Calcium in PDB 3o4p: Dfpase at 0.85 Angstrom Resolution (H Atoms Included)

All present enzymatic activity of Dfpase at 0.85 Angstrom Resolution (H Atoms Included):
3.1.8.2;

The structure of Dfpase at 0.85 Angstrom Resolution (H Atoms Included), PDB code: 3o4p was solved by D.Liebschner, M.Elias, J.Koepke, C.Lecomte, B.Guillot, C.Jelsch, E.Chabriere, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.80 / 0.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.114, 81.849, 86.467, 90.00, 90.00, 90.00
R / Rfree (%)	10.3 / 12.1

The binding sites of Calcium atom in the Dfpase at 0.85 Angstrom Resolution (H Atoms Included) (pdb code 3o4p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Dfpase at 0.85 Angstrom Resolution (H Atoms Included), PDB code: 3o4p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dfpase at 0.85 Angstrom Resolution (H Atoms Included)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dfpase at 0.85 Angstrom Resolution (H Atoms Included) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca491 b:4.7 occ:1.00 OD1 A:ASN120 2.3 6.7 1.0 OE2 A:GLU21 2.3 6.5 1.0 O A:HOH604 2.3 5.4 1.0 OD1 A:ASP229 2.4 6.4 1.0 OD1 A:ASN175 2.4 5.5 1.0 O A:HOH502 2.5 5.6 1.0 O A:HOH524 2.5 6.9 1.0 H1 A:HOH524 2.6 30.0 1.0 H2 A:HOH502 3.0 30.0 1.0 H1 A:HOH604 3.1 30.0 1.0 H1 A:HOH502 3.1 30.0 1.0 H2 A:HOH511 3.3 30.0 1.0 CD A:GLU21 3.4 5.6 1.0 CG A:ASN175 3.4 4.8 1.0 CG A:ASP229 3.4 5.5 1.0 HD22 A:ASN175 3.5 5.4 1.0 CG A:ASN120 3.5 6.1 1.0 OE1 A:GLU21 3.7 5.6 1.0 HB2 A:ASP121 3.7 4.7 1.0 ND2 A:ASN175 3.8 5.4 1.0 O A:HOH511 3.8 7.8 1.0 OD2 A:ASP229 3.9 6.9 1.0 HD22 A:ASN120 3.9 7.0 1.0 HD21 A:ASN272 3.9 5.5 1.0 ND2 A:ASN120 4.1 7.0 1.0 ND2 A:ASN272 4.3 5.5 1.0 HD22 A:ASN272 4.4 5.5 1.0 O A:ASN120 4.5 4.4 1.0 HA A:ASP229 4.5 4.8 1.0 OD2 A:ASP121 4.5 5.2 1.0 HB2 A:ASN272 4.6 4.9 1.0 CB A:ASP121 4.6 4.7 1.0 C A:ASP229 4.6 4.7 1.0 HB3 A:ASN120 4.6 5.2 1.0 CG A:GLU21 4.7 6.3 1.0 HA A:ASN175 4.7 4.5 1.0 HG3 A:GLU21 4.7 6.3 1.0 CB A:ASP229 4.7 5.0 1.0 HD21 A:ASN175 4.7 5.4 1.0 CB A:ASN120 4.7 5.2 1.0 O A:ALA74 4.7 5.7 1.0 HB2 A:ALA74 4.7 6.8 1.0 CB A:ASN175 4.7 5.0 1.0 H1 A:HOH511 4.7 30.0 1.0 N A:GLY230 4.8 4.8 1.0 HA2 A:GLY230 4.8 4.6 1.0 C A:ASN175 4.8 4.4 1.0 OG A:SER271 4.8 5.7 0.8 CA A:ASP229 4.8 4.8 1.0 N A:GLY176 4.9 4.5 1.0 CG A:ASP121 4.9 4.6 1.0 C A:ASN120 4.9 4.0 1.0 H A:GLY230 4.9 4.8 1.0 H A:GLY176 4.9 4.5 1.0 HD21 A:ASN120 5.0 7.0 1.0 CA A:ASN175 5.0 4.5 1.0 O A:ASP229 5.0 6.3 1.0 HA2 A:GLY176 5.0 4.5 1.0

Calcium binding site 2 out of 2 in the Dfpase at 0.85 Angstrom Resolution (H Atoms Included)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dfpase at 0.85 Angstrom Resolution (H Atoms Included) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca492 b:4.6 occ:1.00 OD2 A:ASP232 2.2 6.8 1.0 O A:HOH615 2.2 5.8 1.0 O A:HOH623 2.3 5.5 1.0 O A:LEU273 2.3 4.8 1.0 O A:HOH509 2.3 6.3 1.0 ND1 A:HIS274 2.4 5.4 1.0 H2 A:HOH509 2.8 30.0 1.0 H2 A:HOH623 2.8 30.0 1.0 H1 A:HOH509 2.8 30.0 1.0 H2 A:HOH615 2.9 30.0 1.0 H1 A:HOH615 2.9 30.0 1.0 H1 A:HOH623 3.0 30.0 1.0 HA A:HIS274 3.2 4.4 1.0 CG A:ASP232 3.2 5.5 1.0 CE1 A:HIS274 3.3 5.9 1.0 HE1 A:HIS274 3.4 5.9 1.0 C A:LEU273 3.4 4.5 1.0 CG A:HIS274 3.5 4.7 1.0 HB2 A:HIS274 3.5 4.6 1.0 OD1 A:ASP232 3.6 6.0 1.0 CB A:HIS274 3.7 4.6 1.0 CA A:HIS274 3.8 4.4 1.0 HG2 A:PRO23 4.0 5.3 1.0 H A:LEU273 4.0 4.9 1.0 OD1 A:ASN272 4.1 4.9 1.0 N A:HIS274 4.1 4.5 1.0 O A:PRO23 4.1 5.0 1.0 O A:HOH683 4.2 7.1 1.0 O A:MET231 4.2 5.0 1.0 O A:HOH614 4.4 5.7 1.0 HB2 A:ASP232 4.4 5.5 1.0 O A:HOH551 4.4 6.3 1.0 CB A:ASP232 4.4 5.5 1.0 NE2 A:HIS274 4.5 6.5 1.0 CD2 A:HIS274 4.5 5.9 1.0 HE22 A:GLN77 4.6 5.8 1.0 N A:LEU273 4.6 4.9 1.0 CA A:LEU273 4.7 5.4 1.0 HB3 A:HIS274 4.7 4.6 1.0 H1 A:HOH538 4.7 30.0 1.0 HD2 A:PRO23 4.8 4.9 1.0 H2 A:HOH614 4.8 30.0 1.0 CG A:ASN272 4.9 4.7 1.0 CD1 A:LEU273 4.9 11.6 0.7 CG A:PRO23 4.9 5.3 1.0 H A:HIS274 4.9 4.6 1.0 HE21 A:GLN77 5.0 5.8 1.0

M.Elias, D.Liebschner, J.Koepke, C.Lecomte, B.Guillot, C.Jelsch, E.Chabriere. Hydrogen Atoms in Protein Structures: High-Resolution X-Ray Diffraction Structure of the Dfpase. Bmc Res Notes V. 6 308 2013.
ISSN: ESSN 1756-0500
PubMed: 23915572
DOI: 10.1186/1756-0500-6-308