Zinc in PDB 5z0c: Nerol Dehydrogenase From Persicaria Minor

The structure of Nerol Dehydrogenase From Persicaria Minor, PDB code: 5z0c was solved by C.S.Tan, C.L.Ng, Z.Zainal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.37 / 1.54
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.000, 54.030, 79.370, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 18.8

The binding sites of Zinc atom in the Nerol Dehydrogenase From Persicaria Minor (pdb code 5z0c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Nerol Dehydrogenase From Persicaria Minor, PDB code: 5z0c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Nerol Dehydrogenase From Persicaria Minor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nerol Dehydrogenase From Persicaria Minor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:18.1 occ:1.00 SG A:CYS104 2.3 19.1 1.0 SG A:CYS107 2.3 18.4 1.0 SG A:CYS118 2.4 17.2 1.0 SG A:CYS110 2.4 17.3 1.0 CB A:CYS118 3.3 15.4 1.0 CB A:CYS107 3.4 20.8 1.0 CB A:CYS104 3.5 19.4 1.0 CB A:CYS110 3.5 18.1 1.0 N A:CYS104 3.5 17.2 1.0 CA A:CYS104 3.9 17.9 1.0 N A:HIS105 3.9 18.6 1.0 N A:CYS107 4.0 20.7 1.0 O A:HOH622 4.0 27.9 1.0 CA A:CYS118 4.0 15.8 1.0 N A:CYS110 4.2 16.9 1.0 CA A:CYS107 4.2 21.1 1.0 C A:CYS104 4.3 19.9 1.0 CA A:CYS110 4.4 16.9 1.0 N A:SER106 4.4 22.0 1.0 CD A:PRO119 4.5 20.7 1.0 CB A:SER103 4.6 15.4 1.0 C A:SER106 4.7 27.1 1.0 C A:SER103 4.7 18.6 1.0 C A:CYS118 4.9 16.0 1.0 C A:CYS107 4.9 21.0 1.0 CA A:HIS105 4.9 20.7 1.0 OG A:SER103 4.9 14.8 1.0 N A:PRO119 4.9 16.7 1.0 O A:CYS107 5.0 22.4 1.0

Zinc binding site 2 out of 2 in the Nerol Dehydrogenase From Persicaria Minor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nerol Dehydrogenase From Persicaria Minor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:20.2 occ:1.00 O A:HOH637 2.1 19.1 1.0 CE1 A:HIS73 2.2 15.5 1.0 SG A:CYS51 2.3 18.8 1.0 SG A:CYS167 2.4 19.6 1.0 NE2 A:HIS73 2.9 24.5 1.0 ND1 A:HIS73 3.2 20.3 1.0 CB A:CYS51 3.3 17.4 1.0 CB A:CYS167 3.5 17.0 1.0 O A:HOH853 3.8 50.6 1.0 O A:HOH840 3.8 40.8 1.0 OG A:SER53 4.0 23.9 1.0 CB A:SER53 4.1 20.3 1.0 CD2 A:HIS73 4.1 19.0 1.0 SG A:CYS99 4.2 12.6 0.5 O A:HOH721 4.3 37.0 1.0 CG A:HIS73 4.3 16.4 1.0 O A:HOH828 4.5 47.0 1.0 CA A:CYS51 4.8 15.4 1.0 NH2 A:ARG349 4.8 20.9 1.0 CA A:CYS167 4.9 13.9 1.0 N A:SER53 5.0 16.3 1.0 OE2 A:GLU74 5.0 19.0 1.0

C.S.Tan, M.Hassan, Z.A.Mohamed Hussein, I.Ismail, K.L.Ho, C.L.Ng, Z.Zainal. Structural and Kinetic Studies of A Novel Nerol Dehydrogenase From Persicaria Minor, A Nerol-Specific Enzyme For Citral Biosynthesis. Plant Physiol. Biochem. V. 123 359 2017.
ISSN: ISSN 1873-2690
PubMed: 29304481
DOI: 10.1016/J.PLAPHY.2017.12.033