Zinc in PDB 3wid: Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp

All present enzymatic activity of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp:
1.1.1.47;

The structure of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp, PDB code: 3wid was solved by H.Sakuraba, Y.Kanoh, K.Yoneda, T.Ohshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.27 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.172, 90.346, 120.370, 90.00, 90.84, 90.00
R / Rfree (%)	19.7 / 25.1

The binding sites of Zinc atom in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp (pdb code 3wid). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp, PDB code: 3wid:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:36.8 occ:1.00 OD2 A:ASP116 2.1 49.2 1.0 SG A:CYS110 2.2 32.0 1.0 SG A:CYS99 2.4 34.3 1.0 SG A:CYS102 2.5 34.4 1.0 CG A:ASP116 3.1 37.1 1.0 CB A:CYS110 3.3 39.2 1.0 CB A:CYS102 3.3 34.8 1.0 CB A:CYS99 3.4 40.6 1.0 CB A:ASP116 3.6 37.1 1.0 CA A:CYS110 3.6 35.6 1.0 N A:CYS99 3.9 34.5 1.0 N A:SER111 4.1 37.7 1.0 OD1 A:ASP116 4.1 39.9 1.0 N A:CYS102 4.2 34.5 1.0 CA A:CYS99 4.2 36.3 1.0 C A:CYS110 4.3 34.6 1.0 CA A:CYS102 4.3 35.6 1.0 N A:GLY97 4.4 39.4 1.0 N A:LYS117 4.5 49.2 1.0 CA A:GLY97 4.5 35.5 1.0 N A:LYS98 4.5 39.5 1.0 N A:ILE112 4.6 42.0 1.0 C A:ASP116 4.6 47.0 1.0 C A:GLY97 4.7 35.5 1.0 CA A:ASP116 4.7 42.1 1.0 C A:CYS99 4.9 33.9 1.0 N A:CYS110 4.9 40.2 1.0 CB A:LYS117 4.9 45.9 1.0 C A:LYS98 4.9 35.0 1.0 O A:CYS99 5.0 36.2 1.0

Zinc binding site 2 out of 4 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4002 b:31.5 occ:1.00 OD2 B:ASP116 2.1 31.5 1.0 SG B:CYS110 2.2 29.6 1.0 SG B:CYS99 2.2 31.8 1.0 SG B:CYS102 2.3 32.5 1.0 CB B:CYS110 3.1 30.7 1.0 CG B:ASP116 3.2 33.4 1.0 CB B:CYS102 3.3 33.2 1.0 CB B:CYS99 3.4 33.6 1.0 CA B:CYS110 3.5 29.7 1.0 CB B:ASP116 3.8 34.1 1.0 N B:CYS99 4.0 28.0 1.0 N B:SER111 4.2 29.3 1.0 OD1 B:ASP116 4.2 33.0 1.0 N B:CYS102 4.2 29.8 1.0 CA B:CYS99 4.2 29.6 1.0 C B:CYS110 4.2 28.7 1.0 CA B:CYS102 4.4 30.2 1.0 N B:ILE112 4.5 34.9 1.0 N B:LYS98 4.6 31.1 1.0 N B:GLY97 4.6 34.0 1.0 N B:LYS117 4.6 43.0 1.0 CA B:GLY97 4.7 34.1 1.0 N B:CYS110 4.8 29.7 1.0 C B:ASP116 4.8 43.1 1.0 C B:CYS99 4.8 29.7 1.0 CB B:LYS117 4.8 36.7 1.0 C B:GLY97 4.8 31.3 1.0 CB B:ILE112 4.9 36.1 1.0 CA B:ASP116 4.9 37.5 1.0 O B:CYS99 4.9 29.5 1.0

Zinc binding site 3 out of 4 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:34.6 occ:1.00 OD2 C:ASP116 2.0 31.7 1.0 SG C:CYS110 2.3 34.3 1.0 SG C:CYS102 2.4 33.5 1.0 SG C:CYS99 2.4 34.4 1.0 CG C:ASP116 3.0 35.7 1.0 CB C:CYS99 3.3 28.9 1.0 CB C:CYS110 3.3 36.0 1.0 CB C:CYS102 3.4 30.7 1.0 CB C:ASP116 3.5 37.4 1.0 CA C:CYS110 3.7 37.6 1.0 N C:CYS99 4.0 28.2 1.0 N C:SER111 4.0 31.1 1.0 OD1 C:ASP116 4.1 34.9 1.0 CA C:CYS99 4.1 32.2 1.0 N C:CYS102 4.2 34.6 1.0 C C:CYS110 4.3 30.4 1.0 CA C:CYS102 4.4 35.9 1.0 N C:LYS117 4.4 45.6 1.0 N C:GLY97 4.5 39.1 1.0 N C:LYS98 4.5 36.8 1.0 CA C:GLY97 4.6 35.9 1.0 N C:ILE112 4.6 35.9 1.0 C C:ASP116 4.6 42.0 1.0 CA C:ASP116 4.7 38.0 1.0 C C:GLY97 4.8 38.3 1.0 CB C:LYS117 4.8 39.9 1.0 C C:CYS99 4.8 34.2 1.0 CB C:ILE112 4.9 43.9 1.0 N C:CYS110 5.0 37.5 1.0

Zinc binding site 4 out of 4 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with Nadp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4002 b:38.7 occ:1.00 OD2 D:ASP116 2.0 49.6 1.0 SG D:CYS110 2.3 34.2 1.0 SG D:CYS102 2.3 35.2 1.0 SG D:CYS99 2.4 33.0 1.0 CG D:ASP116 3.1 42.9 1.0 CB D:CYS110 3.2 34.8 1.0 CB D:CYS99 3.4 30.1 1.0 CB D:CYS102 3.5 36.6 1.0 CA D:CYS110 3.6 34.7 1.0 CB D:ASP116 3.6 45.0 1.0 N D:CYS99 3.9 33.2 1.0 N D:SER111 4.0 35.4 1.0 OD1 D:ASP116 4.1 40.6 1.0 N D:CYS102 4.1 34.0 1.0 CA D:CYS99 4.2 30.7 1.0 C D:CYS110 4.3 30.4 1.0 CA D:CYS102 4.3 36.1 1.0 N D:LYS98 4.5 38.0 1.0 N D:LYS117 4.5 46.4 1.0 N D:GLY97 4.6 43.2 1.0 CA D:GLY97 4.6 39.3 1.0 C D:ASP116 4.6 49.8 1.0 N D:ILE112 4.7 39.2 1.0 CA D:ASP116 4.8 44.8 1.0 C D:GLY97 4.8 37.6 1.0 C D:CYS99 4.9 31.4 1.0 N D:CYS110 4.9 37.2 1.0 CB D:ILE112 4.9 42.1 1.0 O D:CYS99 4.9 29.7 1.0

Y.Kanoh, S.Uehara, H.Iwata, K.Yoneda, T.Ohshima, H.Sakuraba. Structural Insight Into Glucose Dehydrogenase From the Thermoacidophilic Archaeon Thermoplasma Volcanium Acta Crystallogr.,Sect.D V. 70 1271 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714002363