Zinc in PDB 8v36: Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Nadh

The structure of Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Nadh, PDB code: 8v36 was solved by M.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.90 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.307, 87.556, 134.197, 90, 90, 90
R / Rfree (%)	22.3 / 28.1

The binding sites of Zinc atom in the Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Nadh (pdb code 8v36). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Nadh, PDB code: 8v36:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Nadh


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 Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:59.5 occ:1.00 NE2 B:HIS411 2.0 58.1 1.0 O A:HOH618 2.0 56.8 1.0 O B:HOH635 2.1 52.7 1.0 OE1 A:GLN248 2.2 57.9 1.0 NE2 A:HIS126 2.2 56.8 1.0 NE2 A:HIS251 2.2 66.8 1.0 CE1 B:HIS411 3.0 60.4 1.0 CD2 B:HIS411 3.0 55.5 1.0 CD A:GLN248 3.1 60.7 1.0 CE1 A:HIS126 3.1 57.8 1.0 CD2 A:HIS126 3.2 57.0 1.0 CE1 A:HIS251 3.2 70.7 1.0 CD2 A:HIS251 3.2 67.7 1.0 NE2 A:GLN248 3.3 60.8 1.0 ND1 B:HIS411 4.1 57.9 1.0 CG B:HIS411 4.1 58.1 1.0 ND1 A:HIS126 4.3 56.4 1.0 CG A:HIS126 4.3 57.7 1.0 ND1 A:HIS251 4.3 69.5 1.0 CG A:HIS251 4.4 68.3 1.0 OG A:SER226 4.4 99.9 1.0 CG A:GLN248 4.5 59.9 1.0 CB A:SER226 4.9 101.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Nadh


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 Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:67.9 occ:1.00 NE2 B:HIS251 2.1 80.9 1.0 O B:HOH632 2.1 74.0 1.0 NE2 B:HIS126 2.2 73.4 1.0 O B:HOH636 2.3 52.8 1.0 OE1 B:GLN248 2.3 70.9 1.0 NE2 A:HIS411 2.4 73.5 1.0 CD2 B:HIS251 3.0 83.1 1.0 CE1 B:HIS251 3.1 77.3 1.0 CD2 B:HIS126 3.1 72.0 1.0 CE1 B:HIS126 3.2 74.3 1.0 CD B:GLN248 3.3 71.7 1.0 CD2 A:HIS411 3.3 73.2 1.0 CE1 A:HIS411 3.3 74.2 1.0 NE2 B:GLN248 3.6 68.7 1.0 CG B:HIS251 4.2 83.4 1.0 ND1 B:HIS251 4.2 82.5 1.0 ND1 B:HIS126 4.3 75.5 1.0 CG B:HIS126 4.3 74.2 1.0 ND1 A:HIS411 4.4 72.9 1.0 CG A:HIS411 4.5 70.5 1.0 OG B:SER226 4.5 123.2 1.0 CG B:GLN248 4.7 73.0 1.0 CA B:GLN248 5.0 73.3 1.0

L.Burchill, A.Kaur, A.Nastasovici, M.Lee, S.J.Williams. Structural and Kinetic Insights Into the Stereospecific Oxidation of R -2,3-Dihydroxypropanesulfonate By Dhps-3-Dehydrogenase From Cupriavidus Pinatubonensis. Chem Sci 2024.
ISSN: ISSN 2041-6520
PubMed: 39263660
DOI: 10.1039/D4SC05114A