Zinc in PDB 9cp8: Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Product (R-Sulfolactate) and Nadh

The structure of Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Product (R-Sulfolactate) and Nadh, PDB code: 9cp8 was solved by M.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.88 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.078, 75.592, 84.995, 90, 117.28, 90
R / Rfree (%)	15 / 17.6

The binding sites of Zinc atom in the Crystal Structure of Dhps-3-Dehydrogenase, Hpsn From Cupriavidus Pinatubonensis in Complex with Product (R-Sulfolactate) and Nadh (pdb code 9cp8). 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 (R-Sulfolactate) and Nadh, PDB code: 9cp8:
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 (R-Sulfolactate) 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 (R-Sulfolactate) and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:14.5 occ:1.00 NE2 B:HIS411 2.0 12.6 1.0 O2 A:3SL502 2.1 13.8 1.0 NE2 A:HIS251 2.1 13.7 1.0 OE1 A:GLN248 2.1 14.5 1.0 O3S A:3SL502 2.2 13.1 1.0 OD2 A:ASP352 2.2 14.1 1.0 CE1 B:HIS411 2.9 14.2 1.0 C2 A:3SL502 3.1 13.9 1.0 CG A:ASP352 3.1 12.9 1.0 CD2 B:HIS411 3.1 12.9 1.0 CE1 A:HIS251 3.1 13.5 1.0 CD A:GLN248 3.1 14.4 1.0 CD2 A:HIS251 3.1 13.4 1.0 NE2 A:GLN248 3.4 15.0 1.0 S A:3SL502 3.4 13.8 1.0 OD1 A:ASP352 3.6 13.8 1.0 C3 A:3SL502 3.6 13.1 1.0 ND1 B:HIS411 4.1 14.3 1.0 CB A:ASP352 4.1 12.7 1.0 O2S A:3SL502 4.2 13.4 1.0 CG B:HIS411 4.2 14.0 1.0 ND1 A:HIS251 4.2 14.0 1.0 CG A:HIS251 4.2 13.5 1.0 C1 A:3SL502 4.3 15.9 1.0 O1S A:3SL502 4.5 13.6 1.0 CG A:GLN248 4.5 15.1 1.0 OG A:SER226 4.8 13.8 1.0 SD B:MET408 4.8 15.8 1.0 NZ A:LYS353 4.8 14.1 1.0 O12 A:3SL502 4.9 15.7 1.0 CB A:GLN248 5.0 14.8 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 (R-Sulfolactate) 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 (R-Sulfolactate) and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:16.5 occ:1.00 O2 B:3SL502 2.0 15.2 1.0 OE1 B:GLN248 2.1 16.4 1.0 NE2 A:HIS411 2.1 15.0 1.0 NE2 B:HIS251 2.1 15.6 1.0 OD2 B:ASP352 2.2 15.3 1.0 O3S B:3SL502 2.2 15.6 1.0 CE1 A:HIS411 3.0 16.0 1.0 C2 B:3SL502 3.0 15.9 1.0 CE1 B:HIS251 3.1 14.8 1.0 CG B:ASP352 3.1 17.0 1.0 CD B:GLN248 3.1 16.6 1.0 CD2 A:HIS411 3.1 15.9 1.0 CD2 B:HIS251 3.1 16.6 1.0 NE2 B:GLN248 3.4 16.9 1.0 S B:3SL502 3.4 15.6 1.0 OD1 B:ASP352 3.5 14.8 1.0 C3 B:3SL502 3.6 14.7 1.0 CB B:ASP352 4.1 14.4 1.0 ND1 A:HIS411 4.1 15.9 1.0 ND1 B:HIS251 4.2 15.6 1.0 O2S B:3SL502 4.2 15.5 1.0 CG A:HIS411 4.2 15.7 1.0 CG B:HIS251 4.2 15.9 1.0 C1 B:3SL502 4.3 16.7 1.0 O1S B:3SL502 4.5 15.6 1.0 CG B:GLN248 4.5 17.1 1.0 OG B:SER226 4.8 16.3 1.0 NZ B:LYS353 4.8 16.9 1.0 O11 B:3SL502 4.8 17.1 1.0 SD A:MET408 4.8 18.8 1.0 CB B:GLN248 5.0 18.0 1.0 CG1 B:VAL348 5.0 14.8 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