Sodium in PDB 3gdg: 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: 3gdg 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)	19.86 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.707, 112.089, 107.292, 90.00, 98.28, 90.00
R / Rfree (%)	22.8 / 29.6

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

Sodium binding site 1 out of 2 in the Crystal Structure of the Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1002 b:10.7 occ:1.00 O A:HOH419 2.1 7.9 1.0 O A:ARG267 2.1 19.8 1.0 O D:HOH668 2.2 16.1 1.0 O D:ARG267 2.3 19.8 1.0 O D:HOH269 2.3 10.4 1.0 O A:HOH304 2.4 6.0 1.0 C A:ARG267 3.0 13.7 1.0 OXT A:ARG267 3.2 14.1 1.0 C D:ARG267 3.3 10.6 1.0 OXT D:ARG267 3.6 10.5 1.0 CG2 D:ILE165 3.8 10.8 1.0 O A:THR265 4.0 10.1 1.0 CG2 A:ILE165 4.1 7.7 1.0 O D:THR265 4.1 9.9 1.0 CA A:ARG267 4.3 12.8 1.0 CA D:ARG267 4.6 10.2 1.0 O D:HOH281 4.6 10.9 1.0 O D:TYR264 4.6 9.3 1.0 C D:THR265 4.6 9.9 1.0 N A:ARG267 4.6 11.9 1.0 C A:THR265 4.7 10.1 1.0 CA D:THR265 4.7 9.3 1.0 O A:TYR264 4.7 8.4 1.0 N D:ARG267 4.8 10.1 1.0 O D:HOH303 4.8 1.8 1.0 CA A:THR265 4.8 9.6 1.0 CB D:ILE165 4.9 10.8 1.0 O A:HOH338 4.9 10.3 1.0 CB A:ARG267 5.0 12.7 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 B:Na1001 b:31.2 occ:1.00 O C:ARG267 2.0 19.8 1.0 O B:HOH317 2.2 5.2 1.0 O B:ARG267 2.3 19.8 1.0 O B:HOH327 2.3 16.5 1.0 O B:HOH298 2.5 34.4 1.0 O B:HOH296 2.6 22.5 1.0 C C:ARG267 2.8 10.6 1.0 C B:ARG267 3.1 10.1 1.0 OXT C:ARG267 3.3 9.4 1.0 OXT B:ARG267 3.3 10.3 1.0 CA C:ARG267 4.0 11.1 1.0 O C:THR265 4.2 11.9 1.0 O C:TYR264 4.3 12.0 1.0 N C:ARG267 4.3 9.9 1.0 CA B:ARG267 4.4 10.0 1.0 CB C:ARG267 4.4 10.7 1.0 CG2 B:ILE165 4.5 9.3 1.0 C C:THR265 4.5 11.9 1.0 O C:HOH332 4.6 5.7 1.0 O C:HOH339 4.6 14.1 1.0 CA C:THR265 4.7 12.2 1.0 CG2 C:ILE165 4.7 7.5 1.0 O B:TYR264 4.7 11.4 1.0 N B:ARG267 4.8 9.4 1.0 CB B:ARG267 4.8 9.6 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