Calcium in PDB 2hib: Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization

The structure of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization, PDB code: 2hib was solved by M.G.Rudolph, D.Roeser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.83 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.890, 109.110, 43.492, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 23.8

The structure of Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization also contains other interesting chemical elements:

Iodine

(I)

11 atoms

The binding sites of Calcium atom in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization (pdb code 2hib). 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, C336S Mutant, Iodide Co- Crystallization, PDB code: 2hib:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


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, C336S Mutant, Iodide Co- Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca1001 b:26.8 occ:1.00 O X:HOH1045 2.2 26.9 1.0 O X:ASN293 2.4 27.7 1.0 OE2 X:GLU130 2.4 25.1 1.0 O X:ALA298 2.4 25.8 1.0 O X:GLY296 2.4 25.2 1.0 OE2 X:GLU300 2.4 26.6 1.0 CD X:GLU300 3.4 26.9 1.0 CD X:GLU130 3.4 25.2 1.0 C X:ALA298 3.5 26.3 1.0 C X:ASN293 3.6 26.2 1.0 CG X:GLU300 3.7 26.9 1.0 N X:ALA298 3.7 25.9 1.0 C X:GLY296 3.7 25.7 1.0 O X:ILE294 3.7 25.7 1.0 C X:ILE294 4.0 26.1 1.0 CG X:GLU130 4.0 24.6 1.0 CA X:ALA298 4.2 25.8 1.0 CA X:ILE294 4.3 25.9 1.0 C X:VAL295 4.3 26.6 1.0 N X:GLY296 4.3 26.7 1.0 CB X:ASN297 4.4 25.7 1.0 OE1 X:GLU130 4.4 25.4 1.0 N X:ILE294 4.4 26.0 1.0 O X:GLY332 4.4 27.1 1.0 CB X:ASN293 4.5 26.2 1.0 C X:ASN297 4.5 25.9 1.0 OE1 X:GLU300 4.5 25.8 1.0 NH2 X:ARG364 4.5 24.0 1.0 O X:VAL295 4.6 27.2 1.0 N X:VAL295 4.6 25.9 1.0 N X:ASN297 4.6 25.4 1.0 CA X:ASN293 4.6 26.6 1.0 CA X:GLY296 4.6 25.9 1.0 N X:TRP299 4.6 26.4 1.0 CA X:ASN297 4.7 25.6 1.0 CA X:VAL295 4.7 26.8 1.0 CB X:ALA298 4.8 25.0 1.0 C X:TRP299 4.9 26.1 1.0 CA X:TRP299 5.0 26.7 1.0

Calcium binding site 2 out of 2 in the Human Formylglycine Generating Enzyme, C336S Mutant, Iodide Co- Crystallization


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, C336S Mutant, Iodide Co- Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca1002 b:26.0 occ:1.00 O X:ILE260 2.3 25.7 1.0 O X:PHE275 2.3 26.7 1.0 OD1 X:ASN259 2.3 23.6 1.0 O X:HOH1022 2.4 24.2 1.0 O X:HOH1080 2.5 31.0 1.0 OD1 X:ASP273 2.5 30.3 1.0 OD2 X:ASP273 2.5 29.3 1.0 CG X:ASP273 2.8 29.0 1.0 C X:ILE260 3.5 26.2 1.0 C X:PHE275 3.5 27.1 1.0 CG X:ASN259 3.6 24.8 1.0 N X:ILE260 3.8 25.2 1.0 OE1 X:GLN262 4.1 29.6 1.0 C X:ASN259 4.2 25.0 1.0 CA X:ILE260 4.2 25.7 1.0 CA X:ASN259 4.3 25.1 1.0 CB X:ASP273 4.3 27.4 1.0 CA X:PHE275 4.4 26.3 1.0 NE2 X:GLN262 4.4 26.9 1.0 ND2 X:ASN259 4.4 22.7 1.0 N X:PHE275 4.5 27.1 1.0 N X:GLN276 4.5 28.4 1.0 CB X:PHE275 4.5 25.8 1.0 N X:TRP261 4.5 26.9 1.0 CB X:ASN259 4.5 24.3 1.0 O X:TYR334 4.6 28.9 1.0 O X:GLN276 4.6 29.2 1.0 CA X:GLN276 4.6 29.4 1.0 CD X:GLN262 4.6 28.8 1.0 OD1 X:ASN269 4.7 30.3 1.0 ND2 X:ASN269 4.7 25.8 1.0 CA X:TRP261 4.7 27.6 1.0 C X:GLN276 4.9 29.2 1.0 O X:GLY277 4.9 29.1 1.0 CB X:TYR334 4.9 28.7 1.0 O X:ASN259 4.9 23.8 1.0

D.Roeser, B.Schmidt, A.Preusser-Kunze, M.G.Rudolph. Probing the Oxygen-Binding Site of the Human Formylglycine-Generating Enzyme Using Halide Ions. Acta Crystallogr.,Sect.D V. 63 621 2007.
ISSN: ISSN 0907-4449
PubMed: 17452787
DOI: 10.1107/S0907444907009961