Zinc in PDB 1czf: Endo-Polygalacturonase II From Aspergillus Niger

All present enzymatic activity of Endo-Polygalacturonase II From Aspergillus Niger:
3.2.1.15;

The structure of Endo-Polygalacturonase II From Aspergillus Niger, PDB code: 1czf was solved by Y.Van Santen, K.H.Kalk, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.68
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.497, 201.241, 49.065, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.1

The binding sites of Zinc atom in the Endo-Polygalacturonase II From Aspergillus Niger (pdb code 1czf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Endo-Polygalacturonase II From Aspergillus Niger, PDB code: 1czf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Endo-Polygalacturonase II From Aspergillus Niger


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Endo-Polygalacturonase II From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:7.8 occ:1.00 O A:HOH588 2.0 6.3 1.0 OD2 A:ASP110 2.1 7.4 1.0 OD1 A:ASP110 2.4 5.4 1.0 CG A:ASP110 2.6 5.3 1.0 O A:HOH538 4.1 10.6 1.0 CB A:ASP110 4.1 5.0 1.0 CG A:ARG113 4.1 4.2 1.0 O A:HOH959 4.2 30.8 1.0 CD A:ARG113 4.5 3.7 1.0 O A:HOH508 4.7 4.5 1.0 O A:ASP110 4.8 4.4 1.0 NE A:ARG113 4.9 4.2 1.0 CA A:ASP110 5.0 4.9 1.0

Zinc binding site 2 out of 6 in the Endo-Polygalacturonase II From Aspergillus Niger


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Endo-Polygalacturonase II From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:8.9 occ:1.00 O A:HOH702 2.1 12.9 1.0 O A:HOH553 2.1 7.2 1.0 O A:HOH572 2.1 12.2 1.0 O A:HOH535 2.1 7.5 1.0 NE2 A:HIS223 2.2 6.3 1.0 O A:HOH578 2.3 10.2 1.0 CE1 A:HIS223 3.1 6.8 1.0 CD2 A:HIS223 3.2 4.8 1.0 O A:GLN200 3.8 5.6 1.0 OE1 A:GLU252 3.9 7.9 1.0 O A:HOH854 4.1 29.5 1.0 O A:HOH637 4.1 14.4 1.0 O A:HOH607 4.2 12.6 1.0 ND1 A:HIS223 4.2 6.2 1.0 O A:HOH558 4.2 6.5 1.0 O A:HOH548 4.3 10.9 1.0 CG A:HIS223 4.3 6.3 1.0 O A:HOH853 4.4 27.2 1.0 ND1 A:HIS177 4.4 12.9 1.0 O A:HOH983 4.5 35.7 1.0 CE1 A:HIS177 4.5 14.4 1.0 C A:GLN200 4.8 4.5 1.0 CD A:GLU252 4.9 7.5 1.0

Zinc binding site 3 out of 6 in the Endo-Polygalacturonase II From Aspergillus Niger


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Endo-Polygalacturonase II From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:9.9 occ:1.00 O A:HOH674 2.1 15.1 1.0 NE2 A:HIS96 2.1 11.2 1.0 O A:HOH606 2.1 10.5 1.0 O A:HOH636 2.1 12.1 1.0 CE1 A:HIS96 2.9 11.6 1.0 CD2 A:HIS96 3.2 11.4 1.0 OE2 A:GLU95 3.9 18.5 1.0 OG A:SER136 4.0 6.5 1.0 ND1 A:HIS96 4.1 11.5 1.0 CB A:SER136 4.3 6.4 1.0 CG A:HIS96 4.3 9.6 1.0 CD A:GLU95 4.5 16.6 1.0 CG A:GLU95 4.8 14.1 1.0

Zinc binding site 4 out of 6 in the Endo-Polygalacturonase II From Aspergillus Niger


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Endo-Polygalacturonase II From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:7.4 occ:1.00 OD2 B:ASP336 2.0 7.9 1.0 OD1 B:ASP308 2.0 5.5 1.0 O B:HOH562 2.1 13.9 1.0 CG B:ASP308 2.8 6.4 1.0 CG B:ASP336 2.8 7.2 1.0 OD2 B:ASP308 2.9 7.1 1.0 OD1 B:ASP336 3.1 7.9 1.0 O B:HOH637 3.9 20.5 1.0 O B:HOH577 4.1 9.3 1.0 CB B:ASP308 4.2 5.7 1.0 CB B:ASP336 4.2 5.8 1.0 O B:HOH702 4.2 20.2 1.0 O B:HOH850 4.4 27.6 1.0 CA B:ASP308 4.6 4.8 1.0 O B:HOH600 4.6 12.1 1.0 O B:ASP336 4.7 5.0 1.0

Zinc binding site 5 out of 6 in the Endo-Polygalacturonase II From Aspergillus Niger


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Endo-Polygalacturonase II From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:13.3 occ:1.00 O B:HOH674 2.1 18.3 1.0 NE2 B:HIS223 2.1 6.9 1.0 O B:HOH603 2.1 8.8 1.0 O B:HOH619 2.2 14.8 1.0 O B:HOH677 2.2 21.6 1.0 O B:HOH635 2.3 15.0 1.0 CE1 B:HIS223 3.1 7.4 1.0 CD2 B:HIS223 3.2 6.7 1.0 O B:GLN200 3.8 5.5 1.0 OE1 B:GLU252 3.9 11.4 1.0 O B:HOH975 4.1 33.9 1.0 O B:HOH574 4.2 14.1 1.0 ND1 B:HIS223 4.2 6.4 1.0 O B:HOH803 4.2 25.7 1.0 O B:HOH625 4.2 13.3 1.0 CG B:HIS223 4.3 6.1 1.0 O B:HOH543 4.3 9.4 1.0 ND1 B:HIS177 4.5 16.7 1.0 CE1 B:HIS177 4.6 18.1 1.0 C B:GLN200 4.8 5.0 1.0 CD B:GLU252 4.9 11.4 1.0

Zinc binding site 6 out of 6 in the Endo-Polygalacturonase II From Aspergillus Niger


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Endo-Polygalacturonase II From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:10.0 occ:1.00 NE2 B:HIS96 2.1 10.6 1.0 O B:HOH687 2.2 16.9 1.0 O B:HOH650 2.2 16.4 1.0 O B:HOH779 2.3 24.1 1.0 CE1 B:HIS96 2.8 12.6 1.0 CD2 B:HIS96 3.3 10.9 1.0 ND1 B:HIS96 4.0 12.5 1.0 OG B:SER136 4.0 7.0 1.0 OE2 B:GLU95 4.1 18.9 1.0 CB B:SER136 4.3 6.6 1.0 CG B:HIS96 4.3 9.6 1.0 CD B:GLU95 4.5 16.6 1.0 CG B:GLU95 4.7 14.4 1.0

Y.Van Santen, J.A.Benen, K.H.Schroter, K.H.Kalk, S.Armand, J.Visser, B.W.Dijkstra. 1.68-A Crystal Structure of Endopolygalacturonase II From Aspergillus Niger and Identification of Active Site Residues By Site-Directed Mutagenesis. J.Biol.Chem. V. 274 30474 1999.
ISSN: ISSN 0021-9258
PubMed: 10521427
DOI: 10.1074/JBC.274.43.30474