Zinc in PDB 2nvb: Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs)

All present enzymatic activity of Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs):
1.1.1.2;

The structure of Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs), PDB code: 2nvb was solved by E.Goihberg, S.Tel-Or, M.Peretz, F.Frolow, O.Dym, Y.Burstein, Israel Structural Proteomics Center (Ispc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.60 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.598, 125.008, 167.111, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 27.8

The binding sites of Zinc atom in the Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs) (pdb code 2nvb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs), PDB code: 2nvb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn354 b:52.7 occ:1.00 OD2 A:ASP150 1.9 34.7 1.0 NE2 A:HIS59 2.2 27.3 1.0 SG A:CYS37 2.6 39.0 1.0 C4N A:NAP353 3.0 81.0 1.0 CG A:ASP150 3.0 35.4 1.0 OG A:SER39 3.0 47.1 1.0 CD2 A:HIS59 3.2 27.1 1.0 CE1 A:HIS59 3.2 25.7 1.0 CB A:CYS37 3.3 38.0 1.0 C5N A:NAP353 3.3 80.9 1.0 OD1 A:ASP150 3.5 37.7 1.0 C3N A:NAP353 3.7 82.4 1.0 CB A:SER39 3.8 43.1 1.0 O7N A:NAP353 4.0 86.7 1.0 OE2 A:GLU60 4.1 19.8 1.0 C7N A:NAP353 4.2 84.7 1.0 CB A:ASP150 4.2 32.1 1.0 C6N A:NAP353 4.2 79.2 1.0 ND1 A:HIS59 4.4 25.7 1.0 CG A:HIS59 4.4 27.6 1.0 CE A:MET151 4.4 28.2 1.0 CD A:GLU60 4.6 19.8 1.0 C2N A:NAP353 4.6 79.8 1.0 CA A:CYS37 4.7 37.4 1.0 CG A:GLU60 4.8 21.5 1.0 N1N A:NAP353 4.8 77.9 1.0 N A:SER39 4.9 40.3 1.0

Zinc binding site 2 out of 4 in the Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1354 b:49.9 occ:1.00 OD2 B:ASP150 2.2 33.0 1.0 NE2 B:HIS59 2.3 30.7 1.0 SG B:CYS37 2.3 25.9 1.0 CE1 B:HIS59 3.1 28.9 1.0 OG B:SER39 3.2 38.6 1.0 CG B:ASP150 3.2 32.8 1.0 CB B:CYS37 3.2 28.6 1.0 C4N B:NAP1353 3.3 65.8 1.0 CD2 B:HIS59 3.4 29.3 1.0 C3N B:NAP1353 3.6 66.3 1.0 CB B:SER39 3.6 36.5 1.0 OD1 B:ASP150 3.7 36.4 1.0 O7N B:NAP1353 3.8 65.6 1.0 C7N B:NAP1353 3.8 66.7 1.0 C5N B:NAP1353 3.8 64.9 1.0 ND1 B:HIS59 4.3 29.5 1.0 C2N B:NAP1353 4.4 64.9 1.0 CB B:ASP150 4.4 29.0 1.0 CG B:HIS59 4.5 29.1 1.0 OE2 B:GLU60 4.5 22.9 1.0 C6N B:NAP1353 4.5 65.0 1.0 CE B:MET151 4.5 12.8 1.0 CA B:CYS37 4.7 29.1 1.0 N7N B:NAP1353 4.7 68.8 1.0 N B:SER39 4.7 32.3 1.0 N1N B:NAP1353 4.8 64.2 1.0 CA B:SER39 4.8 34.2 1.0 CD B:GLU60 4.8 24.3 1.0

Zinc binding site 3 out of 4 in the Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2354 b:69.0 occ:1.00 OD2 C:ASP150 2.1 38.5 1.0 NE2 C:HIS59 2.2 37.9 1.0 SG C:CYS37 2.6 43.0 1.0 CE1 C:HIS59 2.9 37.0 1.0 CG C:ASP150 2.9 39.5 1.0 OG C:SER39 3.2 50.2 1.0 OD1 C:ASP150 3.2 42.5 1.0 CD2 C:HIS59 3.3 36.4 1.0 CB C:CYS37 3.5 40.9 1.0 O7N C:NAP2353 3.7 90.3 1.0 C4N C:NAP2353 3.7 87.6 1.0 C7N C:NAP2353 3.7 90.0 1.0 C3N C:NAP2353 3.7 88.8 1.0 CB C:SER39 3.8 47.9 1.0 ND1 C:HIS59 4.1 37.1 1.0 CB C:ASP150 4.2 37.2 1.0 OE2 C:GLU60 4.2 36.9 1.0 CG C:HIS59 4.3 37.2 1.0 C5N C:NAP2353 4.4 87.1 1.0 N7N C:NAP2353 4.4 91.8 1.0 CE C:MET151 4.5 34.2 1.0 C2N C:NAP2353 4.5 86.6 1.0 CD C:GLU60 4.8 35.2 1.0 CG C:GLU60 4.8 33.5 1.0 CA C:CYS37 5.0 40.0 1.0

Zinc binding site 4 out of 4 in the Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Contribution of PRO275 to the Thermostability of the Alcohol Dehydrogenases (Adhs) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3354 b:78.0 occ:1.00 OD2 D:ASP150 2.3 49.2 1.0 SG D:CYS37 3.0 58.8 1.0 CG D:ASP150 3.3 47.2 1.0 OG D:SER39 3.3 66.2 1.0 CB D:CYS37 3.5 57.0 1.0 CB D:SER39 3.5 65.0 1.0 C4N D:NAP3353 3.6 87.9 1.0 OD1 D:ASP150 3.7 48.6 1.0 C3N D:NAP3353 4.0 89.5 1.0 ND1 D:HIS59 4.1 71.0 1.0 C5N D:NAP3353 4.1 86.8 1.0 O7N D:NAP3353 4.2 92.1 1.0 C7N D:NAP3353 4.3 91.1 1.0 OE2 D:GLU60 4.3 50.8 1.0 CB D:ASP150 4.5 45.0 1.0 CE D:MET151 4.5 47.4 1.0 CA D:SER39 4.8 64.3 1.0 C2N D:NAP3353 4.8 87.3 1.0 CD D:GLU60 4.8 51.9 1.0 C6N D:NAP3353 4.8 85.5 1.0 N D:SER39 4.8 63.0 1.0 CE1 D:HIS59 4.9 71.8 1.0 CG D:HIS59 4.9 68.9 1.0 CA D:CYS37 4.9 56.2 1.0 CB D:HIS59 5.0 64.5 1.0

E.Goihberg, O.Dym, S.Tel-Or, L.Shimon, F.Frolow, M.Peretz, Y.Burstein. Thermal Stabilization of the Protozoan Entamoeba Histolytica Alcohol Dehydrogenase By A Single Proline Substitution Proteins V. 72 711 2008.
ISSN: ISSN 0887-3585
PubMed: 18260103
DOI: 10.1002/PROT.21946