Zinc in PDB 7lgp: Dape Enzyme From Shigella Flexneri

Enzymatic activity of Dape Enzyme From Shigella Flexneri

All present enzymatic activity of Dape Enzyme From Shigella Flexneri:
3.5.1.18;

Protein crystallography data

The structure of Dape Enzyme From Shigella Flexneri, PDB code: 7lgp was solved by J.Osipiuk, M.Endres, D.P.Becker, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.68 / 1.91
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.141, 180.141, 200.091, 90, 90, 120
R / Rfree (%) 15.9 / 18.7

Other elements in 7lgp:

The structure of Dape Enzyme From Shigella Flexneri also contains other interesting chemical elements:

Sodium (Na) 3 atoms
Chlorine (Cl) 15 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Dape Enzyme From Shigella Flexneri (pdb code 7lgp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dape Enzyme From Shigella Flexneri, PDB code: 7lgp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7lgp

Go back to Zinc Binding Sites List in 7lgp
Zinc binding site 1 out of 2 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dape Enzyme From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:31.7
occ:1.00
OD1 A:ASP99 1.9 32.4 1.0
OE1 A:GLU162 2.0 29.2 1.0
NE2 A:HIS66 2.0 29.0 1.0
O A:HOH672 2.0 24.8 1.0
CD A:GLU162 2.7 29.0 1.0
OE2 A:GLU162 2.7 28.0 1.0
CG A:ASP99 2.8 34.4 1.0
CE1 A:HIS66 3.0 28.4 1.0
CD2 A:HIS66 3.0 28.7 1.0
OD2 A:ASP99 3.1 41.5 1.0
OE1 A:GLU133 3.7 35.7 1.0
OE2 A:GLU134 3.7 40.1 1.0
O A:HOH872 3.8 45.6 1.0
O A:HOH814 4.1 49.4 1.0
ND1 A:HIS66 4.1 27.8 1.0
CG A:HIS66 4.1 28.7 1.0
CG A:GLU162 4.2 28.6 1.0
CB A:ASP99 4.2 31.7 1.0
SD A:MET100 4.3 29.0 1.0
CG A:MET100 4.3 28.8 1.0
CD A:GLU133 4.3 34.3 1.0
CD A:GLU134 4.4 36.3 1.0
CB A:MET100 4.5 27.7 1.0
CD A:PRO163 4.5 27.4 1.0
CA A:ASP99 4.6 29.4 1.0
C A:ASP99 4.6 29.6 1.0
CB A:GLU162 4.8 28.5 1.0
OE2 A:GLU133 4.8 34.6 1.0
N A:MET100 4.9 29.0 1.0
O A:ASP99 4.9 30.0 1.0
OE1 A:GLU134 5.0 35.5 1.0
CA A:GLU162 5.0 27.6 1.0

Zinc binding site 2 out of 2 in 7lgp

Go back to Zinc Binding Sites List in 7lgp
Zinc binding site 2 out of 2 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dape Enzyme From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:38.8
occ:1.00
OD1 B:ASP99 1.9 39.8 1.0
OE1 B:GLU162 2.0 35.0 1.0
NE2 B:HIS66 2.1 31.1 1.0
O B:HOH619 2.1 34.5 1.0
CD B:GLU162 2.7 33.8 1.0
OE2 B:GLU162 2.8 33.5 1.0
CG B:ASP99 2.9 40.0 1.0
CE1 B:HIS66 3.0 31.9 1.0
CD2 B:HIS66 3.2 30.2 1.0
OD2 B:ASP99 3.2 46.6 1.0
OE1 B:GLU133 3.7 36.5 1.0
OE2 B:GLU134 3.7 41.5 1.0
O B:HOH799 4.1 40.1 1.0
CG B:GLU162 4.1 34.5 1.0
ND1 B:HIS66 4.2 31.2 1.0
CB B:ASP99 4.2 38.2 1.0
CG B:HIS66 4.3 29.3 1.0
O B:HOH828 4.3 53.4 1.0
CD B:GLU133 4.3 33.0 1.0
SD B:MET100 4.3 31.8 1.0
CG B:MET100 4.3 32.2 1.0
CD B:GLU134 4.4 39.2 1.0
CB B:MET100 4.4 31.2 1.0
CD B:PRO163 4.5 32.1 1.0
O B:THR324 4.5 43.7 1.0
CA B:ASP99 4.6 37.0 1.0
C B:ASP99 4.6 36.1 1.0
CB B:GLU162 4.7 32.0 1.0
OE2 B:GLU133 4.8 34.8 1.0
OE1 B:GLU134 4.8 42.0 1.0
O B:ASP99 4.9 34.8 1.0
N B:MET100 4.9 34.4 1.0
CA B:GLU162 4.9 32.7 1.0

Reference:

J.Osipiuk, M.Endres, D.P.Becker, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Dape Enzyme From Shigella Flexneri To Be Published.
Page generated: Wed Mar 3 16:22:15 2021

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