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Calcium in PDB 3edf: Structural Base For Cyclodextrin Hydrolysis

Enzymatic activity of Structural Base For Cyclodextrin Hydrolysis

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

Protein crystallography data

The structure of Structural Base For Cyclodextrin Hydrolysis, PDB code: 3edf 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) 19.57 / 1.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.542, 111.107, 106.602, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Base For Cyclodextrin Hydrolysis (pdb code 3edf). 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: 3edf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3edf

Go back to Calcium Binding Sites List in 3edf
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:Ca602

b:12.5
occ:1.00
 O A:TYR315 2.3 12.2 1.0
OG A:SER222 2.4 13.2 1.0
O A:HOH825 2.4 13.2 1.0
O A:THR270 2.4 10.8 1.0
OD1 A:ASP280 2.4 13.3 1.0
O A:HOH858 2.4 15.4 1.0
OD2 A:ASP280 2.5 11.8 1.0
CG A:ASP280 2.8 14.4 1.0
C A:THR270 3.3 11.6 1.0
C A:TYR315 3.5 12.1 1.0
CB A:SER222 3.6 12.4 1.0
O A:SER222 3.8 14.0 1.0
CA A:THR270 4.1 12.6 1.0
N A:LYS271 4.1 13.4 1.0
CA A:SER222 4.2 11.5 1.0
O A:HOH845 4.2 14.9 1.0
CB A:ASP280 4.3 12.6 1.0
CB A:TYR315 4.3 11.3 1.0
CA A:LYS271 4.3 13.7 1.0
C A:SER222 4.3 12.4 1.0
N A:SER316 4.4 11.2 1.0
CA A:TYR315 4.4 10.8 1.0
O A:GLY272 4.4 13.8 1.0
CA A:SER316 4.4 13.3 1.0
O A:HOH940 4.6 14.7 1.0
O A:PHE269 4.6 12.6 1.0
O A:LEU281 4.6 12.7 1.0
C A:LYS271 4.7 13.1 1.0
OD1 A:ASN241 4.8 19.1 1.0
OE1 A:GLN283 4.8 14.8 1.0
O A:LYS271 4.9 13.6 1.0
CB A:THR270 5.0 12.4 1.0
O A:HOH834 5.0 14.5 1.0

Calcium binding site 2 out of 4 in 3edf

Go back to Calcium Binding Sites List in 3edf
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:Ca603

b:15.6
occ:1.00
 OD1 A:ASP125 2.3 17.5 1.0
OD1 A:ASP146 2.4 15.4 1.0
OD1 A:ASN124 2.4 16.8 1.0
O A:ASP121 2.4 18.3 1.0
O A:GLY144 2.4 14.5 1.0
OD1 A:ASN119 2.5 16.2 1.0
O A:HOH897 2.6 14.7 1.0
CG A:ASN119 3.3 15.9 1.0
C A:ASP121 3.4 19.0 1.0
CG A:ASP146 3.4 15.3 1.0
C A:GLY144 3.5 14.7 1.0
CG A:ASN124 3.6 18.2 1.0
CG A:ASP125 3.6 16.8 1.0
ND2 A:ASN119 3.9 17.4 1.0
CB A:ASP146 3.9 15.2 1.0
N A:ASP125 3.9 16.4 1.0
CA A:GLY144 4.0 15.2 1.0
CA A:PRO122 4.1 19.2 1.0
N A:PRO122 4.1 19.2 1.0
N A:ASP121 4.2 19.2 1.0
CA A:ASP125 4.2 16.7 1.0
ND2 A:ASN124 4.2 17.8 1.0
C A:ASN124 4.3 16.9 1.0
CA A:ASP121 4.3 19.8 1.0
OD2 A:ASP125 4.4 17.2 1.0
O A:ARG194 4.4 15.4 1.0
CB A:ASN119 4.4 16.0 1.0
C A:PRO122 4.5 18.7 1.0
OD2 A:ASP146 4.5 15.3 1.0
CB A:ASP125 4.5 16.5 1.0
N A:ASN124 4.5 16.8 1.0
C A:GLY145 4.5 13.8 1.0
CA A:ASN119 4.5 17.0 1.0
CB A:ASP121 4.6 20.7 1.0
O A:GLY145 4.6 14.1 1.0
N A:GLY145 4.6 13.2 1.0
O A:PRO122 4.7 18.0 1.0
CA A:ASN124 4.7 16.9 1.0
CB A:ASN124 4.7 17.1 1.0
N A:ASP146 4.7 14.8 1.0
O A:ASN124 4.8 17.4 1.0
C A:ASN119 4.9 17.9 1.0
N A:GLY120 4.9 17.7 1.0
CA A:GLY145 4.9 14.3 1.0
CA A:ASP146 5.0 14.8 1.0

