Calcium in PDB 5nxl: Formylglycine Generating Enzyme From T. Curvata in Complex with Ag(I)

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

The structure of Formylglycine Generating Enzyme From T. Curvata in Complex with Ag(I), PDB code: 5nxl 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)	39.63 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.947, 65.572, 99.501, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.8

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

Silver

(Ag)

1 atom

The binding sites of Calcium atom in the Formylglycine Generating Enzyme From T. Curvata in Complex with Ag(I) (pdb code 5nxl). 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 Ag(I), PDB code: 5nxl:
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 Ag(I)


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 Ag(I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca415 b:14.2 occ:1.00 OD1 A:ASN188 2.3 13.9 1.0 O A:ILE189 2.3 11.7 1.0 O A:HOH542 2.4 12.5 1.0 O A:TYR204 2.4 15.5 1.0 O A:HOH553 2.5 16.6 1.0 OD2 A:ASP202 2.5 17.3 1.0 OD1 A:ASP202 2.5 14.6 1.0 CG A:ASP202 2.9 16.5 1.0 C A:ILE189 3.5 13.0 1.0 CG A:ASN188 3.5 12.9 1.0 C A:TYR204 3.6 20.6 1.0 N A:ILE189 3.8 12.7 1.0 C A:ASN188 4.1 11.0 1.0 CA A:ILE189 4.2 11.0 1.0 CA A:ASN188 4.2 12.1 1.0 OE1 A:GLN191 4.3 15.5 1.0 CA A:TYR204 4.3 19.2 1.0 CB A:TYR204 4.3 17.3 1.0 N A:TYR204 4.3 17.6 1.0 OD2 A:ASP198 4.4 15.7 1.0 CB A:ASP202 4.4 16.1 1.0 ND2 A:ASN188 4.4 11.8 1.0 CB A:ASN188 4.4 13.5 1.0 OD1 A:ASP198 4.5 16.2 1.0 NE2 A:GLN191 4.5 13.6 1.0 O A:PHE267 4.5 13.9 1.0 N A:TRP190 4.5 11.8 1.0 N A:THR205 4.6 16.5 1.0 CA A:TRP190 4.7 13.4 1.0 CB A:PHE267 4.7 13.0 1.0 CD A:GLN191 4.7 14.6 1.0 O A:GLY206 4.8 12.5 1.0 CA A:THR205 4.9 13.1 1.0 CG A:ASP198 4.9 18.9 1.0 O A:ASN188 4.9 15.0 1.0 CA A:GLY200 5.0 20.6 1.0

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


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 Ag(I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca416 b:19.0 occ:1.00 O A:VAL227 2.6 11.3 1.0 O A:GLY225 2.6 13.0 1.0 O A:VAL223 2.7 13.8 1.0 O A:ASN222 3.1 14.1 1.0 O A:HOH526 3.2 14.1 1.0 OE2 A:GLU229 3.2 14.1 1.0 O A:GLY265 3.3 14.0 1.0 C A:VAL223 3.4 12.1 1.0 C A:VAL227 3.7 12.5 1.0 C A:GLY225 3.7 10.8 1.0 N A:GLY225 3.7 12.6 1.0 CD A:GLU229 3.7 18.6 1.0 O A:GLY264 3.9 13.4 1.0 C A:GLY264 3.9 9.7 1.0 CA A:GLY264 3.9 9.2 1.0 C A:ALA224 4.0 15.2 1.0 CA A:VAL223 4.0 12.1 1.0 CG A:GLU229 4.1 9.9 1.0 C A:ASN222 4.1 12.6 1.0 N A:VAL227 4.1 11.9 1.0 N A:ALA224 4.2 10.8 1.0 O A:LYS263 4.2 13.4 1.0 CA A:GLY225 4.3 12.6 1.0 CA A:ALA224 4.3 12.8 1.0 C A:GLY265 4.4 12.6 1.0 N A:GLY265 4.5 12.4 1.0 OE1 A:GLU229 4.5 14.4 1.0 O A:ALA224 4.5 14.3 1.0 CA A:VAL227 4.5 9.6 1.0 N A:TRP228 4.5 13.9 1.0 N A:VAL223 4.6 11.2 1.0 CA A:TRP228 4.7 11.1 1.0 N A:ASN226 4.8 11.2 1.0 CZ2 A:TRP160 4.8 10.9 1.0 C A:TRP228 4.9 9.1 1.0 N A:GLY264 4.9 11.4 1.0 C A:LYS263 5.0 13.0 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