 4.9 20.1 1.0 C1 B:DMJ1773 4.9 25.1 1.0

P.Tiels, E.Baranova, K.Piens, C.De Visscher, G.Pynaert, W.Nerinckx, J.Stout, F.Fudalej, P.Hulpiau, S.Tannler, S.Geysens, A.Van Hecke, A.Valevska, W.Vervecken, H.Remaut, N.Callewaert. A Bacterial Glycosidase Enables Mannose-6-Phosphate Modification and Improved Cellular Uptake of Yeast-Produced Recombinant Human Lysosomal Enzymes. Nat.Biotechnol. V. 30 1225 2012.
ISSN: ISSN 1087-0156
PubMed: 23159880
DOI: 10.1038/NBT.2427