Calcium binding site 3 out of 4 in 3edf

Go back to Calcium Binding Sites List in 3edf
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:Ca602

b:15.1
occ:1.00
 O B:TYR315 2.4 13.9 1.0
O B:HOH1240 2.4 14.8 1.0
O B:HOH1224 2.4 16.0 1.0
O B:THR270 2.4 14.2 1.0
OD1 B:ASP280 2.4 14.3 1.0
OG B:SER222 2.5 13.8 1.0
OD2 B:ASP280 2.5 13.4 1.0
CG B:ASP280 2.8 16.0 1.0
C B:THR270 3.3 13.7 1.0
C B:TYR315 3.5 13.7 1.0
CB B:SER222 3.7 14.9 1.0
O B:SER222 3.8 15.3 1.0
CA B:THR270 4.1 14.2 1.0
N B:LYS271 4.1 14.3 1.0
O B:HOH1214 4.2 16.1 1.0
CA B:SER222 4.2 14.6 1.0
CB B:ASP280 4.3 15.2 1.0
CB B:TYR315 4.3 13.1 1.0
CA B:LYS271 4.4 14.2 1.0
C B:SER222 4.4 13.9 1.0
O B:GLY272 4.4 14.5 1.0
N B:SER316 4.4 13.5 1.0
CA B:TYR315 4.4 13.7 1.0
CA B:SER316 4.5 13.9 1.0
O B:PHE269 4.5 13.7 1.0
O B:LEU281 4.6 16.0 1.0
O B:HOH1288 4.6 17.4 1.0
C B:LYS271 4.6 14.6 1.0
OD1 B:ASN241 4.8 19.9 1.0
OE1 B:GLN283 4.8 18.9 1.0
O B:LYS271 4.9 14.6 1.0
CB B:THR270 5.0 14.4 1.0
CA B:ASP280 5.0 15.6 1.0

Calcium binding site 4 out of 4 in 3edf

Go back to Calcium Binding Sites List in 3edf
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:Ca603

b:19.2
occ:1.00
 OD1 B:ASN124 2.3 19.7 1.0
OD1 B:ASP146 2.4 20.4 1.0
OD1 B:ASP125 2.4 20.2 1.0
O B:ASP121 2.4 22.7 1.0
O B:GLY144 2.5 16.6 1.0
OD1 B:ASN119 2.5 19.9 1.0
O B:HOH1254 2.6 17.1 1.0
C B:ASP121 3.3 22.8 1.0
CG B:ASN119 3.4 18.8 1.0
CG B:ASP146 3.4 17.7 1.0
CG B:ASN124 3.5 20.9 1.0
C B:GLY144 3.5 17.1 1.0
CG B:ASP125 3.6 21.0 1.0
CB B:ASP146 3.8 17.2 1.0
ND2 B:ASN119 3.9 18.4 1.0
N B:ASP125 3.9 21.1 1.0
CA B:GLY144 4.0 17.5 1.0
N B:PRO122 4.1 23.1 1.0
CA B:PRO122 4.1 22.9 1.0
N B:ASP121 4.2 22.6 1.0
ND2 B:ASN124 4.2 20.8 1.0
CA B:ASP121 4.2 23.9 1.0
C B:ASN124 4.2 21.4 1.0
CA B:ASP125 4.2 20.6 1.0
O B:ARG194 4.4 19.3 1.0
OD2 B:ASP125 4.4 20.8 1.0
OD2 B:ASP146 4.4 17.8 1.0
CB B:ASN119 4.5 17.2 1.0
C B:PRO122 4.5 22.7 1.0
N B:ASN124 4.5 22.5 1.0
CA B:ASN119 4.6 17.9 1.0
CB B:ASP125 4.6 20.5 1.0
C B:GLY145 4.6 17.1 1.0
CB B:ASP121 4.6 24.1 1.0
O B:PRO122 4.6 22.2 1.0
O B:GLY145 4.7 16.6 1.0
N B:GLY145 4.7 17.0 1.0
CA B:ASN124 4.7 21.4 1.0
CB B:ASN124 4.7 21.4 1.0
O B:ASN124 4.7 20.7 1.0
N B:ASP146 4.8 16.5 1.0
C B:ASN119 4.9 19.0 1.0
CA B:GLY145 4.9 16.3 1.0
N B:GLY120 5.0 18.9 1.0
CA B:ASP146 5.0 16.7 1.0

Reference:

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
Page generated: Tue Jul 8 11:51:30 2025

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