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

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

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

Protein crystallography data

The structure of Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+, Adp and Carbaphosphonate, PDB code: 1nvf 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) 26.07 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 206.500, 136.400, 40.400, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 24.2

Other elements in 1nvf:

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

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 3 in 1nvf

Go back to Zinc Binding Sites List in 1nvf
Zinc binding site 1 out of 3 in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+, Adp 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+, Adp and Carbaphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:32.2
occ:1.00
 NE2 A:HIS287 2.1 38.0 1.0
NE2 A:HIS271 2.2 47.3 1.0
OE2 A:GLU194 2.2 40.2 1.0
O5 A:CRB500 2.2 24.5 1.0
O4 A:CRB500 2.4 27.3 1.0
CD2 A:HIS287 3.0 40.6 1.0
C4 A:CRB500 3.0 35.2 1.0
CD2 A:HIS271 3.1 43.6 1.0
C5 A:CRB500 3.1 28.3 1.0
CE1 A:HIS287 3.1 32.8 1.0
CD A:GLU194 3.1 25.1 1.0
CE1 A:HIS271 3.3 57.0 1.0
OE1 A:GLU194 3.4 31.4 1.0
OD2 A:ASP146 3.7 39.2 1.0
CG2 A:VAL291 4.1 36.2 1.0
CG A:HIS287 4.2 34.9 1.0
ND1 A:HIS287 4.2 37.9 1.0
CG A:HIS271 4.3 36.9 1.0
ND1 A:HIS271 4.3 52.7 1.0
C6 A:CRB500 4.4 31.6 1.0
CG A:GLU194 4.5 37.5 1.0
C3 A:CRB500 4.5 32.4 1.0
O A:HOH722 4.7 45.5 1.0
CG A:ASP146 4.8 34.1 1.0
NZ A:LYS197 4.8 42.1 1.0

Zinc binding site 2 out of 3 in 1nvf

Go back to Zinc Binding Sites List in 1nvf
Zinc binding site 2 out of 3 in the Crystal Structure of 3-Dehydroquinate Synthase (Dhqs) in Complex with ZN2+, Adp 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+, Adp and Carbaphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:29.2
occ:1.00
 NE2 B:HIS287 2.0 34.0 1.0
OE2 B:GLU194 2.2 43.6 1.0
NE2 B:HIS271 2.3 11.8 1.0
O4 B:CRB501 2.3 30.5 1.0
O5 B:CRB501 2.3 29.6 1.0
CD2 B:HIS287 2.9 27.5 1.0
C4 B:CRB501 3.0 16.7 1.0
CE1 B:HIS287 3.1 34.3 1.0
CD B:GLU194 3.1 13.2 1.0
CD2 B:HIS271 3.1 20.8 1.0
C5 B:CRB501 3.1 23.9 1.0
CE1 B:HIS271 3.3 26.7 1.0
OE1 B:GLU194 3.4 6.9 1.0
OD2 B:ASP146 3.8 45.5 1.0
CG B:HIS287 4.1 28.1 1.0
CG2 B:VAL291 4.1 30.2 1.0
ND1 B:HIS287 4.1 30.1 1.0
CG B:HIS271 4.3 17.7 1.0
ND1 B:HIS271 4.4 16.7 1.0
CG B:GLU194 4.4 22.9 1.0
C6 B:CRB501 4.4 7.5 1.0
C3 B:CRB501 4.5 11.3 1.0
O B:HOH619 4.8 13.4 1.0
CG B:ASP146 4.8 39.1 1.0
NZ B:LYS197 4.9 23.2 1.0

Zinc binding site 3 out of 3 in 1nvf

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


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+, Adp and Carbaphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:33.1
occ:1.00
 OE2 C:GLU194 2.0 38.1 1.0
NE2 C:HIS287 2.1 20.5 1.0
O4 C:CRB502 2.3 10.4 1.0
O5 C:CRB502 2.4 27.0 1.0
NE2 C:HIS271 2.4 16.9 1.0
CD2 C:HIS287 2.9 22.8 1.0
CD C:GLU194 3.0 17.0 1.0
C4 C:CRB502 3.2 18.3 1.0
CE1 C:HIS287 3.2 25.2 1.0
C5 C:CRB502 3.2 15.2 1.0
CD2 C:HIS271 3.3 22.6 1.0
OE1 C:GLU194 3.3 14.1 1.0
CE1 C:HIS271 3.4 36.1 1.0
OD2 C:ASP146 3.6 39.2 1.0
CG C:HIS287 4.2 23.7 1.0
ND1 C:HIS287 4.2 29.2 1.0
CG2 C:VAL291 4.3 12.4 1.0
CG C:GLU194 4.3 35.1 1.0
CG C:HIS271 4.5 21.0 1.0
ND1 C:HIS271 4.5 25.3 1.0
C3 C:CRB502 4.6 11.7 1.0
CG C:ASP146 4.6 31.2 1.0
C6 C:CRB502 4.6 10.0 1.0
O C:HOH2615 4.7 19.9 1.0
NZ C:LYS197 4.8 19.6 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 16:10:44 2021

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