Calcium in PDB 2gvv: Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa)

All present enzymatic activity of Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa):
3.1.8.2;

The structure of Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa), PDB code: 2gvv was solved by J.C.H.Chen, M.M.Blum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.600, 83.020, 87.470, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.6

The binding sites of Calcium atom in the Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa) (pdb code 2gvv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa), PDB code: 2gvv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:12.1 occ:1.00 OAA A:DI9502 2.2 22.8 0.8 OD1 A:ASN175 2.4 14.7 1.0 OD1 A:ASP229 2.4 14.2 1.0 O A:HOH532 2.4 13.2 1.0 OE2 A:GLU21 2.4 16.3 1.0 OD1 A:ASN120 2.4 18.6 1.0 O A:HOH531 2.5 11.9 1.0 CG A:ASN175 3.4 14.5 1.0 CD A:GLU21 3.4 16.6 1.0 CG A:ASN120 3.5 17.9 1.0 PAE A:DI9502 3.5 27.1 0.8 CG A:ASP229 3.5 15.1 1.0 NAM A:DI9502 3.8 21.8 0.8 OE1 A:GLU21 3.8 14.3 1.0 ND2 A:ASN175 3.8 13.6 1.0 ND2 A:ASN120 3.9 21.4 1.0 OD2 A:ASP229 4.0 15.8 1.0 ND2 A:ASN272 4.4 11.9 1.0 OD2 A:ASP121 4.5 13.5 1.0 OAD A:DI9502 4.5 28.4 0.8 C A:ASP229 4.6 15.3 1.0 OAF A:DI9502 4.6 27.5 0.8 O A:ASN120 4.7 15.0 1.0 CB A:ASN175 4.7 14.3 1.0 CG A:GLU21 4.7 15.1 1.0 CB A:ASP229 4.7 13.2 1.0 N A:GLY230 4.8 13.9 1.0 CB A:ASP121 4.8 12.2 1.0 CB A:ASN120 4.8 15.5 1.0 O A:ASP229 4.8 16.5 1.0 O A:ALA74 4.8 14.2 1.0 CA A:ASP229 4.8 13.6 1.0 C A:ASN175 4.9 13.7 1.0 CAG A:DI9502 4.9 30.9 0.8 CG A:ASP121 4.9 12.6 1.0 OG A:SER271 5.0 18.3 1.0

Calcium binding site 2 out of 2 in the Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Diisopropyl Fluorophosphatase (Dfpase) in Complex with Dicyclopentylphosphoroamidate (Dcppa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:14.1 occ:1.00 OD2 A:ASP232 2.2 16.7 1.0 O A:HOH551 2.2 15.9 1.0 O A:HOH514 2.3 14.9 1.0 O A:LEU273 2.3 13.1 1.0 O A:HOH548 2.4 15.6 1.0 ND1 A:HIS274 2.5 16.5 1.0 CG A:ASP232 3.2 17.4 1.0 CE1 A:HIS274 3.4 16.5 1.0 CG A:HIS274 3.5 15.4 1.0 C A:LEU273 3.5 14.3 1.0 OD1 A:ASP232 3.7 17.3 1.0 CB A:HIS274 3.8 13.3 1.0 CA A:HIS274 3.9 15.1 1.0 OD1 A:ASN272 4.0 12.1 1.0 O A:HOH550 4.1 15.9 1.0 N A:HIS274 4.2 13.7 1.0 O A:PRO23 4.2 14.0 1.0 O A:MET231 4.2 16.2 1.0 O A:HOH552 4.4 17.1 1.0 O A:HOH533 4.4 17.0 1.0 CB A:ASP232 4.5 14.9 1.0 NE2 A:HIS274 4.6 14.5 1.0 CD2 A:HIS274 4.7 15.1 1.0 N A:LEU273 4.7 13.7 1.0 CA A:LEU273 4.7 14.4 1.0 CG A:ASN272 4.9 10.9 1.0 CD1 A:LEU273 5.0 24.2 1.0 CG A:PRO23 5.0 14.2 1.0

M.M.Blum, F.Lohr, A.Richardt, H.Ruterjans, J.C.Chen. Binding of A Designed Substrate Analogue to Diisopropyl Fluorophosphatase: Implications For the Phosphotriesterase Mechanism. J.Am.Chem.Soc. V. 128 12750 2006.
ISSN: ISSN 0002-7863
PubMed: 17002369
DOI: 10.1021/JA061887N