Calcium in PDB 7cdy: Crystal Structure of Glucose Dehydrogenase

The structure of Crystal Structure of Glucose Dehydrogenase, PDB code: 7cdy was solved by S.Jia, D.Xu, W.Wang, T.Ran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.48 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.364, 88.612, 80.77, 90, 106.42, 90
R / Rfree (%)	16.6 / 18.1

The binding sites of Calcium atom in the Crystal Structure of Glucose Dehydrogenase (pdb code 7cdy). 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 Glucose Dehydrogenase, PDB code: 7cdy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Glucose Dehydrogenase


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 Glucose Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:9.5 occ:1.00 O A:TYR227 2.3 9.7 1.0 O A:HOH850 2.4 11.5 1.0 O A:HOH614 2.4 10.6 1.0 O A:HOH662 2.4 9.2 1.0 OE2 A:GLU217 2.4 12.3 1.0 OE1 A:GLU217 2.5 11.2 1.0 O A:HOH685 2.5 10.2 1.0 CD A:GLU217 2.8 10.2 1.0 C A:TYR227 3.5 9.7 1.0 HB3 A:TYR227 3.5 10.2 1.0 HD3 A:PRO257 3.9 14.2 1.0 HD21 A:ASN219 4.0 10.8 0.0 H A:TRP229 4.1 9.1 1.0 CG A:GLU217 4.3 15.1 1.0 CA A:TYR227 4.3 8.8 1.0 CB A:TYR227 4.3 10.2 1.0 HA3 A:GLY228 4.4 9.8 1.0 O A:HOH593 4.4 14.5 1.0 HA A:TYR227 4.4 8.8 1.0 HB2 A:TRP229 4.5 8.3 1.0 N A:GLY228 4.5 9.6 1.0 O A:ALA232 4.6 10.6 1.0 O A:GLY189 4.6 9.2 1.0 N A:TRP229 4.6 9.1 1.0 O A:HOH670 4.6 11.9 1.0 OE1 A:GLU209 4.6 9.6 1.0 O A:GLU255 4.6 10.9 0.6 O A:GLU255 4.6 10.6 0.4 HG2 A:GLU217 4.7 15.1 1.0 ND2 A:ASN219 4.7 10.8 1.0 HG3 A:GLU217 4.7 15.1 1.0 OD1 A:ASN219 4.7 10.5 1.0 HB2 A:TYR227 4.8 10.2 1.0 O A:HOH636 4.8 12.1 1.0 HD2 A:TYR227 4.8 12.1 1.0 CD A:PRO257 4.8 14.2 1.0 O A:HOH558 4.8 11.7 1.0 HG3 A:PRO257 4.8 17.0 1.0 CA A:GLY228 4.8 9.8 1.0 HB3 A:PRO257 4.8 15.9 1.0 HA A:THR233 4.8 10.0 1.0 HB3 A:ALA232 4.9 11.5 1.0 HB3 A:GLU217 4.9 12.3 1.0 C A:GLY228 5.0 9.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Glucose Dehydrogenase


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 Glucose Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:16.5 occ:1.00 O B:TYR227 2.3 13.8 1.0 O B:HOH630 2.4 17.1 1.0 O B:HOH650 2.4 13.7 1.0 O B:HOH792 2.4 24.2 1.0 OE1 B:GLU217 2.5 15.3 1.0 O B:HOH565 2.6 22.4 1.0 OE2 B:GLU217 2.6 26.1 1.0 CD B:GLU217 2.9 21.7 1.0 HB3 B:TYR227 3.3 12.1 1.0 C B:TYR227 3.4 11.7 1.0 HD21 B:ASN219 3.8 12.7 0.0 HD3 B:PRO257 3.8 19.0 1.0 CB B:TYR227 4.1 12.1 1.0 CA B:TYR227 4.1 12.7 1.0 HA B:TYR227 4.2 12.7 1.0 H B:TRP229 4.3 13.3 1.0 HA3 B:GLY228 4.3 14.8 1.0 O B:HOH613 4.3 28.2 1.0 CG B:GLU217 4.4 27.5 1.0 N B:GLY228 4.5 12.6 1.0 HD2 B:TYR227 4.5 12.6 1.0 O B:ALA232 4.5 25.9 1.0 HB2 B:TYR227 4.5 12.1 1.0 O B:GLY189 4.5 12.9 1.0 O B:HOH632 4.6 24.0 1.0 O B:GLU255 4.6 16.1 1.0 ND2 B:ASN219 4.6 12.7 1.0 OD1 B:ASN219 4.6 14.0 1.0 HB2 B:TRP229 4.6 14.2 1.0 OE1 B:GLU209 4.6 13.8 1.0 N B:TRP229 4.7 13.3 1.0 HB3 B:PRO257 4.8 18.6 1.0 CD B:PRO257 4.8 19.0 1.0 CA B:GLY228 4.8 14.8 1.0 HG3 B:PRO257 4.8 21.3 1.0 O B:HOH512 4.8 25.1 1.0 HA B:THR233 4.8 28.5 1.0 HG3 B:GLU217 4.8 27.5 1.0 HG2 B:GLU217 4.8 27.5 1.0 O B:HOH787 4.8 27.6 1.0 HB3 B:GLU217 5.0 19.0 1.0

S.Jia, D.Xu, W.Wang, T.Ran. Structure of Glucose Dehydrogenase at 1.33 Angstroms To Be Published.