Calcium in PDB 1y1i: Hyuman Formylglycine Generating Enzyme, Reduced Form

The structure of Hyuman Formylglycine Generating Enzyme, Reduced Form, PDB code: 1y1i 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)	31.40 / 2.61
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.633, 109.365, 43.364, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 25.2

The binding sites of Calcium atom in the Hyuman Formylglycine Generating Enzyme, Reduced Form (pdb code 1y1i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Hyuman Formylglycine Generating Enzyme, Reduced Form, PDB code: 1y1i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Hyuman Formylglycine Generating Enzyme, Reduced Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hyuman Formylglycine Generating Enzyme, Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca1001 b:24.1 occ:1.00 O X:HOH1095 2.2 29.2 1.0 OE2 X:GLU130 2.3 22.5 1.0 O X:ALA298 2.4 21.4 1.0 O X:ASN293 2.4 24.8 1.0 O X:GLY296 2.4 24.0 1.0 OE2 X:GLU300 2.5 28.8 1.0 CD X:GLU300 3.4 24.1 1.0 CD X:GLU130 3.4 25.7 1.0 CG X:GLU300 3.5 24.1 1.0 C X:ALA298 3.5 22.7 1.0 C X:ASN293 3.6 25.1 1.0 O X:ILE294 3.6 27.2 1.0 C X:GLY296 3.7 24.3 1.0 N X:ALA298 3.7 22.9 1.0 CG X:GLU130 4.0 26.5 1.0 C X:ILE294 4.0 26.1 1.0 O X:GLY332 4.1 23.7 1.0 CA X:ALA298 4.2 22.3 1.0 N X:GLY296 4.3 25.2 1.0 C X:VAL295 4.3 25.4 1.0 CA X:ILE294 4.4 25.9 1.0 CB X:ASN297 4.4 23.4 1.0 N X:ILE294 4.4 25.3 1.0 OE1 X:GLU300 4.5 20.4 1.0 OE1 X:GLU130 4.5 23.8 1.0 CB X:ASN293 4.5 25.5 1.0 C X:ASN297 4.6 23.0 1.0 N X:ASN297 4.6 23.7 1.0 N X:TRP299 4.6 23.3 1.0 CA X:GLY296 4.6 25.0 1.0 O X:VAL295 4.6 25.1 1.0 N X:VAL295 4.6 25.9 1.0 NH2 X:ARG364 4.7 24.4 1.0 CA X:ASN293 4.7 25.2 1.0 CA X:VAL295 4.7 25.7 1.0 CA X:ASN297 4.7 23.1 1.0 CB X:ALA298 4.8 22.4 1.0 C X:TRP299 4.9 24.2 1.0 CA X:TRP299 4.9 23.8 1.0 CB X:GLU300 5.0 24.7 1.0 O X:TRP299 5.0 23.9 1.0

Calcium binding site 2 out of 2 in the Hyuman Formylglycine Generating Enzyme, Reduced Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hyuman Formylglycine Generating Enzyme, Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca1002 b:19.6 occ:1.00 O X:PHE275 2.2 27.4 1.0 OD2 X:ASP273 2.3 21.6 1.0 O X:ILE260 2.3 27.1 1.0 OD1 X:ASN259 2.4 28.2 1.0 O X:HOH1027 2.4 18.1 1.0 O X:HOH1032 2.4 21.2 1.0 OD1 X:ASP273 2.5 23.1 1.0 CG X:ASP273 2.8 22.4 1.0 C X:PHE275 3.4 28.0 1.0 C X:ILE260 3.5 26.4 1.0 CG X:ASN259 3.6 25.8 1.0 N X:ILE260 3.7 25.4 1.0 OE1 X:GLN262 3.9 28.3 1.0 CA X:ILE260 4.2 25.5 1.0 C X:ASN259 4.2 24.7 1.0 CB X:ASP273 4.3 23.1 1.0 CA X:PHE275 4.3 26.4 1.0 N X:GLN276 4.4 29.8 1.0 CA X:ASN259 4.4 24.6 1.0 CA X:GLN276 4.4 31.1 1.0 N X:PHE275 4.4 25.8 1.0 ND2 X:ASN259 4.4 26.2 1.0 CB X:PHE275 4.4 25.9 1.0 O X:TYR334 4.4 25.6 1.0 ND2 X:ASN269 4.5 26.2 1.0 OD1 X:ASN269 4.5 26.3 1.0 N X:TRP261 4.5 26.9 1.0 O X:GLN276 4.6 32.9 1.0 CB X:ASN259 4.6 24.6 1.0 O X:GLY277 4.7 32.2 1.0 CD X:GLN262 4.7 28.8 1.0 C X:GLN276 4.7 31.7 1.0 NE2 X:GLN262 4.8 28.9 1.0 CA X:TRP261 4.8 27.1 1.0 CB X:TYR334 4.9 26.5 1.0 CA X:GLY271 5.0 26.6 1.0 CG X:ASN269 5.0 25.9 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