Calcium in PDB 6ddu: Mouse Beta-Mannosidase Bound to Beta-D-Mannose (Manba)

All present enzymatic activity of Mouse Beta-Mannosidase Bound to Beta-D-Mannose (Manba):
3.2.1.25;

The structure of Mouse Beta-Mannosidase Bound to Beta-D-Mannose (Manba), PDB code: 6ddu was solved by H.Gytz, J.Liang, Y.Liang, A.Gorelik, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.39 / 2.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.162, 65.651, 104.531, 90.00, 92.73, 90.00
R / Rfree (%)	19.9 / 24.6

The binding sites of Calcium atom in the Mouse Beta-Mannosidase Bound to Beta-D-Mannose (Manba) (pdb code 6ddu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Mouse Beta-Mannosidase Bound to Beta-D-Mannose (Manba), PDB code: 6ddu:

Calcium binding site 1 out of 1 in the Mouse Beta-Mannosidase Bound to Beta-D-Mannose (Manba)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse Beta-Mannosidase Bound to Beta-D-Mannose (Manba) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:75.8 occ:1.00 O A:PRO523 2.5 41.5 1.0 OD1 A:ASN509 2.5 52.0 1.0 O A:SER525 2.7 51.3 1.0 O A:TYR528 2.7 41.8 1.0 O A:THR508 2.8 45.5 1.0 O A:ASP530 2.9 36.5 1.0 H A:SER525 3.2 63.3 1.0 HG22 A:ILE531 3.4 59.8 1.0 HB3 A:SER525 3.4 61.5 1.0 N A:SER525 3.4 52.8 1.0 HG23 A:ILE531 3.4 59.8 1.0 C A:PRO523 3.5 49.3 1.0 HA A:ASN509 3.5 54.9 1.0 C A:SER525 3.6 46.7 1.0 C A:THR508 3.7 44.1 1.0 C A:TYR528 3.7 44.6 1.0 CG A:ASN509 3.7 52.7 1.0 HA3 A:GLY529 3.8 50.9 1.0 CG2 A:ILE531 3.8 49.9 1.0 CA A:SER525 3.9 50.4 1.0 O A:HOH1009 3.9 53.5 1.0 C A:TYR524 3.9 54.2 1.0 HA A:TYR524 4.0 61.2 1.0 C A:ASP530 4.0 34.9 1.0 HA A:PRO523 4.0 58.4 1.0 CB A:SER525 4.1 51.3 1.0 N A:ASP530 4.1 42.2 1.0 HB2 A:TYR528 4.1 64.5 1.0 C A:GLY529 4.1 43.5 1.0 H A:ASP530 4.1 50.7 1.0 H A:TYR528 4.2 57.9 1.0 CA A:ASN509 4.2 45.8 1.0 N A:ASN509 4.3 44.4 1.0 CA A:TYR524 4.3 51.0 1.0 N A:TYR524 4.3 51.8 1.0 HB2 A:PRO507 4.3 46.1 1.0 HG21 A:ILE531 4.3 59.8 1.0 CA A:GLY529 4.3 42.4 1.0 CA A:PRO523 4.4 48.6 1.0 N A:GLY529 4.4 44.6 1.0 H A:THR508 4.4 44.9 1.0 CB A:ASN509 4.6 49.4 1.0 O A:GLY529 4.6 47.3 1.0 HD21 A:ASN509 4.6 64.0 1.0 O A:ASP522 4.6 57.8 1.0 N A:THR508 4.6 37.4 1.0 O A:TYR524 4.6 56.7 1.0 ND2 A:ASN509 4.6 53.3 1.0 HA A:ILE531 4.6 44.5 1.0 CA A:TYR528 4.6 48.5 1.0 CA A:ASP530 4.7 40.7 1.0 CA A:THR508 4.7 39.5 1.0 HB2 A:SER525 4.7 61.5 1.0 CB A:TYR528 4.8 53.7 1.0 N A:TYR528 4.8 48.2 1.0 HA A:SER525 4.8 60.5 1.0 HA A:THR508 4.8 47.5 1.0 N A:ILE526 4.9 40.2 1.0 N A:ILE531 4.9 33.5 1.0 HB3 A:TYR528 4.9 64.5 1.0 H A:ASN509 5.0 53.3 1.0 HA A:ILE526 5.0 47.0 1.0 OG A:SER525 5.0 52.5 1.0

H.Gytz, J.Liang, Y.Liang, A.Gorelik, K.Illes, B.Nagar. The Structure of Mammalian Beta-Mannosidase Provides Insight Into Beta-Mannosidosis and Nystagmus. Febs J. V. 286 1319 2019.
ISSN: ISSN 1742-4658
PubMed: 30552791
DOI: 10.1111/FEBS.14731