Sodium 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:

Chlorine (Cl) 15 atoms
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dape Enzyme From Shigella Flexneri (pdb code 7lgp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dape Enzyme From Shigella Flexneri, PDB code: 7lgp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7lgp

Go back to Sodium Binding Sites List in 7lgp
Sodium binding site 1 out of 3 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dape Enzyme From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:61.0
occ:1.00
O A:HOH830 2.3 52.9 1.0
O A:HOH760 2.3 49.0 1.0
O A:THR122 2.4 44.3 1.0
O A:GLN57 2.5 46.8 1.0
C A:THR122 3.3 44.2 1.0
C A:GLN57 3.5 44.7 1.0
N A:GLN57 3.8 44.0 1.0
OE1 A:GLN57 3.9 57.6 0.6
CA A:THR122 3.9 45.5 1.0
CB A:GLN57 3.9 49.7 0.6
CA A:GLN57 4.0 46.6 0.6
CA A:GLN57 4.0 45.2 0.4
CB A:GLN57 4.1 46.5 0.4
O A:HOH906 4.1 60.9 1.0
N A:GLY123 4.3 41.9 1.0
O A:GLY123 4.3 39.1 1.0
O A:HOH799 4.5 44.8 1.0
O A:HIS121 4.5 43.2 1.0
CA A:GLY123 4.5 39.8 1.0
CD A:GLN57 4.6 54.8 0.6
C A:GLY123 4.6 38.7 1.0
N A:GLY58 4.6 44.0 1.0
CB A:THR122 4.8 48.5 1.0
CG A:GLN57 4.8 53.6 0.6
CA A:GLY58 5.0 45.8 1.0

Sodium binding site 2 out of 3 in 7lgp

Go back to Sodium Binding Sites List in 7lgp
Sodium binding site 2 out of 3 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dape Enzyme From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:57.9
occ:1.00
O B:HOH650 2.2 52.2 1.0
O B:THR122 2.5 39.5 1.0
O B:HOH766 2.7 42.4 1.0
O B:GLN57 2.8 38.2 1.0
O B:HOH617 3.6 38.9 1.0
C B:THR122 3.7 35.9 1.0
C B:GLN57 3.8 36.4 1.0
OE1 B:GLN57 3.8 43.5 1.0
CA B:GLY58 4.1 37.7 1.0
O B:HOH770 4.2 38.8 1.0
N B:GLY58 4.4 35.8 1.0
O B:HOH858 4.4 59.0 1.0
O B:HOH829 4.5 54.5 1.0
CA B:THR122 4.6 36.8 1.0
N B:GLY123 4.6 35.3 1.0
CA B:GLY123 4.7 33.9 1.0
CD B:GLN57 4.7 43.1 1.0
N B:GLU59 4.9 37.0 1.0
CB B:THR122 4.9 39.5 1.0
CA B:GLN57 4.9 39.1 1.0

Sodium binding site 3 out of 3 in 7lgp

Go back to Sodium Binding Sites List in 7lgp
Sodium binding site 3 out of 3 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dape Enzyme From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na511

b:57.6
occ:1.00
O B:ASN223 2.3 44.2 1.0
O B:HOH816 2.5 53.2 1.0
O B:PHE226 2.5 42.4 1.0
O B:HOH857 2.7 57.4 1.0
O B:HOH846 2.7 61.4 1.0
C B:PHE226 3.3 43.3 1.0
C B:ASN223 3.5 52.0 1.0
N B:ASN223 3.8 55.3 1.0
N B:PRO227 4.0 43.2 1.0
N B:PHE226 4.1 45.1 1.0
CA B:PRO227 4.1 45.7 1.0
O B:GLU224 4.2 50.4 1.0
C B:GLU224 4.3 52.8 1.0
CA B:ASN223 4.3 53.2 1.0
CA B:PHE226 4.3 43.6 1.0
N B:GLU224 4.5 52.3 1.0
C B:GLY222 4.6 55.6 1.0
CA B:GLU224 4.6 54.9 1.0
N B:PHE225 4.7 49.3 1.0
C B:PHE225 4.7 47.9 1.0
O B:GLN221 4.8 61.8 1.0
CA B:GLY222 4.9 55.9 1.0
C B:PRO227 4.9 45.5 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 15:35:23 2021

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