Zinc in PDB 3ce9: Crystal Structure of Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution

The structure of Crystal Structure of Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution, PDB code: 3ce9 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.94 / 2.37
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.740, 125.810, 133.230, 90.00, 102.33, 90.00
R / Rfree (%)	18.8 / 21.4

The binding sites of Zinc atom in the Crystal Structure of Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution (pdb code 3ce9). 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 Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution, PDB code: 3ce9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution


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 Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:46.8 occ:1.00 NE2 A:HIS266 2.0 50.0 1.0 OD1 A:ASP171 2.1 43.2 1.0 NE2 A:HIS250 2.1 39.2 1.0 O A:HOH436 2.3 53.4 1.0 O A:HOH465 2.7 52.5 1.0 CG A:ASP171 2.9 44.8 1.0 CD2 A:HIS250 3.0 38.0 1.0 CE1 A:HIS266 3.0 52.3 1.0 CD2 A:HIS266 3.0 43.6 1.0 OD2 A:ASP171 3.1 49.8 1.0 CE1 A:HIS250 3.3 44.9 1.0 OD1 A:ASP124 3.9 52.6 1.0 ND1 A:HIS266 4.1 51.2 1.0 CG A:HIS266 4.1 45.5 1.0 CG A:HIS250 4.2 42.6 1.0 ND1 A:HIS250 4.3 43.8 1.0 CB A:ASP171 4.4 45.5 1.0 OD2 A:ASP124 4.4 55.9 1.0 CG A:ASP124 4.5 48.6 1.0 CG2 A:VAL270 4.6 40.6 1.0 O A:HOH464 4.6 50.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution


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 Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:48.9 occ:1.00 OD1 B:ASP171 1.8 42.2 1.0 NE2 B:HIS250 2.1 39.6 1.0 O B:HOH433 2.1 58.5 1.0 NE2 B:HIS266 2.2 49.9 1.0 CG B:ASP171 2.6 44.6 1.0 OD2 B:ASP171 2.8 49.7 1.0 O B:HOH435 2.9 48.6 1.0 CD2 B:HIS250 3.0 38.1 1.0 CE1 B:HIS250 3.1 44.9 1.0 CD2 B:HIS266 3.2 43.9 1.0 CE1 B:HIS266 3.2 52.4 1.0 OD1 B:ASP124 3.8 52.7 1.0 CB B:ASP171 4.1 45.4 1.0 CG B:HIS250 4.2 42.7 1.0 ND1 B:HIS250 4.2 43.9 1.0 OD2 B:ASP124 4.3 55.8 1.0 CG B:HIS266 4.3 45.8 1.0 ND1 B:HIS266 4.3 51.1 1.0 CG B:ASP124 4.4 48.6 1.0 CG2 B:VAL270 4.6 40.9 1.0 CA B:ASP171 4.7 44.9 1.0 O B:ASP171 5.0 48.8 1.0 O B:ALA245 5.0 53.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution


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 Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn400 b:47.0 occ:1.00 OD1 C:ASP171 2.0 42.9 1.0 NE2 C:HIS266 2.1 49.9 1.0 NE2 C:HIS250 2.2 39.0 1.0 O C:HOH457 2.2 55.4 1.0 O C:HOH432 2.7 51.3 1.0 CG C:ASP171 2.8 44.7 1.0 OD2 C:ASP171 2.9 50.0 1.0 CD2 C:HIS250 3.0 38.0 1.0 CD2 C:HIS266 3.1 43.9 1.0 CE1 C:HIS266 3.1 52.3 1.0 CE1 C:HIS250 3.3 44.9 1.0 OD1 C:ASP124 3.8 52.4 1.0 ND1 C:HIS266 4.2 51.2 1.0 CG C:HIS266 4.2 45.4 1.0 CG C:HIS250 4.2 42.5 1.0 CB C:ASP171 4.3 45.5 1.0 ND1 C:HIS250 4.3 44.0 1.0 OD2 C:ASP124 4.4 55.9 1.0 CG C:ASP124 4.4 48.4 1.0 CG2 C:VAL270 4.6 40.9 1.0 CA C:ASP171 4.9 45.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution


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 Glycerol Dehydrogenase (NP_348253.1) From Clostridium Acetobutylicum at 2.37 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn400 b:42.2 occ:1.00 OD1 D:ASP171 2.0 42.7 1.0 NE2 D:HIS250 2.1 38.8 1.0 NE2 D:HIS266 2.2 49.7 1.0 O D:HOH424 2.2 48.3 1.0 CG D:ASP171 2.8 44.5 1.0 OD2 D:ASP171 3.0 49.4 1.0 CD2 D:HIS250 3.0 37.3 1.0 CE1 D:HIS266 3.1 52.6 1.0 CD2 D:HIS266 3.2 43.8 1.0 CE1 D:HIS250 3.2 44.8 1.0 OD1 D:ASP124 3.8 52.3 1.0 CG D:HIS250 4.2 42.5 1.0 ND1 D:HIS250 4.2 43.6 1.0 CB D:ASP171 4.3 45.5 1.0 ND1 D:HIS266 4.3 51.4 1.0 CG D:HIS266 4.3 45.6 1.0 OD2 D:ASP124 4.4 55.8 1.0 CG D:ASP124 4.4 48.5 1.0 CG2 D:VAL270 4.7 40.6 1.0 O D:ALA245 4.8 52.8 1.0 O D:HOH437 4.9 40.6 1.0 CA D:ASP171 4.9 44.9 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.