Calcium in PDB 3edd: Structural Base For Cyclodextrin Hydrolysis

All present enzymatic activity of Structural Base For Cyclodextrin Hydrolysis:
3.2.1.54;

The structure of Structural Base For Cyclodextrin Hydrolysis, PDB code: 3edd was solved by S.Buedenbender, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.61 / 2.65
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	183.758, 183.758, 233.272, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 26.7

The binding sites of Calcium atom in the Structural Base For Cyclodextrin Hydrolysis (pdb code 3edd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural Base For Cyclodextrin Hydrolysis, PDB code: 3edd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structural Base For Cyclodextrin Hydrolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Base For Cyclodextrin Hydrolysis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca700 b:40.4 occ:1.00 O A:GLY144 2.3 41.0 1.0 OD1 A:ASP125 2.3 43.9 1.0 OD1 A:ASN124 2.4 44.6 1.0 OD1 A:ASP146 2.4 43.0 1.0 O A:ASP121 2.4 44.1 1.0 OD1 A:ASN119 2.6 41.9 1.0 C A:GLY144 3.4 41.0 1.0 CG A:ASP146 3.4 42.9 1.0 C A:ASP121 3.4 43.9 1.0 CG A:ASN119 3.5 41.5 1.0 CG A:ASP125 3.6 44.2 1.0 CG A:ASN124 3.6 44.2 1.0 N A:ASP125 3.8 44.1 1.0 CB A:ASP146 3.8 42.8 1.0 CA A:GLY144 3.9 40.7 1.0 ND2 A:ASN119 4.0 41.2 1.0 C A:ASN124 4.0 44.0 1.0 CA A:ASP125 4.2 44.2 1.0 N A:PRO122 4.2 43.9 1.0 O A:ARG194 4.2 37.9 1.0 CA A:PRO122 4.2 43.9 1.0 ND2 A:ASN124 4.3 44.2 1.0 O A:ASN124 4.3 43.9 1.0 N A:ASP121 4.4 43.3 1.0 OD2 A:ASP125 4.4 44.7 1.0 CA A:ASP121 4.4 43.7 1.0 CB A:ASP125 4.5 44.2 1.0 C A:GLY145 4.5 42.0 1.0 N A:GLY145 4.5 41.3 1.0 OD2 A:ASP146 4.5 42.9 1.0 N A:ASN124 4.5 44.0 1.0 CA A:ASN124 4.6 44.0 1.0 C A:PRO122 4.6 43.9 1.0 O A:GLY145 4.6 42.1 1.0 CB A:ASN119 4.6 41.1 1.0 N A:ASP146 4.6 42.4 1.0 CB A:ASN124 4.7 44.0 1.0 CA A:ASN119 4.7 41.1 1.0 CB A:ASP121 4.7 43.8 1.0 CA A:GLY145 4.8 41.7 1.0 O A:PRO122 4.8 43.9 1.0 CA A:ASP146 4.9 42.8 1.0

Calcium binding site 2 out of 4 in the Structural Base For Cyclodextrin Hydrolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Base For Cyclodextrin Hydrolysis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:49.1 occ:1.00 O A:THR270 2.3 42.1 1.0 O A:TYR315 2.4 36.6 1.0 OD1 A:ASP280 2.6 39.7 1.0 OD2 A:ASP280 2.6 40.5 1.0 CG A:ASP280 3.0 39.5 1.0 C A:THR270 3.3 42.1 1.0 C A:TYR315 3.5 36.5 1.0 O A:SER222 3.9 33.4 1.0 CB A:SER222 4.1 33.2 1.0 CA A:SER316 4.1 36.4 1.0 CA A:THR270 4.2 42.1 1.0 N A:SER316 4.2 36.5 1.0 O A:LEU281 4.2 38.1 1.0 N A:LYS271 4.2 42.3 1.0 OE1 A:GLN283 4.4 39.6 1.0 CA A:LYS271 4.4 42.5 1.0 CA A:SER222 4.4 33.3 1.0 CB A:ASP280 4.5 39.2 1.0 C A:SER222 4.5 33.4 1.0 CA A:TYR315 4.6 36.5 1.0 CB A:TYR315 4.6 36.4 1.0 O A:HOH708 4.8 13.2 1.0 ND2 A:ASN241 4.8 45.6 1.0 C A:SER316 4.8 36.3 1.0 C A:LYS271 4.8 42.5 1.0 O A:PHE269 4.8 42.2 1.0 O A:GLY272 4.9 42.4 1.0 CB A:THR270 5.0 42.0 1.0

