Cadmium in PDB 1ib4: Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5

All present enzymatic activity of Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5:
3.2.1.15;

The structure of Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5, PDB code: 1ib4 was solved by S.W.Cho, W.Shin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.10 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.100, 96.400, 57.770, 90.00, 107.30, 90.00
R / Rfree (%)	16.8 / 21.7

The binding sites of Cadmium atom in the Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5 (pdb code 1ib4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5, PDB code: 1ib4:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd935 b:8.4 occ:1.00 OE2 B:GLU95 1.9 34.0 1.0 NE2 A:HIS202 2.3 8.7 1.0 OD1 A:ASP231 2.6 26.1 1.0 CD B:GLU95 2.6 36.0 1.0 OE1 B:GLU95 2.7 38.5 1.0 CD2 A:HIS202 3.2 6.4 1.0 O A:HOH1249 3.3 40.3 1.0 CE1 A:HIS202 3.4 8.4 1.0 CG A:ASP231 3.4 15.5 1.0 OD2 A:ASP231 3.7 25.1 1.0 N B:GLY100 3.9 18.7 1.0 CG B:GLU95 4.1 29.4 1.0 O A:HOH1305 4.2 39.4 1.0 O A:GLN179 4.4 24.8 1.0 CG A:HIS202 4.4 10.1 1.0 ND1 A:HIS202 4.4 10.1 1.0 CB A:ASP231 4.5 8.8 1.0 CA B:GLY99 4.6 11.9 1.0 C B:GLY99 4.6 16.3 1.0 CA B:GLY100 4.6 17.7 1.0 O A:HOH1232 4.8 49.5 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd936 b:11.7 occ:1.00 O B:HOH1309 1.7 41.3 1.0 OE2 A:GLU95 2.2 52.4 1.0 NE2 B:HIS202 2.5 9.8 1.0 OE1 A:GLU95 2.6 54.6 1.0 OD1 B:ASP231 2.7 20.1 1.0 CD A:GLU95 2.8 51.7 1.0 OD2 B:ASP231 3.2 29.2 1.0 CG B:ASP231 3.2 16.6 1.0 CD2 B:HIS202 3.3 6.6 1.0 CE1 B:HIS202 3.6 13.2 1.0 N A:GLY100 4.2 18.1 1.0 O B:HOH1114 4.2 51.8 1.0 CG A:GLU95 4.3 36.7 1.0 CB B:ASP231 4.4 10.9 1.0 CG B:HIS202 4.5 8.2 1.0 O B:GLN179 4.6 15.9 1.0 CA A:GLY99 4.6 21.1 1.0 ND1 B:HIS202 4.6 15.7 1.0 C A:GLY99 4.9 21.7 1.0 CA A:GLY100 4.9 15.7 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Polygalacturonase From Aspergillus Aculeatus at PH4.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd937 b:27.9 occ:1.00 OD2 B:ASP313 2.4 33.6 1.0 OD2 B:ASP285 2.4 51.7 1.0 CG B:ASP313 3.1 26.7 1.0 OD1 B:ASP313 3.2 22.2 1.0 CG B:ASP285 3.6 35.1 1.0 O B:HOH1262 3.8 55.0 1.0 OD1 B:ASP285 4.4 33.9 1.0 CB B:ASP285 4.5 18.2 1.0 CB B:ASP313 4.6 13.0 1.0 O B:HOH1042 4.7 22.5 1.0 CA B:ASP285 5.0 13.5 1.0

S.W.Cho, S.Lee, W.Shin. The X-Ray Structure of Aspergillus Aculeatus Polygalacturonase and A Modeled Structure of the Polygalacturonase-Octagalacturonate Complex. J.Mol.Biol. V. 311 863 2001.
ISSN: ISSN 0022-2836
PubMed: 11518536
DOI: 10.1006/JMBI.2001.4919