Calcium in PDB 2eae: Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products

All present enzymatic activity of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products:
3.2.1.63;

The structure of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products, PDB code: 2eae was solved by M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, R.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.63 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.519, 70.878, 170.979, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.9

The binding sites of Calcium atom in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products (pdb code 2eae). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products, PDB code: 2eae:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:26.8 occ:1.00 O A:HOH1232 2.3 26.6 1.0 O A:HOH1094 2.3 20.4 1.0 O A:HOH1181 2.4 26.4 1.0 OD2 A:ASP689 2.5 22.9 1.0 OE1 A:GLU519 2.5 24.4 1.0 O A:HOH1183 2.6 29.6 1.0 OE2 A:GLU519 2.7 21.8 1.0 CD A:GLU519 2.9 24.7 1.0 CG A:ASP689 3.4 20.8 1.0 OD1 A:ASP689 3.6 20.6 1.0 O A:HOH1044 4.1 28.0 1.0 O A:HOH1310 4.2 31.9 1.0 NE A:ARG819 4.2 19.7 1.0 NE2 A:GLN584 4.3 25.3 1.0 OD1 A:ASP588 4.3 22.8 1.0 CG A:GLU519 4.4 25.1 1.0 OD1 A:ASN796 4.6 24.9 1.0 CE2 A:TYR515 4.7 21.4 1.0 CD A:ARG819 4.7 20.6 1.0 CB A:ASP689 4.8 20.1 1.0 O A:ASN783 4.9 20.6 1.0 CD2 A:TYR515 4.9 20.6 1.0 OE1 A:GLU591 4.9 34.1 1.0 CZ A:ARG819 5.0 20.4 1.0 NH2 A:ARG819 5.0 21.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum in Complexes with Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:47.4 occ:1.00 O A:LEU392 2.6 18.0 1.0 O A:SER385 2.7 20.5 1.0 OE1 A:GLU76 2.8 25.7 1.0 O A:HOH1152 3.0 22.1 1.0 O A:GLY56 3.2 24.3 1.0 CG2 A:ILE399 3.5 22.5 1.0 O A:PRO393 3.6 17.9 1.0 C A:LEU392 3.6 18.6 1.0 CD A:GLU76 3.8 26.3 1.0 C A:SER385 3.9 20.1 1.0 C A:PRO393 3.9 18.6 1.0 CB A:GLU76 3.9 23.7 1.0 CB A:SER390 3.9 21.8 1.0 OG A:SER390 4.0 22.9 1.0 C A:GLY56 4.2 23.7 1.0 N A:SER394 4.2 19.3 1.0 CG A:GLU76 4.4 25.6 1.0 CA A:PRO393 4.5 18.4 1.0 CA A:LEU392 4.5 19.3 1.0 N A:PRO393 4.5 18.2 1.0 N A:LEU392 4.6 20.2 1.0 CA A:SER394 4.6 19.3 1.0 CB A:LEU392 4.6 20.8 1.0 CA A:SER386 4.7 21.2 1.0 N A:SER386 4.7 19.8 1.0 CA A:SER385 4.8 19.6 1.0 OE2 A:GLU76 4.8 25.7 1.0 CA A:GLY56 4.9 22.6 1.0 O A:GLY398 5.0 20.2 1.0

M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, R.Kato. Structural Basis on the Catalytic Reaction Mechanism of Novel 1,2-Alpha-L-Fucosidase (Afca) From Bifidobacterium Bifidum J.Biol.Chem. V. 282 18497 2007.
ISSN: ISSN 0021-9258
PubMed: 17459873
DOI: 10.1074/JBC.M702246200