Calcium in PDB 1y1e: Human Formylglycine Generating Enzyme

The structure of Human Formylglycine Generating Enzyme, PDB code: 1y1e was solved by M.G.Rudolph, A.Dickmanns, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.80 / 1.73
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.956, 110.014, 43.474, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.2

The binding sites of Calcium atom in the Human Formylglycine Generating Enzyme (pdb code 1y1e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Formylglycine Generating Enzyme, PDB code: 1y1e:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 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 Human Formylglycine Generating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca1001 b:21.7 occ:1.00 OE2 X:GLU130 2.3 21.0 1.0 O X:ALA298 2.4 20.1 1.0 O X:ASN293 2.4 21.9 1.0 O X:HOH1007 2.4 20.5 1.0 O X:GLY296 2.5 21.1 1.0 OE2 X:GLU300 2.5 24.7 1.0 CD X:GLU130 3.3 22.5 1.0 CD X:GLU300 3.4 21.9 1.0 C X:ALA298 3.5 21.3 1.0 N X:ALA298 3.6 21.6 1.0 C X:ASN293 3.6 22.1 1.0 CG X:GLU300 3.7 23.4 1.0 C X:GLY296 3.7 21.2 1.0 CG X:GLU130 3.9 19.5 1.0 CA X:ALA298 4.0 21.2 1.0 O X:ILE294 4.0 23.1 1.0 C X:ILE294 4.2 22.8 1.0 O X:GLY332 4.3 23.2 1.0 OE1 X:GLU130 4.3 21.7 1.0 CB X:ASN297 4.3 22.5 1.0 CA X:ILE294 4.4 22.8 1.0 N X:GLY296 4.4 21.6 1.0 C X:ASN297 4.4 21.5 1.0 N X:ILE294 4.4 22.3 1.0 C X:VAL295 4.4 22.3 1.0 CB X:ASN293 4.4 21.3 1.0 OE1 X:GLU300 4.5 22.6 1.0 N X:ASN297 4.5 21.0 1.0 NH2 X:ARG364 4.6 23.7 1.0 N X:TRP299 4.6 21.9 1.0 CA X:GLY296 4.6 21.2 1.0 CA X:ASN293 4.6 21.5 1.0 CA X:ASN297 4.6 21.9 1.0 CB X:ALA298 4.6 21.4 1.0 O X:VAL295 4.6 22.4 1.0 N X:VAL295 4.7 23.1 1.0 CA X:VAL295 4.9 22.7 1.0 C X:TRP299 4.9 21.9 1.0 CA X:TRP299 4.9 22.0 1.0

Calcium binding site 2 out of 2 in 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 Human Formylglycine Generating Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca1002 b:21.1 occ:1.00 O X:ILE260 2.3 22.1 1.0 OD1 X:ASN259 2.3 22.4 1.0 O X:PHE275 2.4 22.4 1.0 OD2 X:ASP273 2.4 23.6 1.0 OD1 X:ASP273 2.5 24.1 1.0 O X:HOH1013 2.5 22.7 1.0 O X:HOH1011 2.5 22.3 1.0 CG X:ASP273 2.8 23.7 1.0 C X:ILE260 3.5 22.4 1.0 C X:PHE275 3.6 21.9 1.0 CG X:ASN259 3.6 21.5 1.0 N X:ILE260 3.8 21.5 1.0 OE1 X:GLN262 4.1 24.1 1.0 C X:ASN259 4.2 20.4 1.0 CA X:ILE260 4.2 22.0 1.0 CB X:ASP273 4.3 23.4 1.0 CA X:ASN259 4.3 20.8 1.0 CA X:PHE275 4.4 21.9 1.0 N X:PHE275 4.4 21.6 1.0 NE2 X:GLN262 4.4 23.5 1.0 CB X:PHE275 4.4 21.4 1.0 ND2 X:ASN259 4.5 20.3 1.0 N X:TRP261 4.5 22.4 1.0 CB X:ASN259 4.5 20.9 1.0 N X:GLN276 4.6 22.8 1.0 O X:TYR334 4.6 24.6 1.0 OD1 X:ASN269 4.6 25.8 1.0 ND2 X:ASN269 4.6 20.8 1.0 CD X:GLN262 4.6 24.1 1.0 CA X:GLN276 4.7 23.4 1.0 O X:GLN276 4.7 23.1 1.0 CA X:TRP261 4.7 23.3 1.0 O X:GLY277 4.9 22.6 1.0 C X:GLN276 4.9 22.9 1.0 O X:ASN259 4.9 19.6 1.0 CB X:TYR334 4.9 24.3 1.0

T.Dierks, A.Dickmanns, A.Preusser-Kunze, B.Schmidt, M.Mariappan, K.Von Figura, R.Ficner, M.G.Rudolph. Molecular Basis For Multiple Sulfatase Deficiency and Mechanism For Formylglycine Generation of the Human Formylglycine-Generating Enzyme. Cell(Cambridge,Mass.) V. 121 541 2005.
ISSN: ISSN 0092-8674
PubMed: 15907468
DOI: 10.1016/J.CELL.2005.03.001