Calcium in PDB 2eab: Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum (Apo Form)

All present enzymatic activity of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum (Apo Form):
3.2.1.63;

The structure of Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum (Apo Form), PDB code: 2eab 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)	35.05 / 1.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.183, 112.035, 98.317, 90.00, 94.74, 90.00
R / Rfree (%)	17.5 / 18.9

The binding sites of Calcium atom in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum (Apo Form) (pdb code 2eab). 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 (Apo Form), PDB code: 2eab:
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 (Apo Form)


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 (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca899 b:8.3 occ:1.00 O A:SER385 2.7 6.9 1.0 OE2 A:GLU76 2.7 6.3 1.0 O A:LEU392 2.7 5.9 1.0 O A:GLY56 2.9 7.3 1.0 O A:HOH5069 3.0 7.6 1.0 CG2 A:ILE399 3.5 7.2 1.0 CD A:GLU76 3.7 6.4 1.0 C A:LEU392 3.7 6.0 1.0 O A:PRO393 3.7 5.7 1.0 OG A:SER390 3.8 7.4 1.0 CB A:GLU76 3.8 6.0 1.0 C A:SER385 3.9 6.9 1.0 CB A:SER390 3.9 7.5 1.0 C A:PRO393 4.0 5.7 1.0 C A:GLY56 4.1 7.1 1.0 CG A:GLU76 4.3 6.5 1.0 N A:SER394 4.4 5.7 1.0 CA A:LEU392 4.5 6.0 1.0 N A:LEU392 4.5 6.2 1.0 CA A:PRO393 4.6 6.2 1.0 N A:PRO393 4.6 6.2 1.0 CB A:LEU392 4.6 6.0 1.0 OE1 A:GLU76 4.7 6.8 1.0 CA A:SER386 4.7 6.8 1.0 N A:SER386 4.7 6.4 1.0 CA A:GLY56 4.7 7.3 1.0 CA A:SER394 4.8 5.9 1.0 CA A:SER385 4.8 6.9 1.0 O A:GLY398 4.9 6.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum (Apo Form)


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 (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca899 b:7.9 occ:1.00 OE1 B:GLU76 2.6 6.3 1.0 O B:SER385 2.7 6.4 1.0 O B:LEU392 2.7 5.8 1.0 O B:GLY56 2.9 7.1 1.0 O B:HOH5044 3.0 7.4 1.0 CG2 B:ILE399 3.5 6.2 1.0 CD B:GLU76 3.7 6.0 1.0 C B:LEU392 3.7 5.9 1.0 OG B:SER390 3.8 7.0 1.0 O B:PRO393 3.8 5.4 1.0 CB B:GLU76 3.8 5.7 1.0 CB B:SER390 3.9 6.9 1.0 C B:SER385 3.9 6.2 1.0 C B:GLY56 4.0 6.7 1.0 C B:PRO393 4.0 5.5 1.0 CG B:GLU76 4.3 5.7 1.0 N B:SER394 4.5 5.4 1.0 N B:LEU392 4.5 6.2 1.0 CA B:LEU392 4.5 5.9 1.0 N B:PRO393 4.6 6.0 1.0 CA B:PRO393 4.6 6.0 1.0 OE2 B:GLU76 4.6 6.6 1.0 CB B:LEU392 4.6 6.3 1.0 CA B:GLY56 4.7 6.6 1.0 CA B:SER386 4.7 6.1 1.0 N B:SER386 4.7 6.0 1.0 CA B:SER385 4.8 6.3 1.0 CA B:SER394 4.8 5.7 1.0 O B:GLY398 5.0 5.7 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