Zinc in PDB 3gdf: Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum.

All present enzymatic activity of Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum.:
1.1.1.138;

The structure of Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum., PDB code: 3gdf was solved by D.Nuess, P.Goettig, I.Magler, U.Denk, M.Breitenbach, P.B.Schneider, H.Brandstetter, B.Simon-Nobbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.012, 106.536, 132.783, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 26.2

The binding sites of Zinc atom in the Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum. (pdb code 3gdf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum., PDB code: 3gdf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:46.9 occ:1.00 NE2 A:HIS127 2.0 33.6 1.0 OE2 A:GLU123 2.0 13.9 1.0 CE1 A:HIS127 2.7 33.8 1.0 CD A:GLU123 2.9 27.3 1.0 CD2 A:HIS127 3.1 35.4 1.0 CG A:GLU123 3.1 19.4 1.0 ND1 A:HIS127 3.8 34.2 1.0 CG A:HIS127 4.1 30.4 1.0 OE1 A:GLU123 4.1 28.7 1.0 CB A:GLU123 4.6 17.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:43.9 occ:1.00 O A:ARG267 2.1 25.9 1.0 O D:ARG267 2.1 22.6 1.0 O A:HOH376 2.4 24.9 1.0 O D:HOH366 2.5 23.8 1.0 O A:HOH551 2.9 41.2 1.0 C A:ARG267 3.1 21.5 1.0 C D:ARG267 3.1 18.2 1.0 OXT A:ARG267 3.5 24.2 1.0 OXT D:ARG267 3.5 17.6 1.0 O D:THR265 4.1 25.6 1.0 CG2 A:ILE165 4.1 15.1 1.0 CG2 D:ILE165 4.1 20.4 1.0 CA A:ARG267 4.4 21.9 1.0 CA D:ARG267 4.4 17.9 1.0 O A:THR265 4.5 23.2 1.0 N A:ARG267 4.5 18.9 1.0 O A:TYR264 4.6 17.8 1.0 C A:THR265 4.6 16.9 1.0 C D:THR265 4.7 20.5 1.0 N D:ARG267 4.7 20.2 1.0 CA A:THR265 4.7 13.7 1.0 O D:HOH490 4.8 35.4 1.0 O D:TYR264 4.8 15.8 1.0 CA D:THR265 4.9 17.0 1.0 CB D:ILE165 5.0 17.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:41.4 occ:1.00 O C:ARG267 1.9 21.5 1.0 O B:ARG267 2.1 22.4 1.0 O C:HOH436 2.3 12.6 1.0 O C:HOH552 2.6 34.2 1.0 O C:HOH349 2.6 30.9 1.0 C C:ARG267 2.9 18.6 1.0 C B:ARG267 3.1 18.4 1.0 OXT C:ARG267 3.2 21.2 1.0 OXT B:ARG267 3.5 15.9 1.0 O C:THR265 4.0 16.2 1.0 CG2 B:ILE165 4.0 5.7 1.0 O B:THR265 4.2 19.2 1.0 CA C:ARG267 4.3 19.4 1.0 CG2 C:ILE165 4.3 19.1 1.0 CA B:ARG267 4.4 20.0 1.0 O C:TYR264 4.6 21.9 1.0 N C:ARG267 4.6 15.3 1.0 C C:THR265 4.6 16.5 1.0 C B:THR265 4.7 15.8 1.0 N B:ARG267 4.7 14.5 1.0 O B:TYR264 4.8 16.4 1.0 CA C:THR265 4.8 15.2 1.0 CB B:ILE165 4.9 13.4 1.0 CA B:THR265 4.9 18.0 1.0 CB C:ARG267 4.9 19.9 1.0 CB C:ILE165 5.0 18.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:38.3 occ:1.00 NE2 B:HIS127 1.9 32.5 1.0 OE2 B:GLU123 2.1 24.2 1.0 CE1 B:HIS127 2.6 25.5 1.0 CD B:GLU123 3.0 20.4 1.0 CD2 B:HIS127 3.2 32.0 1.0 CG B:GLU123 3.2 18.4 1.0 ND1 B:HIS127 3.8 30.0 1.0 OE1 B:GLU123 4.1 18.4 1.0 CG B:HIS127 4.1 26.7 1.0 CB B:GLU123 4.6 16.8 1.0

D.Nuss, P.Goettig, I.Magler, U.Denk, M.Breitenbach, P.B.Schneider, H.Brandstetter, B.Simon-Nobbe. Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum: Implications For Oligomerisation and Catalysis. Biochimie V. 92 985 2010.
ISSN: ISSN 0300-9084
PubMed: 20420880
DOI: 10.1016/J.BIOCHI.2010.04.012