Calcium in PDB 3pe7: Oligogalacturonate Lyase in Complex with Manganese

The structure of Oligogalacturonate Lyase in Complex with Manganese, PDB code: 3pe7 was solved by D.W.Abbott, H.J.Gilbert, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.650, 75.510, 78.510, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.7

The structure of Oligogalacturonate Lyase in Complex with Manganese also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Oligogalacturonate Lyase in Complex with Manganese (pdb code 3pe7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Oligogalacturonate Lyase in Complex with Manganese, PDB code: 3pe7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Oligogalacturonate Lyase in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Oligogalacturonate Lyase in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca390 b:17.6 occ:1.00 O A:MET1 2.3 19.4 1.0 O A:HOH589 2.4 17.9 1.0 O A:HOH599 2.4 21.0 1.0 OD1 A:ASP57 2.4 13.2 1.0 O A:HOH668 2.4 28.4 1.0 CG A:ASP57 3.3 13.7 1.0 C A:MET1 3.4 19.1 1.0 OD2 A:ASP57 3.5 15.9 1.0 N A:MET1 4.0 19.9 1.0 O A:HOH484 4.1 58.2 1.0 CA A:MET1 4.2 19.4 1.0 N A:ALA2 4.4 18.4 1.0 O A:ASP57 4.6 12.8 1.0 CA A:ALA2 4.6 17.8 1.0 CB A:MET1 4.7 20.1 1.0 CB A:ALA2 4.7 17.7 1.0 CB A:ASP57 4.7 12.7 1.0 O A:HOH596 4.8 29.9 1.0 O A:HOH398 4.8 28.4 1.0

Calcium binding site 2 out of 2 in the Oligogalacturonate Lyase in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Oligogalacturonate Lyase in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca391 b:10.9 occ:1.00 OE2 A:GLU272 2.3 11.2 1.0 OD1 A:ASP270 2.4 15.1 1.0 OD2 A:ASP270 2.8 13.3 1.0 CG A:ASP270 2.9 12.6 1.0 CD A:GLU272 3.4 13.3 1.0 OE1 A:GLU272 4.1 17.9 1.0 CB A:GLU272 4.3 14.3 1.0 CG A:GLU272 4.3 14.0 1.0 CB A:ASP270 4.4 11.7 1.0 CD A:PRO271 4.6 14.4 1.0 N A:GLU272 4.7 14.6 1.0 NH1 A:ARG196 4.7 11.7 1.0 O A:SER250 4.8 10.8 1.0 O A:HOH423 4.8 16.0 0.5

D.W.Abbott, H.J.Gilbert, A.B.Boraston. The Active Site of Oligogalacturonate Lyase Provides Unique Insights Into Cytoplasmic Oligogalacturonate Beta-Elimination. J.Biol.Chem. V. 285 39029 2010.
ISSN: ISSN 0021-9258
PubMed: 20851883
DOI: 10.1074/JBC.M110.153981