Calcium in PDB 3fcx: Crystal Structure of Human Esterase D

All present enzymatic activity of Crystal Structure of Human Esterase D:
3.1.2.12;

The structure of Crystal Structure of Human Esterase D, PDB code: 3fcx was solved by D.Wu, Y.Li, G.Song, D.Zhang, N.Shaw, Z.J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.16 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.542, 70.724, 65.014, 90.00, 108.84, 90.00
R / Rfree (%)	17.6 / 19.6

The structure of Crystal Structure of Human Esterase D also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

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

Calcium binding site 1 out of 3 in the Crystal Structure of Human Esterase D


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 Human Esterase D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca284 b:26.7 occ:1.00 O A:HOH544 2.4 38.8 1.0 O A:HOH554 2.4 44.0 1.0 N A:GLN227 3.3 16.9 1.0 N A:HIS260 3.5 12.9 1.0 CB A:ASP259 3.5 13.5 1.0 CB A:HIS260 3.7 13.4 1.0 CB A:GLN227 3.9 18.1 1.0 CA A:ASP226 3.9 16.4 1.0 O A:ASP225 4.0 17.8 1.0 C A:ASP226 4.1 16.5 1.0 CA A:GLN227 4.2 17.4 1.0 CA A:ASP259 4.2 13.3 1.0 CA A:HIS260 4.2 13.0 1.0 OD1 A:ASP226 4.2 15.6 1.0 C A:ASP259 4.3 13.1 1.0 O A:HOH634 4.4 51.0 1.0 CG A:ASP259 4.5 14.0 1.0 CG A:ASP226 4.7 15.5 1.0 C A:ASP225 4.8 17.4 1.0 N A:ASP226 4.8 16.9 1.0 CB A:ASP226 4.9 16.1 1.0 CG A:HIS260 5.0 14.3 1.0 OD2 A:ASP259 5.0 15.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Human Esterase D


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 Human Esterase D within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca283 b:35.5 occ:1.00 OD1 B:ASN281 2.8 36.7 1.0 NZ B:LYS39 2.8 31.4 1.0 O B:GLY75 2.8 13.5 1.0 O B:HIS74 3.3 13.9 1.0 CD B:LYS39 3.5 28.3 1.0 CD B:PRO46 3.5 16.6 1.0 CG B:ASN281 3.5 35.5 1.0 C B:GLY75 3.6 13.2 1.0 CE B:LYS39 3.7 24.0 1.0 ND2 B:ASN281 3.7 37.0 1.0 CA B:GLY75 3.9 13.5 1.0 CG B:PRO46 4.1 16.6 1.0 C B:HIS74 4.2 13.9 1.0 N B:GLY75 4.5 13.8 1.0 CD2 B:LEU76 4.6 14.2 1.0 N B:LEU76 4.7 12.8 1.0 N B:PRO46 4.8 16.5 1.0 CB B:ASN281 4.8 34.3 1.0 CG B:LYS39 4.9 24.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Human Esterase D


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 Human Esterase D within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca284 b:28.6 occ:1.00 O B:VAL107 2.8 11.3 1.0 O B:GLY104 2.8 11.0 1.0 N B:MET120 3.3 12.3 1.0 O B:TYR118 3.3 14.4 1.0 C B:TYR118 3.3 15.0 1.0 CB B:MET120 3.5 11.8 1.0 CG B:MET120 3.5 12.6 1.0 C B:GLY104 3.6 10.5 1.0 CB B:TYR118 3.6 17.1 1.0 CA B:TYR118 3.7 16.3 1.0 N B:ARG119 3.8 14.0 1.0 CA B:GLY104 3.8 10.4 1.0 C B:VAL107 3.9 11.1 1.0 CD2 B:TYR118 3.9 24.3 1.0 CA B:MET120 4.0 11.8 1.0 N B:VAL107 4.0 10.5 1.0 CG2 B:VAL107 4.0 11.9 1.0 C B:ARG119 4.3 12.8 1.0 CG B:TYR118 4.3 20.9 1.0 CA B:ARG119 4.3 13.4 1.0 CA B:VAL107 4.5 11.0 1.0 N B:TYR106 4.6 10.1 1.0 N B:PHE105 4.9 10.4 1.0 N B:TYR121 4.9 11.4 1.0 CB B:VAL107 4.9 11.0 1.0 N B:ASP108 4.9 11.6 1.0 N B:ALA109 4.9 12.2 1.0 C B:TYR106 5.0 10.4 1.0 CA B:TYR106 5.0 10.2 1.0 C B:MET120 5.0 11.6 1.0 O B:HOH338 5.0 11.7 1.0

D.Wu, Y.Li, G.Song, D.Zhang, N.Shaw, Z.J.Liu. Crystal Structure of Human Esterase D: A Potential Genetic Marker of Retinoblastoma Faseb J. V. 23 1441 2009.
ISSN: ISSN 0892-6638
PubMed: 19126594
DOI: 10.1096/FJ.08-125286