Calcium in PDB 7bbv: Pectate Lyase B From Verticillium Dahliae

The structure of Pectate Lyase B From Verticillium Dahliae, PDB code: 7bbv was solved by J.Safran, O.Habrylo, J.Bouckaert, C.Pau Roblot, F.Senechal, J.Pelloux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.52 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.89, 59.69, 93.87, 90, 96.35, 90
R / Rfree (%)	17.2 / 19.6

The binding sites of Calcium atom in the Pectate Lyase B From Verticillium Dahliae (pdb code 7bbv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pectate Lyase B From Verticillium Dahliae, PDB code: 7bbv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pectate Lyase B From Verticillium Dahliae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pectate Lyase B From Verticillium Dahliae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.2 occ:0.79 OD2 A:ASP155 2.2 27.6 1.0 O A:HOH568 2.4 37.1 1.0 OG B:SER288 2.4 29.1 1.0 OD1 A:ASP122 2.4 25.1 1.0 O A:HOH830 2.4 30.3 1.0 O B:HOH790 2.5 31.3 1.0 OD2 A:ASP151 2.5 35.2 1.0 OD2 A:ASP122 2.6 22.3 1.0 CG A:ASP122 2.8 21.8 1.0 CG A:ASP155 3.4 26.7 1.0 CB B:SER288 3.4 34.2 1.0 CG A:ASP151 3.5 31.9 1.0 HB2 B:SER288 3.5 41.0 1.0 HB3 B:SER288 3.6 41.0 1.0 H A:GLY152 3.7 25.5 1.0 HB2 A:ASP155 3.7 26.1 1.0 HA3 A:GLY152 3.9 23.7 1.0 CB A:ASP155 4.0 21.8 1.0 HB3 A:ASP155 4.0 26.1 1.0 OD1 A:ASP151 4.1 33.4 1.0 HB3 A:ASP151 4.1 33.9 1.0 O A:HOH681 4.2 37.3 1.0 N A:GLY152 4.2 21.2 1.0 CB A:ASP122 4.3 22.1 1.0 O B:HOH644 4.4 38.3 1.0 CB A:ASP151 4.4 28.2 1.0 OD1 A:ASP155 4.5 26.4 1.0 HD22 A:LEU178 4.5 32.9 1.0 HD21 A:LEU178 4.5 32.9 1.0 CA A:GLY152 4.6 19.7 1.0 HB3 A:ASP122 4.7 26.6 1.0 O B:HOH581 4.7 42.5 1.0 O A:HOH645 4.7 33.0 1.0 H B:SER288 4.7 42.0 1.0 HB2 A:ASP122 4.8 26.6 1.0 CA B:SER288 4.8 33.2 1.0 HB3 A:LEU178 4.8 25.9 1.0 O A:HOH622 4.9 27.2 1.0 HH12 A:ARG208 4.9 32.7 1.0

Calcium binding site 2 out of 2 in the Pectate Lyase B From Verticillium Dahliae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pectate Lyase B From Verticillium Dahliae within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:32.8 occ:0.69 O B:HOH505 2.1 35.6 1.0 O B:HOH742 2.3 43.0 1.0 OD2 B:ASP155 2.3 33.0 1.0 OD2 B:ASP151 2.4 36.8 1.0 OD1 B:ASP122 2.5 33.2 1.0 OD2 B:ASP122 2.5 36.1 1.0 O B:HOH789 2.5 50.7 1.0 CG B:ASP122 2.8 37.6 1.0 O B:HOH623 2.9 53.0 1.0 CG B:ASP155 3.4 31.6 1.0 CG B:ASP151 3.5 34.9 1.0 H41 B:PEG402 3.6 42.8 0.7 HB2 B:ASP155 3.6 32.4 1.0 H B:GLY152 3.7 35.9 1.0 O B:HOH541 3.7 62.3 1.0 HB3 B:ASP155 3.9 32.4 1.0 CB B:ASP155 3.9 27.0 1.0 HB3 B:ASP151 3.9 43.4 1.0 H42 B:PEG402 4.1 42.8 0.7 C4 B:PEG402 4.1 35.6 0.7 HO4 B:PEG402 4.1 48.8 0.7 HA3 B:GLY152 4.2 31.2 1.0 OD1 B:ASP151 4.3 42.2 1.0 CB B:ASP151 4.3 36.2 1.0 O B:HOH700 4.3 41.3 1.0 CB B:ASP122 4.3 30.3 1.0 O4 B:PEG402 4.3 40.6 0.7 N B:GLY152 4.4 29.9 1.0 O B:HOH908 4.4 50.4 1.0 OD1 B:ASP155 4.5 31.1 1.0 HB3 B:ASP122 4.6 36.3 1.0 HB2 B:ASP122 4.7 36.3 1.0 HD23 B:LEU178 4.7 43.0 1.0 CA B:GLY152 4.8 26.0 1.0 HD22 B:LEU178 4.8 43.0 1.0 HB2 B:ASP151 4.8 43.4 1.0 O B:HOH835 4.9 70.0 1.0

J.Safran, O.Habrylo, J.Bouckaert, C.Pau Roblot, F.Senechal, J.Pelloux. Structural and Biochemical Characterization of An Unusual Pectin/Pectate Lyase From Verticillium Dahliae To Be Published.