Zinc in PDB 9cp7: Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Product Analogue (L-Cysteate) and Nadh

The structure of Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Product Analogue (L-Cysteate) and Nadh, PDB code: 9cp7 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 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.931, 76.339, 85.076, 90, 117.04, 90
R / Rfree (%)	14.8 / 17.7

The binding sites of Zinc atom in the Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Product Analogue (L-Cysteate) and Nadh (pdb code 9cp7). 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 Product Analogue (L-Cysteate) and Nadh, PDB code: 9cp7:
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 Product Analogue (L-Cysteate) and 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 Product Analogue (L-Cysteate) and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:17.0 occ:1.00 NE2 B:HIS411 2.0 14.4 1.0 N A:OCS502 2.1 15.8 1.0 NE2 A:HIS251 2.1 15.0 1.0 OE1 A:GLN248 2.2 16.7 1.0 OD2 A:OCS502 2.2 15.0 1.0 OD2 A:ASP352 2.2 18.8 1.0 CE1 B:HIS411 2.9 16.2 1.0 CA A:OCS502 3.1 16.5 1.0 CG A:ASP352 3.1 16.3 1.0 CE1 A:HIS251 3.1 15.9 1.0 CD2 B:HIS411 3.1 14.1 1.0 CD A:GLN248 3.1 18.4 1.0 CD2 A:HIS251 3.2 15.8 1.0 SG A:OCS502 3.3 16.7 1.0 NE2 A:GLN248 3.4 18.6 1.0 CB A:OCS502 3.5 16.0 1.0 OD1 A:ASP352 3.6 18.6 1.0 ND1 B:HIS411 4.0 15.8 1.0 OD1 A:OCS502 4.1 15.3 1.0 CB A:ASP352 4.1 14.8 1.0 CG B:HIS411 4.2 15.4 1.0 ND1 A:HIS251 4.2 14.9 1.0 CG A:HIS251 4.3 14.9 1.0 C A:OCS502 4.4 19.1 1.0 OD3 A:OCS502 4.4 15.6 1.0 CG A:GLN248 4.5 19.1 1.0 SD B:MET408 4.7 19.2 1.0 OG A:SER226 4.8 18.8 1.0 NZ A:LYS353 4.8 17.5 1.0 O A:OCS502 4.9 19.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Product Analogue (L-Cysteate) and 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 Product Analogue (L-Cysteate) and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:19.1 occ:1.00 N B:OCS502 2.1 16.7 1.0 NE2 A:HIS411 2.1 17.5 1.0 NE2 B:HIS251 2.1 18.1 1.0 OE1 B:GLN248 2.2 16.7 1.0 OD2 B:OCS502 2.2 18.4 1.0 OD2 B:ASP352 2.3 20.7 1.0 CE1 A:HIS411 3.0 18.9 1.0 CA B:OCS502 3.1 17.1 1.0 CE1 B:HIS251 3.1 17.9 1.0 CD2 B:HIS251 3.1 19.1 1.0 CD2 A:HIS411 3.1 17.5 1.0 CG B:ASP352 3.1 19.8 1.0 CD B:GLN248 3.1 20.2 1.0 SG B:OCS502 3.3 18.3 1.0 NE2 B:GLN248 3.4 21.0 1.0 CB B:OCS502 3.5 17.0 1.0 OD1 B:ASP352 3.6 18.8 1.0 OD1 B:OCS502 4.1 18.5 1.0 ND1 A:HIS411 4.2 17.8 1.0 CB B:ASP352 4.2 17.5 1.0 ND1 B:HIS251 4.2 19.5 1.0 CG A:HIS411 4.2 17.5 1.0 CG B:HIS251 4.2 18.1 1.0 C B:OCS502 4.3 21.3 1.0 OD3 B:OCS502 4.4 18.4 1.0 CG B:GLN248 4.5 20.9 1.0 SD A:MET408 4.7 22.7 1.0 OG B:SER226 4.7 20.4 1.0 NZ B:LYS353 4.8 21.8 1.0 OXT B:OCS502 4.8 22.2 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