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Zinc in PDB 4guj: 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate

Enzymatic activity of 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate

All present enzymatic activity of 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate:
4.2.1.10;

Protein crystallography data

The structure of 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate, PDB code: 4guj was solved by S.H.Light, G.Minasov, M.-E.Duban, L.Shuvalova, K.Kwon, A.Lavie, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.66 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.620, 74.966, 63.042, 90.00, 100.49, 90.00
R / Rfree (%) 15.5 / 18.2

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate (pdb code 4guj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate, PDB code: 4guj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4guj

Go back to Zinc Binding Sites List in 4guj
Zinc binding site 1 out of 3 in the 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:22.2
occ:0.60
 O A:HOH503 2.0 31.9 1.0
O A:HOH504 2.1 23.9 1.0
O A:HOH502 2.1 38.3 1.0
NE2 A:HIS134 2.2 25.3 1.0
O A:HOH560 2.2 36.1 1.0
CD2 A:HIS134 3.0 24.9 1.0
CE1 A:HIS134 3.3 23.8 1.0
O A:HOH580 3.9 44.8 1.0
OD1 A:ASP106 4.2 25.9 1.0
CG A:HIS134 4.2 22.3 1.0
ND1 A:HIS134 4.3 21.8 1.0
OH A:TYR130 4.4 24.0 1.0
O A:HOH571 4.6 38.0 1.0

Zinc binding site 2 out of 3 in 4guj

Go back to Zinc Binding Sites List in 4guj
Zinc binding site 2 out of 3 in the 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:21.9
occ:0.80
 O B:HOH437 2.0 28.1 1.0
O B:HOH448 2.0 27.3 1.0
O B:HOH433 2.0 25.7 1.0
O B:HOH475 2.0 27.5 1.0
NE2 B:HIS134 2.1 19.5 1.0
O B:HOH438 2.1 24.8 1.0
CD2 B:HIS134 3.0 19.4 1.0
CE1 B:HIS134 3.2 19.2 1.0
O B:HOH503 4.0 38.0 1.0
OD1 B:ASP106 4.0 19.6 1.0
OH B:TYR130 4.2 18.1 1.0
CG B:HIS134 4.2 18.0 1.0
ND1 B:HIS134 4.3 18.4 1.0
O B:HOH586 4.5 38.4 1.0
O B:HOH587 4.5 30.8 1.0
CZ B:TYR130 4.9 16.9 1.0
CG B:ASP106 5.0 18.7 1.0

Zinc binding site 3 out of 3 in 4guj

Go back to Zinc Binding Sites List in 4guj
Zinc binding site 3 out of 3 in the 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.50 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Shikimate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:21.1
occ:0.70
 O B:HOH477 2.1 32.8 1.0
O B:HOH421 2.2 29.5 1.0
ND1 B:HIS146 2.2 18.6 1.0
O B:HOH496 2.2 34.0 1.0
O B:HOH447 2.3 32.7 1.0
CE1 B:HIS146 3.1 20.7 1.0
CG B:HIS146 3.2 17.2 1.0
CB B:HIS146 3.6 16.6 1.0
O B:HOH510 4.2 46.1 1.0
NE2 B:HIS146 4.3 19.1 1.0
CD2 B:HIS146 4.3 18.5 1.0
NZ B:LYS147 4.4 25.5 1.0
OD1 B:ASP144 4.5 17.0 1.0
O B:HOH413 4.8 21.0 1.0
CA B:HIS146 4.9 15.4 1.0

Reference:

S.H.Light, A.Antanasijevic, S.N.Krishna, M.Caffrey, W.F.Anderson, A.Lavie. Crystal Structures of Type I Dehydroquinate Dehydratase in Complex with Quinate and Shikimate Suggest A Novel Mechanism of Schiff Base Formation. Biochemistry V. 53 872 2014.
ISSN: ISSN 0006-2960
PubMed: 24437575
DOI: 10.1021/BI4015506
Page generated: Wed Dec 16 05:20:52 2020

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