Zinc in PDB 7usz: Human Ddah-1, Holo (Zn-Bound) Form

All present enzymatic activity of Human Ddah-1, Holo (Zn-Bound) Form:
3.5.3.18;

The structure of Human Ddah-1, Holo (Zn-Bound) Form, PDB code: 7usz was solved by C.A.Smith, Y.T.Ghebre, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.55 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.968, 47.634, 146.965, 90, 94.61, 90
R / Rfree (%)	15.1 / 19.9

The structure of Human Ddah-1, Holo (Zn-Bound) Form also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Human Ddah-1, Holo (Zn-Bound) Form (pdb code 7usz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Ddah-1, Holo (Zn-Bound) Form, PDB code: 7usz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Ddah-1, Holo (Zn-Bound) Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Ddah-1, Holo (Zn-Bound) Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:37.3 occ:1.00 O A:HOH469 1.9 23.4 1.0 O A:HOH404 2.1 27.5 1.0 O A:HOH418 2.1 26.5 1.0 SG A:CYS274 2.3 18.6 1.0 CB A:CYS274 3.1 17.1 1.0 ND1 A:HIS173 3.8 32.3 1.0 CA A:CYS274 3.9 13.9 1.0 OD1 A:ASP79 4.0 17.0 1.0 OE2 A:GLU78 4.0 19.7 1.0 OD2 A:ASP79 4.1 18.3 1.0 CE1 A:HIS173 4.3 31.1 1.0 CG A:ASP79 4.5 16.1 1.0 O A:ASP269 4.5 22.8 1.0 N A:CYS274 4.5 13.4 1.0 CA A:GLY129 4.6 13.1 1.0

Zinc binding site 2 out of 2 in the Human Ddah-1, Holo (Zn-Bound) Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Ddah-1, Holo (Zn-Bound) Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:34.6 occ:1.00 O B:HOH427 2.0 24.4 1.0 O B:HOH424 2.1 23.8 1.0 O B:HOH414 2.2 32.3 1.0 SG B:CYS274 2.3 24.2 1.0 CB B:CYS274 3.2 20.8 1.0 ND1 B:HIS173 3.8 34.6 1.0 OE1 B:GLU78 3.9 24.4 1.0 CA B:CYS274 4.0 17.1 1.0 OD1 B:ASP79 4.0 19.7 1.0 OD2 B:ASP79 4.1 23.7 1.0 CE1 B:HIS173 4.3 35.7 1.0 O B:ASP269 4.4 28.4 1.0 CG B:ASP79 4.5 22.3 1.0 N B:CYS274 4.6 17.1 1.0 CA B:GLY129 4.6 16.3 1.0 CG B:HIS173 5.0 31.4 1.0

C.A.Smith, A.Ebrahimpour, L.Novikova, D.Farina, A.O.Bailey, W.K.Russell, A.Jain, A.B.Saltzman, A.Malovannaya, B.V.V.Prasad, L.Hu, Y.T.Ghebre. Esomeprazole Covalently Interacts with the Cardiovascular Enzyme Dimethylarginine Dimethylaminohydrolase: Insights Into the Cardiovascular Risk of Proton Pump Inhibitors. Biochim Biophys Acta Gen V.1866 30149 2022SUBJ.
ISSN: ISSN 1872-8006
PubMed: 35472493
DOI: 10.1016/J.BBAGEN.2022.130149