Calcium in PDB 1y4j: Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme

The structure of Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme, PDB code: 1y4j was solved by A.Dickmanns, M.G.Rudolph, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.00 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.078, 100.750, 62.704, 90.00, 101.68, 90.00
R / Rfree (%)	17 / 20.5

The binding sites of Calcium atom in the Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme (pdb code 1y4j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme, PDB code: 1y4j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme


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 the Paralogue of the Human Formylglycine Generating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:23.9 occ:1.00 O A:PHE210 2.3 26.0 1.0 OD1 A:ASN194 2.3 22.0 1.0 O A:LEU195 2.3 22.8 1.0 O A:HOH1006 2.4 20.4 1.0 O A:HOH1018 2.4 23.7 1.0 OD2 A:ASP208 2.5 24.1 1.0 OD1 A:ASP208 2.7 25.2 1.0 CG A:ASP208 2.9 24.0 1.0 C A:PHE210 3.5 27.2 1.0 C A:LEU195 3.5 23.1 1.0 CG A:ASN194 3.5 23.3 1.0 N A:LEU195 3.8 23.7 1.0 OD2 A:ASP204 4.2 28.6 1.0 C A:ASN194 4.3 22.9 1.0 CA A:PHE210 4.3 27.3 1.0 CA A:LEU195 4.3 23.4 1.0 ND2 A:ASN194 4.4 22.3 1.0 CA A:ASN194 4.4 22.9 1.0 N A:PHE210 4.4 27.4 1.0 CB A:PHE210 4.4 28.2 1.0 CB A:ASP208 4.4 27.0 1.0 NE2 A:GLN197 4.5 28.4 1.0 N A:HIS211 4.5 27.3 1.0 OE1 A:GLN197 4.5 27.6 1.0 N A:TRP196 4.5 23.8 1.0 CB A:ASN194 4.5 22.3 1.0 O A:TRP257 4.6 21.9 1.0 OD1 A:ASP204 4.6 27.8 1.0 CA A:HIS211 4.6 27.5 1.0 CA A:TRP196 4.7 24.3 1.0 O A:GLY212 4.9 26.4 1.0 CD A:GLN197 4.9 26.9 1.0 CB A:TRP257 4.9 21.8 1.0 CG A:ASP204 4.9 29.4 1.0 CA A:ALA206 5.0 28.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme


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 the Paralogue of the Human Formylglycine Generating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:30.1 occ:1.00 O A:HOH1047 2.5 31.1 1.0 O A:LEU230 2.6 22.3 1.0 O A:ASP229 2.6 22.6 1.0 O A:GLY232 2.6 20.2 1.0 O A:VAL234 2.6 20.1 1.0 OE2 A:GLU236 2.8 20.7 1.0 C A:LEU230 3.4 22.6 1.0 CD A:GLU236 3.6 22.8 1.0 C A:ASP229 3.7 22.4 1.0 C A:VAL234 3.8 20.8 1.0 C A:GLY232 3.8 21.3 1.0 CA A:LEU230 3.9 22.6 1.0 CG A:GLU236 3.9 21.3 1.0 N A:VAL234 4.0 21.1 1.0 O A:ALA255 4.1 22.0 1.0 N A:GLY232 4.1 22.4 1.0 N A:LEU230 4.2 21.8 1.0 C A:LEU231 4.2 23.0 1.0 N A:LEU231 4.3 23.1 1.0 CA A:VAL234 4.4 20.9 1.0 CA A:GLY254 4.5 23.7 1.0 CA A:GLY232 4.5 21.6 1.0 OE1 A:GLU236 4.6 23.1 1.0 O A:LEU231 4.6 23.3 1.0 CA A:LEU231 4.7 23.3 1.0 CG2 A:VAL234 4.7 22.3 1.0 NH1 A:ARG289 4.8 21.1 1.0 CB A:ASN233 4.8 21.0 1.0 N A:TRP235 4.8 20.5 1.0 C A:GLY254 4.8 23.3 1.0 N A:ASN233 4.8 20.5 1.0 O A:GLY254 4.9 23.7 1.0 CA A:ASP229 4.9 22.2 1.0 C A:ASN233 5.0 20.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:27.5 occ:1.00 O B:PHE210 2.3 29.9 1.0 O B:LEU195 2.3 28.0 1.0 O B:HOH2025 2.4 28.6 1.0 OD1 B:ASN194 2.4 24.4 1.0 O B:HOH2021 2.4 27.9 1.0 OD1 B:ASP208 2.5 27.9 1.0 OD2 B:ASP208 2.6 29.6 1.0 CG B:ASP208 2.9 29.4 1.0 C B:PHE210 3.5 29.6 1.0 C B:LEU195 3.5 27.9 1.0 CG B:ASN194 3.6 26.1 1.0 N B:LEU195 3.9 27.8 1.0 C B:ASN194 4.3 28.0 1.0 OD2 B:ASP204 4.3 33.3 1.0 CA B:PHE210 4.3 30.1 1.0 OE1 B:GLN197 4.3 32.8 1.0 CA B:LEU195 4.3 28.1 1.0 CB B:PHE210 4.4 30.0 1.0 CA B:ASN194 4.4 27.5 1.0 CB B:ASP208 4.5 32.5 1.0 N B:PHE210 4.5 30.4 1.0 ND2 B:ASN194 4.5 24.3 1.0 N B:TRP196 4.5 28.6 1.0 N B:HIS211 4.5 30.2 1.0 O B:TRP257 4.5 27.0 1.0 OD1 B:ASP204 4.5 33.1 1.0 NE2 B:GLN197 4.6 29.8 1.0 CA B:TRP196 4.6 29.4 1.0 CB B:ASN194 4.6 27.5 1.0 CA B:HIS211 4.7 30.8 1.0 O B:GLY212 4.9 28.5 1.0 CD B:GLN197 4.9 31.8 1.0 CB B:TRP257 4.9 25.6 1.0 CG B:ASP204 4.9 34.4 1.0 CA B:ALA206 4.9 34.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Paralogue of the Human Formylglycine Generating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:31.7 occ:1.00 O B:LEU230 2.5 23.1 1.0 O B:VAL234 2.6 21.2 1.0 O B:ASP229 2.6 23.9 1.0 O B:HOH2059 2.7 32.6 1.0 O B:GLY232 2.7 23.7 1.0 OE2 B:GLU236 2.8 24.3 1.0 C B:LEU230 3.3 24.0 1.0 CD B:GLU236 3.6 23.2 1.0 C B:ASP229 3.7 24.5 1.0 C B:VAL234 3.7 22.1 1.0 CA B:LEU230 3.8 23.9 1.0 CG B:GLU236 3.8 21.9 1.0 C B:GLY232 3.8 24.2 1.0 N B:VAL234 4.0 24.2 1.0 O B:ALA255 4.1 23.4 1.0 N B:GLY232 4.2 25.3 1.0 N B:LEU230 4.2 24.0 1.0 C B:LEU231 4.3 25.0 1.0 N B:LEU231 4.3 24.5 1.0 CA B:VAL234 4.4 22.6 1.0 CA B:GLY254 4.5 24.6 1.0 CA B:GLY232 4.6 24.5 1.0 CG2 B:VAL234 4.6 21.9 1.0 O B:LEU231 4.6 25.2 1.0 OE1 B:GLU236 4.6 21.0 1.0 CA B:LEU231 4.7 25.1 1.0 NH1 B:ARG289 4.7 22.3 1.0 N B:TRP235 4.8 21.3 1.0 C B:GLY254 4.8 25.1 1.0 CB B:ASN233 4.9 23.1 1.0 N B:ASN233 4.9 23.9 1.0 CA B:ASP229 4.9 24.2 1.0 CZ2 B:TRP169 4.9 24.1 1.0 C B:TRP235 5.0 21.0 1.0 O B:GLY254 5.0 24.7 1.0 CB B:GLU236 5.0 20.8 1.0 O B:ARG253 5.0 25.5 1.0 C B:ASN233 5.0 23.5 1.0

A.Dickmanns, B.Schmidt, M.G.Rudolph, M.Mariappan, T.Dierks, K.Von Figura, R.Ficner. Crystal Structure of Human Pfge, the Paralog of the C{Alpha}-Formylglycine-Generating Enzyme J.Biol.Chem. V. 280 15180 2005.
ISSN: ISSN 0021-9258
PubMed: 15687489
DOI: 10.1074/JBC.M414317200