Zinc in PDB 1nvb: 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: 1nvb 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	131.550, 84.190, 73.740, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 27.2

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

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Carbaphosphonate (pdb code 1nvb). 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: 1nvb:
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:48.4 occ:1.00 NE2 A:HIS271 2.2 4.7 1.0 NE2 A:HIS287 2.2 4.7 1.0 OE2 A:GLU194 2.2 34.4 1.0 O5 A:CRB500 2.3 32.1 1.0 O4 A:CRB500 2.4 29.8 1.0 CD2 A:HIS287 3.0 4.7 1.0 CD A:GLU194 3.1 16.7 1.0 CE1 A:HIS271 3.1 9.9 1.0 C5 A:CRB500 3.1 16.2 1.0 CD2 A:HIS271 3.2 17.0 1.0 C4 A:CRB500 3.2 18.7 1.0 CE1 A:HIS287 3.2 4.7 1.0 OE1 A:GLU194 3.4 4.7 1.0 C5N A:NAD400 3.6 76.1 1.0 OD2 A:ASP146 3.7 18.1 1.0 C6N A:NAD400 3.7 71.0 1.0 CG A:HIS287 4.2 4.7 1.0 ND1 A:HIS271 4.2 5.0 1.0 ND1 A:HIS287 4.3 6.5 1.0 CG A:HIS271 4.3 4.7 1.0 CG2 A:VAL291 4.4 12.1 1.0 CG A:GLU194 4.4 15.9 1.0 C4N A:NAD400 4.5 75.9 1.0 C6 A:CRB500 4.5 16.4 1.0 C3 A:CRB500 4.6 14.0 1.0 CG A:ASP146 4.8 9.9 1.0 N1N A:NAD400 4.8 65.5 1.0 NZ A:LYS197 4.9 11.4 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:48.3 occ:1.00 NE2 B:HIS287 2.1 8.9 1.0 O5 B:CRB501 2.2 22.1 1.0 OE2 B:GLU194 2.3 37.3 1.0 NE2 B:HIS271 2.3 4.7 1.0 O4 B:CRB501 2.7 14.0 1.0 CD2 B:HIS287 2.9 12.7 1.0 CE1 B:HIS287 3.2 11.7 1.0 C5 B:CRB501 3.2 10.3 1.0 CD2 B:HIS271 3.3 4.7 1.0 CD B:GLU194 3.3 16.8 1.0 CE1 B:HIS271 3.3 4.7 1.0 C4 B:CRB501 3.4 4.7 1.0 OD2 B:ASP146 3.6 12.1 1.0 OE1 B:GLU194 3.6 6.8 1.0 O B:HOH643 3.9 19.5 1.0 CG B:HIS287 4.1 13.4 1.0 ND1 B:HIS287 4.2 10.0 1.0 O B:HOH650 4.3 5.0 1.0 CG B:HIS271 4.4 8.2 1.0 ND1 B:HIS271 4.4 4.7 1.0 C6 B:CRB501 4.6 10.7 1.0 CG2 B:VAL291 4.6 4.7 1.0 CG B:GLU194 4.6 12.6 1.0 CG B:ASP146 4.8 17.8 1.0 C3 B:CRB501 4.8 6.3 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