Calcium in PDB 2pz0: Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) From T. Tengcongensis

The structure of Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) From T. Tengcongensis, PDB code: 2pz0 was solved by L.Shi, J.F.Liu, X.M.An, D.C.Liang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.401, 53.608, 110.885, 90.00, 97.91, 90.00
R / Rfree (%)	22.9 / 23.6

The binding sites of Calcium atom in the Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) From T. Tengcongensis (pdb code 2pz0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) From T. Tengcongensis, PDB code: 2pz0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) From T. Tengcongensis


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 Glycerophosphodiester Phosphodiesterase (Gdpd) From T. Tengcongensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:21.2 occ:1.00 OD1 A:ASP46 2.3 20.6 1.0 OE1 A:GLU119 2.3 18.1 1.0 O2 A:GOL401 2.4 29.0 1.0 O A:HOH628 2.4 14.8 1.0 O A:HOH503 2.5 21.5 1.0 OE2 A:GLU44 2.5 24.6 1.0 C2 A:GOL401 3.3 25.6 1.0 CG A:ASP46 3.3 23.6 1.0 CD A:GLU44 3.4 24.3 1.0 CD A:GLU119 3.5 21.9 1.0 OE1 A:GLU44 3.7 25.8 1.0 OD2 A:ASP46 3.7 20.5 1.0 O1 A:GOL401 3.7 19.3 1.0 CD2 A:HIS59 3.8 24.3 1.0 C3 A:GOL401 3.9 26.1 1.0 C1 A:GOL401 4.0 24.1 1.0 O3 A:GOL401 4.1 32.4 1.0 NE2 A:HIS17 4.2 20.9 1.0 OE2 A:GLU119 4.2 20.4 1.0 CB A:GLU119 4.2 23.6 1.0 NE2 A:HIS59 4.2 25.0 1.0 CG A:GLU119 4.4 21.9 1.0 O A:HOH532 4.5 27.5 1.0 O A:HOH521 4.6 22.6 1.0 CB A:ASP46 4.7 21.4 1.0 CG A:GLU44 4.8 24.1 1.0 CD2 A:HIS17 4.8 21.0 1.0 O A:LEU45 4.9 23.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) From T. Tengcongensis


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 Glycerophosphodiester Phosphodiesterase (Gdpd) From T. Tengcongensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:19.6 occ:1.00 OE1 B:GLU119 2.3 13.5 1.0 OD1 B:ASP46 2.4 15.6 1.0 O2 B:GOL400 2.5 25.5 1.0 OE2 B:GLU44 2.5 15.3 1.0 O B:HOH503 2.5 13.4 1.0 O B:HOH607 2.6 12.7 1.0 CG B:ASP46 3.4 17.1 1.0 CD B:GLU44 3.4 17.3 1.0 CD B:GLU119 3.5 14.5 1.0 C2 B:GOL400 3.5 21.9 1.0 C3 B:GOL400 3.6 27.2 1.0 O1 B:GOL400 3.6 12.2 1.0 OE1 B:GLU44 3.7 15.6 1.0 OD2 B:ASP46 3.7 16.2 1.0 C1 B:GOL400 4.0 20.4 1.0 CD2 B:HIS59 4.0 20.5 1.0 O3 B:GOL400 4.1 33.5 1.0 CB B:GLU119 4.2 17.6 1.0 NE2 B:HIS17 4.2 20.8 1.0 OE2 B:GLU119 4.2 15.4 1.0 CG B:GLU119 4.4 13.7 1.0 O B:HOH545 4.5 32.0 1.0 NE2 B:HIS59 4.5 21.8 1.0 O B:HOH534 4.5 20.8 1.0 CB B:ASP46 4.7 16.4 1.0 CG B:GLU44 4.8 14.1 1.0 CD2 B:HIS17 4.8 19.7 1.0 O B:LEU45 4.9 18.6 1.0

L.Shi, J.F.Liu, X.M.An, D.C.Liang. Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) From Thermoanaerobacter Tengcongensis, A Metal Ion-Dependent Enzyme: Insight Into the Catalytic Mechanism. Proteins V. 72 280 2008.
ISSN: ISSN 0887-3585
PubMed: 18214974
DOI: 10.1002/PROT.21921