Calcium binding site 3 out of 4 in the Structural Base For Cyclodextrin Hydrolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Base For Cyclodextrin Hydrolysis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca700 b:68.1 occ:1.00 O B:GLY144 2.3 49.7 1.0 OD1 B:ASN124 2.3 54.4 1.0 OD1 B:ASP125 2.4 54.7 1.0 OD1 B:ASP146 2.4 50.5 1.0 O B:ASP121 2.4 52.2 1.0 OD1 B:ASN119 2.9 51.2 1.0 C B:GLY144 3.4 49.8 1.0 CG B:ASP146 3.4 50.2 1.0 CG B:ASN124 3.5 54.2 1.0 C B:ASP121 3.6 52.3 1.0 N B:ASP125 3.6 54.4 1.0 CG B:ASP125 3.6 54.8 1.0 CG B:ASN119 3.8 50.6 1.0 CB B:ASP146 3.8 49.9 1.0 CA B:ASP125 3.9 54.6 1.0 O B:ARG194 3.9 44.5 1.0 C B:ASN124 4.0 54.2 1.0 CA B:GLY144 4.0 49.9 1.0 ND2 B:ASN119 4.2 50.5 1.0 ND2 B:ASN124 4.3 54.2 1.0 CA B:PRO122 4.3 52.7 1.0 CB B:ASP125 4.3 54.6 1.0 N B:PRO122 4.4 52.6 1.0 O B:ASN124 4.5 54.2 1.0 CA B:ASN124 4.5 54.1 1.0 OD2 B:ASP125 4.5 55.0 1.0 N B:ASN124 4.5 53.8 1.0 C B:GLY145 4.5 49.7 1.0 N B:GLY145 4.5 49.7 1.0 CB B:ASN124 4.5 54.1 1.0 CA B:ASP121 4.5 52.0 1.0 OD2 B:ASP146 4.6 50.3 1.0 N B:ASP121 4.6 51.8 1.0 C B:PRO122 4.7 52.9 1.0 N B:ASP146 4.7 49.8 1.0 O B:GLY145 4.7 49.7 1.0 CB B:ASP121 4.8 52.0 1.0 CA B:GLY145 4.8 49.7 1.0 CA B:ASP146 4.9 49.9 1.0 O B:PRO122 4.9 52.8 1.0 CB B:ASN119 4.9 50.4 1.0

Calcium binding site 4 out of 4 in the Structural Base For Cyclodextrin Hydrolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Base For Cyclodextrin Hydrolysis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:53.9 occ:1.00 OD2 B:ASP280 2.6 47.3 1.0 O B:HOH845 2.7 36.5 1.0 O B:THR270 2.8 47.5 1.0 O B:TYR315 2.8 39.8 1.0 OD1 B:ASP280 3.1 47.6 1.0 CG B:ASP280 3.2 47.1 1.0 O B:LEU281 3.3 44.7 1.0 OE1 B:GLN283 3.4 44.2 1.0 O B:SER222 3.4 42.3 1.0 NE2 B:GLN283 3.7 44.2 1.0 C B:TYR315 3.8 39.8 1.0 CD B:GLN283 3.9 43.8 1.0 CA B:SER316 4.0 39.6 1.0 C B:THR270 4.0 47.5 1.0 CA B:SER222 4.0 41.9 1.0 CB B:SER222 4.0 41.9 1.0 C B:SER222 4.1 42.2 1.0 N B:SER316 4.2 39.7 1.0 C B:LEU281 4.4 44.8 1.0 N B:LEU281 4.5 45.7 1.0 CB B:ASP280 4.7 46.6 1.0 OG B:SER316 4.7 40.0 1.0 CA B:THR270 4.7 47.5 1.0 C B:SER316 4.7 39.5 1.0 ND2 B:ASN241 4.8 53.5 1.0 O B:HOH803 4.8 11.3 1.0 N B:ASP317 4.8 39.3 1.0 N B:LYS271 4.9 47.6 1.0 CB B:SER316 4.9 39.7 1.0 CA B:LEU281 5.0 45.1 1.0

S.Buedenbender, G.E.Schulz. Structural Base For Enzymatic Cyclodextrin Hydrolysis J.Mol.Biol. V. 385 606 2009.
ISSN: ISSN 0022-2836
PubMed: 19014948
DOI: 10.1016/J.JMB.2008.10.085