Calcium in PDB 1y1j: Human Formylglycine Generating Enzyme, Sulfonic Acid/Desulfurated Form

The structure of Human Formylglycine Generating Enzyme, Sulfonic Acid/Desulfurated Form, PDB code: 1y1j 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)	41.10 / 1.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.180, 109.655, 43.484, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.3

The binding sites of Calcium atom in the Human Formylglycine Generating Enzyme, Sulfonic Acid/Desulfurated Form (pdb code 1y1j). 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, Sulfonic Acid/Desulfurated Form, PDB code: 1y1j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Formylglycine Generating Enzyme, Sulfonic Acid/Desulfurated Form


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, Sulfonic Acid/Desulfurated Form within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca1001 b:9.3 occ:1.00 O X:ALA298 2.3 9.2 1.0 OE2 X:GLU130 2.3 9.6 1.0 O X:ASN293 2.4 8.7 1.0 OE2 X:GLU300 2.4 9.2 1.0 O X:HOH1004 2.4 7.8 1.0 O X:GLY296 2.4 9.3 1.0 CD X:GLU130 3.3 8.8 1.0 CD X:GLU300 3.4 9.6 1.0 C X:ALA298 3.5 9.2 1.0 C X:ASN293 3.6 8.7 1.0 CG X:GLU300 3.6 10.2 1.0 N X:ALA298 3.6 9.1 1.0 C X:GLY296 3.6 8.7 1.0 CG X:GLU130 3.9 8.3 1.0 O X:ILE294 4.0 10.2 1.0 CA X:ALA298 4.1 9.4 1.0 C X:ILE294 4.1 10.5 1.0 CA X:ILE294 4.3 9.9 1.0 O X:GLY332 4.3 9.3 1.0 OE1 X:GLU130 4.3 9.0 1.0 CB X:ASN297 4.3 8.4 1.0 N X:GLY296 4.4 8.4 1.0 N X:ILE294 4.4 9.3 1.0 CB X:ASN293 4.4 8.3 1.0 C X:VAL295 4.4 8.6 1.0 OE1 X:GLU300 4.5 7.8 1.0 C X:ASN297 4.5 9.4 1.0 NH2 X:ARG364 4.5 7.8 1.0 N X:ASN297 4.5 8.5 1.0 N X:TRP299 4.6 7.9 1.0 CA X:GLY296 4.6 8.9 1.0 CA X:ASN293 4.6 8.7 1.0 O X:VAL295 4.6 8.5 1.0 CB X:ALA298 4.7 8.8 1.0 CA X:ASN297 4.7 8.9 1.0 N X:VAL295 4.7 10.5 1.0 CA X:VAL295 4.9 9.6 1.0 C X:TRP299 4.9 7.8 1.0 CA X:TRP299 4.9 8.4 1.0

Calcium binding site 2 out of 2 in the Human Formylglycine Generating Enzyme, Sulfonic Acid/Desulfurated Form


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, Sulfonic Acid/Desulfurated Form within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca1002 b:9.1 occ:1.00 OD1 X:ASN259 2.3 9.9 1.0 O X:ILE260 2.3 10.8 1.0 O X:PHE275 2.3 9.0 1.0 O X:HOH1011 2.4 10.1 1.0 OD2 X:ASP273 2.4 9.4 1.0 O X:HOH1008 2.4 9.4 1.0 OD1 X:ASP273 2.5 9.6 1.0 CG X:ASP273 2.8 10.3 1.0 C X:ILE260 3.5 10.7 1.0 CG X:ASN259 3.5 9.9 1.0 C X:PHE275 3.6 9.8 1.0 N X:ILE260 3.8 10.4 1.0 OE1 X:GLN262 4.1 10.0 1.0 C X:ASN259 4.2 9.3 1.0 CB X:ASP273 4.3 9.6 1.0 CA X:ILE260 4.3 10.5 1.0 CA X:ASN259 4.3 8.7 1.0 CA X:PHE275 4.4 9.1 1.0 ND2 X:ASN259 4.4 9.3 1.0 N X:PHE275 4.4 9.6 1.0 NE2 X:GLN262 4.4 10.0 1.0 CB X:PHE275 4.5 9.0 1.0 O X:TYR334 4.5 10.8 1.0 N X:GLN276 4.5 9.8 1.0 CB X:ASN259 4.5 9.2 1.0 N X:TRP261 4.5 9.8 1.0 O X:GLN276 4.6 11.3 1.0 ND2 X:ASN269 4.6 11.4 1.0 CA X:GLN276 4.6 10.4 1.0 OD1 X:ASN269 4.6 12.3 1.0 CD X:GLN262 4.7 8.0 1.0 CA X:TRP261 4.7 10.6 1.0 C X:GLN276 4.8 10.1 1.0 O X:GLY277 4.9 9.2 1.0 CB X:TYR334 4.9 10.3 1.0 O X:ASN259 4.9 8.7 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