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

Enzymatic activity of Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad

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

Protein crystallography data

The structure of Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad, PDB code: 1nve 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) 25.57 / 2.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.640, 70.350, 144.320, 90.00, 90.78, 90.00
R / Rfree (%) 20.8 / 26.8

Other elements in 1nve:

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

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad (pdb code 1nve). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad, PDB code: 1nve:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1nve

Go back to Zinc Binding Sites List in 1nve
Zinc binding site 1 out of 4 in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad


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 Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:0.3
occ:1.00
 NE2 A:HIS271 2.4 31.8 1.0
NE2 A:HIS287 2.6 45.4 1.0
OE2 A:GLU194 2.7 70.2 1.0
CD A:GLU194 3.2 56.4 1.0
CD2 A:HIS287 3.2 38.0 1.0
CE1 A:HIS271 3.4 43.6 1.0
CD2 A:HIS271 3.4 40.3 1.0
OE1 A:GLU194 3.6 51.7 1.0
OD2 A:ASP146 3.6 46.5 1.0
CE1 A:HIS287 3.7 36.3 1.0
CG A:GLU194 4.1 49.9 1.0
O A:HOH607 4.5 54.6 1.0
CG A:HIS287 4.5 40.4 1.0
CG2 A:VAL291 4.5 53.2 1.0
ND1 A:HIS271 4.5 38.6 1.0
CG A:HIS271 4.6 36.0 1.0
ND1 A:HIS287 4.7 31.6 1.0
C5N A:NAD400 4.7 39.7 1.0
CG A:ASP146 4.7 45.7 1.0

Zinc binding site 2 out of 4 in 1nve

Go back to Zinc Binding Sites List in 1nve
Zinc binding site 2 out of 4 in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad


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 Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:0.1
occ:1.00
 NE2 B:HIS271 2.4 47.9 1.0
OE2 B:GLU194 2.4 55.8 1.0
NE2 B:HIS287 2.4 41.1 1.0
CD B:GLU194 3.0 59.9 1.0
CD2 B:HIS287 3.0 40.2 1.0
CE1 B:HIS271 3.3 48.4 1.0
CD2 B:HIS271 3.4 39.8 1.0
OE1 B:GLU194 3.5 57.8 1.0
CE1 B:HIS287 3.6 42.2 1.0
OD2 B:ASP146 3.7 29.0 1.0
CG B:GLU194 3.9 44.5 1.0
CG2 B:VAL291 4.2 48.1 1.0
CG B:HIS287 4.3 26.5 1.0
ND1 B:HIS271 4.5 40.8 1.0
CG B:HIS271 4.5 42.9 1.0
ND1 B:HIS287 4.6 42.6 1.0
CG B:ASP146 4.9 41.8 1.0
C5N B:NAD401 5.0 33.6 1.0

Zinc binding site 3 out of 4 in 1nve

Go back to Zinc Binding Sites List in 1nve
Zinc binding site 3 out of 4 in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:0.7
occ:1.00
 NE2 C:HIS271 2.5 50.9 1.0
NE2 C:HIS287 2.5 54.4 1.0
OE2 C:GLU194 2.8 82.0 1.0
CD2 C:HIS287 3.2 51.5 1.0
CD C:GLU194 3.2 80.2 1.0
CD2 C:HIS271 3.4 47.0 1.0
CE1 C:HIS271 3.5 57.3 1.0
OD2 C:ASP146 3.6 49.4 1.0
CE1 C:HIS287 3.6 53.2 1.0
OE1 C:GLU194 3.7 85.8 1.0
CG C:GLU194 4.1 69.3 1.0
O C:HOH1623 4.4 48.3 1.0
CG C:HIS287 4.4 44.5 1.0
CG2 C:VAL291 4.5 45.3 1.0
ND1 C:HIS271 4.6 54.3 1.0
CG C:HIS271 4.6 48.4 1.0
ND1 C:HIS287 4.6 49.8 1.0
C5N C:NAD402 4.7 42.5 1.0
CG C:ASP146 4.8 40.1 1.0

Zinc binding site 4 out of 4 in 1nve

Go back to Zinc Binding Sites List in 1nve
Zinc binding site 4 out of 4 in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+ and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1603

b:0.6
occ:1.00
 NE2 D:HIS287 2.6 49.9 1.0
OE2 D:GLU194 2.9 57.9 1.0
NE2 D:HIS271 2.9 31.5 1.0
OD2 D:ASP146 3.1 42.1 1.0
CD2 D:HIS287 3.1 37.8 1.0
CD D:GLU194 3.3 48.8 1.0
OE1 D:GLU194 3.7 39.9 1.0
CE1 D:HIS287 3.8 56.6 1.0
CD2 D:HIS271 3.9 41.3 1.0
CE1 D:HIS271 3.9 44.5 1.0
CG D:GLU194 4.0 32.8 1.0
C5N D:NAD1403 4.1 40.3 1.0
CG D:ASP146 4.1 40.8 1.0
O D:HOH1605 4.3 36.9 1.0
CG D:HIS287 4.4 48.7 1.0
ND1 D:HIS287 4.7 55.0 1.0
OD1 D:ASP146 4.7 40.1 1.0
C4N D:NAD1403 4.8 46.3 1.0
CD1 D:LEU142 4.8 35.2 1.0
CG2 D:VAL291 4.9 38.8 1.0
C6N D:NAD1403 5.0 44.5 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: Mon Jan 25 16:10:45 2021

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