Zinc in PDB 1ped: Bacterial Secondary Alcohol Dehydrogenase (Apo-Form)

All present enzymatic activity of Bacterial Secondary Alcohol Dehydrogenase (Apo-Form):
1.1.1.2;

The structure of Bacterial Secondary Alcohol Dehydrogenase (Apo-Form), PDB code: 1ped was solved by Y.Korkhin, F.Frolow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.400, 102.260, 193.500, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.8

The binding sites of Zinc atom in the Bacterial Secondary Alcohol Dehydrogenase (Apo-Form) (pdb code 1ped). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Bacterial Secondary Alcohol Dehydrogenase (Apo-Form), PDB code: 1ped:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Bacterial Secondary Alcohol Dehydrogenase (Apo-Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacterial Secondary Alcohol Dehydrogenase (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn352 b:54.3 occ:1.00 NE2 A:HIS59 1.7 52.1 1.0 OD2 A:ASP150 2.1 32.6 1.0 OE2 A:GLU60 2.2 30.0 1.0 SG A:CYS37 2.4 32.3 1.0 CE1 A:HIS59 2.5 49.0 1.0 CD2 A:HIS59 2.9 36.7 1.0 CB A:CYS37 3.1 31.1 1.0 CG A:ASP150 3.1 27.1 1.0 CD A:GLU60 3.2 21.6 1.0 CG A:GLU60 3.5 18.8 1.0 CB A:ASP150 3.6 23.3 1.0 ND1 A:HIS59 3.7 48.8 1.0 CG A:HIS59 3.9 36.5 1.0 CE A:MET151 3.9 15.2 1.0 OG A:SER39 4.0 63.0 1.0 OD1 A:ASP150 4.2 35.6 1.0 OE1 A:GLU60 4.3 25.3 1.0 O A:HOH364 4.3 32.3 1.0 O A:HOH432 4.4 40.9 1.0 O A:HOH362 4.5 33.9 1.0 CA A:CYS37 4.5 28.2 1.0 O A:HOH383 4.7 29.5 1.0 CB A:GLU60 4.9 20.1 1.0

Zinc binding site 2 out of 4 in the Bacterial Secondary Alcohol Dehydrogenase (Apo-Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacterial Secondary Alcohol Dehydrogenase (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn352 b:54.5 occ:1.00 NE2 B:HIS59 1.7 50.8 1.0 OD2 B:ASP150 1.9 33.7 1.0 SG B:CYS37 2.4 31.1 1.0 OE2 B:GLU60 2.4 33.5 1.0 CE1 B:HIS59 2.5 45.3 1.0 CD2 B:HIS59 2.9 37.8 1.0 CG B:ASP150 3.0 31.5 1.0 CB B:CYS37 3.2 28.7 1.0 CD B:GLU60 3.4 24.3 1.0 O B:HOH449 3.5 55.1 1.0 CB B:ASP150 3.6 21.4 1.0 CG B:GLU60 3.7 26.7 1.0 ND1 B:HIS59 3.7 44.6 1.0 CE B:MET151 3.9 14.9 1.0 CG B:HIS59 3.9 37.2 1.0 OG B:SER39 3.9 63.9 1.0 OD1 B:ASP150 4.0 39.3 1.0 O B:HOH388 4.2 53.3 1.0 OE1 B:GLU60 4.5 32.3 1.0 CA B:CYS37 4.6 31.2 1.0 O B:HOH353 4.6 26.0 1.0 O B:HOH463 4.8 24.8 1.0

Zinc binding site 3 out of 4 in the Bacterial Secondary Alcohol Dehydrogenase (Apo-Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bacterial Secondary Alcohol Dehydrogenase (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn352 b:61.5 occ:1.00 NE2 C:HIS59 1.7 50.0 1.0 OD2 C:ASP150 2.0 40.0 1.0 SG C:CYS37 2.3 36.3 1.0 OE2 C:GLU60 2.4 38.3 1.0 CE1 C:HIS59 2.5 46.0 1.0 CD2 C:HIS59 2.9 37.1 1.0 CG C:ASP150 3.1 30.3 1.0 CB C:CYS37 3.2 37.1 1.0 CD C:GLU60 3.3 24.6 1.0 CB C:ASP150 3.6 23.6 1.0 CG C:GLU60 3.6 27.2 1.0 ND1 C:HIS59 3.7 46.9 1.0 OG C:SER39 3.9 62.2 1.0 CG C:HIS59 3.9 38.2 1.0 CE C:MET151 4.0 11.7 1.0 OD1 C:ASP150 4.1 43.9 1.0 O C:HOH457 4.1 47.6 1.0 O C:HOH456 4.2 44.2 1.0 O C:HOH384 4.4 42.4 1.0 OE1 C:GLU60 4.4 28.8 1.0 CA C:CYS37 4.6 36.0 1.0

Zinc binding site 4 out of 4 in the Bacterial Secondary Alcohol Dehydrogenase (Apo-Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Bacterial Secondary Alcohol Dehydrogenase (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn352 b:63.2 occ:1.00 NE2 D:HIS59 1.7 48.8 1.0 SG D:CYS37 2.2 42.0 1.0 OD2 D:ASP150 2.2 44.3 1.0 OE2 D:GLU60 2.3 34.3 1.0 CE1 D:HIS59 2.5 43.9 1.0 CD2 D:HIS59 2.9 36.6 1.0 CB D:CYS37 3.0 39.5 1.0 CG D:ASP150 3.3 37.4 1.0 CD D:GLU60 3.3 28.7 1.0 CG D:GLU60 3.6 27.7 1.0 ND1 D:HIS59 3.6 45.6 1.0 CB D:ASP150 3.8 30.8 1.0 OG D:SER39 3.8 65.2 1.0 CG D:HIS59 3.9 36.9 1.0 CE D:MET151 4.0 17.9 1.0 O D:HOH428 4.1 60.2 1.0 O D:HOH437 4.2 56.4 1.0 OD1 D:ASP150 4.3 45.7 1.0 OE1 D:GLU60 4.4 32.4 1.0 CA D:CYS37 4.4 36.9 1.0 O D:HOH445 4.5 40.3 1.0 O D:HOH364 4.6 37.0 1.0 CB D:GLU60 5.0 25.5 1.0

Y.Korkhin, F.Frolow, O.Bogin, M.Peretz, A.J.Kalb, Y.Burstein. Crystalline Alcohol Dehydrogenases From the Mesophilic Bacterium Clostridium Beijerinckii and the Thermophilic Bacterium Thermoanaerobium Brockii: Preparation, Characterization and Molecular Symmetry. Acta Crystallogr.,Sect.D V. 52 882 1996.
ISSN: ISSN 0907-4449
PubMed: 15299659
DOI: 10.1107/S0907444996001461