Calcium in PDB 5nyy: Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II)

All present enzymatic activity of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II):
2.7.11.1;

The structure of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II), PDB code: 5nyy was solved by M.Meury, M.Knop, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.21 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.314, 67.648, 100.021, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 16.7

The structure of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II) also contains other interesting chemical elements:

Cadmium

(Cd)

1 atom

The binding sites of Calcium atom in the Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II) (pdb code 5nyy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II), PDB code: 5nyy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:7.8 occ:1.00 O A:HOH547 2.3 9.1 1.0 OD1 A:ASN188 2.3 7.5 1.0 O A:ILE189 2.3 8.8 1.0 O A:TYR204 2.4 9.7 1.0 O A:HOH582 2.4 8.7 1.0 OD2 A:ASP202 2.5 8.1 1.0 OD1 A:ASP202 2.5 8.9 1.0 CG A:ASP202 2.8 8.9 1.0 C A:ILE189 3.5 8.1 1.0 C A:TYR204 3.5 10.2 1.0 CG A:ASN188 3.6 7.4 1.0 N A:ILE189 3.8 7.7 1.0 C A:ASN188 4.2 6.7 1.0 OE1 A:GLN191 4.2 9.5 1.0 CA A:ILE189 4.3 8.4 1.0 CA A:ASN188 4.3 7.2 1.0 CA A:TYR204 4.3 9.4 1.0 CB A:TYR204 4.3 10.8 1.0 OD2 A:ASP198 4.3 10.6 1.0 CB A:ASP202 4.4 8.4 1.0 N A:TYR204 4.4 9.2 1.0 O A:PHE267 4.4 8.7 1.0 ND2 A:ASN188 4.5 8.0 1.0 CB A:ASN188 4.5 7.2 1.0 NE2 A:GLN191 4.5 9.6 1.0 OD1 A:ASP198 4.5 10.4 1.0 N A:TRP190 4.5 9.3 1.0 N A:THR205 4.5 8.7 0.6 N A:THR205 4.6 10.8 0.4 CA A:THR205 4.6 9.3 0.6 CA A:TRP190 4.7 8.7 1.0 CD A:GLN191 4.7 8.9 1.0 CA A:THR205 4.8 9.6 0.4 CB A:PHE267 4.9 8.5 1.0 CG A:ASP198 4.9 9.0 1.0 O A:GLY206 4.9 9.5 1.0 O A:ASN188 5.0 7.0 1.0 CA A:GLY200 5.0 11.6 1.0

Calcium binding site 2 out of 2 in the Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Formylglycine Generating Enzyme From T. Curvata in Complex with Cd(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:12.2 occ:1.00 O A:VAL227 2.5 7.4 1.0 O A:GLY225 2.6 8.2 1.0 O A:VAL223 2.7 9.7 1.0 O A:ASN222 3.1 7.4 1.0 O A:HOH633 3.1 7.9 1.0 O A:GLY265 3.3 9.0 1.0 OE1 A:GLU229 3.3 8.4 1.0 C A:VAL223 3.4 8.4 1.0 C A:VAL227 3.6 7.2 1.0 C A:GLY225 3.7 6.4 1.0 CA A:GLY264 3.8 8.3 1.0 O A:GLY264 3.8 10.6 1.0 C A:GLY264 3.8 8.6 1.0 N A:GLY225 3.8 7.0 1.0 CD A:GLU229 3.9 7.2 1.0 N A:VAL227 4.0 6.2 1.0 C A:ALA224 4.1 7.5 1.0 CA A:VAL223 4.1 8.1 1.0 C A:ASN222 4.1 6.5 1.0 CG A:GLU229 4.2 7.4 1.0 O A:LYS263 4.2 8.2 1.0 N A:ALA224 4.2 7.7 1.0 CA A:GLY225 4.3 7.4 1.0 C A:GLY265 4.4 7.7 1.0 CA A:ALA224 4.4 7.9 1.0 CA A:VAL227 4.5 6.6 1.0 N A:GLY265 4.5 8.0 1.0 N A:TRP228 4.5 6.8 1.0 O A:ALA224 4.6 7.6 1.0 N A:VAL223 4.6 6.6 1.0 OE2 A:GLU229 4.7 7.3 1.0 CA A:TRP228 4.7 6.8 1.0 N A:ASN226 4.8 6.5 1.0 CZ2 A:TRP160 4.9 7.3 1.0 N A:GLY264 4.9 7.4 1.0 C A:ASN226 4.9 6.3 1.0 C A:LYS263 5.0 7.5 1.0

M.Meury, M.Knop, F.P.Seebeck. Structural Basis For Copper-Oxygen Mediated C-H Bond Activation By the Formylglycine-Generating Enzyme. Angew. Chem. Int. Ed. Engl. V. 56 8115 2017.
ISSN: ESSN 1521-3773
PubMed: 28544744
DOI: 10.1002/ANIE.201702901