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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 1nvb

Go back to Zinc Binding Sites List in 1nvb
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 1nvb

Go back to Zinc Binding Sites List in 1nvb
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

Reference:

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
Page generated: Fri Sep 25 22:47:40 2020
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