Zinc in PDB 1nvd: Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate

All present enzymatic activity of Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate:
4.2.3.4;

The structure of Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate, PDB code: 1nvd was solved by C.E.Nichols, J.Ren, H.K.Lamb, A.R.Hawkins, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.030, 70.030, 197.630, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.7

The structure of Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate (pdb code 1nvd). 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 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate, PDB code: 1nvd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate


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 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:31.1 occ:1.00 OE2 A:GLU194 2.2 23.0 1.0 NE2 A:HIS287 2.2 22.8 1.0 NE2 A:HIS271 2.3 23.4 1.0 O5 A:CRB500 2.5 11.7 1.0 O4 A:CRB500 2.5 27.1 1.0 CD2 A:HIS287 3.0 14.3 1.0 CD A:GLU194 3.1 23.3 1.0 CD2 A:HIS271 3.1 37.2 1.0 C4 A:CRB500 3.3 22.9 1.0 C5 A:CRB500 3.3 19.5 1.0 CE1 A:HIS287 3.4 14.3 1.0 CE1 A:HIS271 3.4 20.2 1.0 OE1 A:GLU194 3.4 18.6 1.0 OD2 A:ASP146 3.8 31.5 1.0 CG A:HIS287 4.3 14.7 1.0 CG2 A:VAL291 4.3 5.9 1.0 CG A:GLU194 4.3 25.5 1.0 CG A:HIS271 4.3 33.7 1.0 ND1 A:HIS287 4.4 21.6 1.0 ND1 A:HIS271 4.4 23.3 1.0 NZ A:LYS197 4.5 24.2 1.0 C6 A:CRB500 4.7 22.0 1.0 C3 A:CRB500 4.7 13.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate


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 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:39.2 occ:1.00 NE2 B:HIS287 2.2 23.6 1.0 NE2 B:HIS271 2.2 28.6 1.0 O5 B:CRB501 2.3 24.7 1.0 OE2 B:GLU194 2.4 35.4 1.0 O4 B:CRB501 2.5 16.3 1.0 CD2 B:HIS271 3.0 14.7 1.0 CD2 B:HIS287 3.0 12.7 1.0 C5 B:CRB501 3.2 25.3 1.0 C4 B:CRB501 3.2 31.1 1.0 CD B:GLU194 3.2 29.0 1.0 CE1 B:HIS287 3.3 35.4 1.0 CE1 B:HIS271 3.4 31.9 1.0 OE1 B:GLU194 3.5 27.1 1.0 OD2 B:ASP146 3.9 30.0 1.0 O B:HOH864 4.2 59.9 1.0 CG B:HIS271 4.2 22.1 1.0 CG2 B:VAL291 4.2 21.4 1.0 CG B:HIS287 4.3 18.1 1.0 ND1 B:HIS287 4.3 23.3 1.0 ND1 B:HIS271 4.4 32.8 1.0 CG B:GLU194 4.5 23.5 1.0 C6 B:CRB501 4.5 12.3 1.0 NZ B:LYS197 4.5 14.8 1.0 C3 B:CRB501 4.7 27.7 1.0

C.E.Nichols, J.Ren, H.K.Lamb, A.R.Hawkins, D.K.Stammers. Ligand-Induced Conformational Changes and A Mechanism For Domain Closure in Aspergillus Nidulans Dehydroquinate Synthase J.Mol.Biol. V. 327 129 2003.
ISSN: ISSN 0022-2836
PubMed: 12614613
DOI: 10.1016/S0022-2836(03)00086-X