Magnesium in PDB 4ksi: Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato

All present enzymatic activity of Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato:
3.4.11.1; 3.4.11.5;

The structure of Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato, PDB code: 4ksi was solved by K.T.Duprez, M.Scranton, L.Walling, L.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.14 / 2.20
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	160.597, 160.597, 104.183, 90.00, 90.00, 120.00
R / Rfree (%)	13.7 / 17.4

The structure of Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato (pdb code 4ksi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato, PDB code: 4ksi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:9.9 occ:1.00 O A:HOH701 1.8 30.2 1.0 OE1 A:GLU429 2.0 25.8 1.0 OD2 A:ASP347 2.0 22.4 1.0 OD1 A:ASP427 2.1 21.2 1.0 O A:ASP427 2.3 17.9 1.0 CD A:GLU429 2.9 26.4 1.0 MG A:MG602 3.0 29.9 1.0 OE2 A:GLU429 3.0 29.8 1.0 CG A:ASP347 3.0 19.3 1.0 C A:ASP427 3.2 18.3 1.0 CG A:ASP427 3.2 19.9 1.0 OD1 A:ASP347 3.4 18.1 1.0 O1 A:SO4603 3.4 33.4 0.8 O A:HOH944 3.5 42.1 1.0 CA A:ASP427 3.6 17.4 1.0 NZ A:LYS354 3.9 22.2 1.0 CB A:ASP427 4.0 17.0 1.0 OD2 A:ASP427 4.0 19.7 1.0 CE A:LYS354 4.1 20.4 1.0 N A:ALA428 4.3 17.9 1.0 N A:GLU429 4.3 17.2 1.0 CG A:GLU429 4.3 21.2 1.0 CB A:ASP347 4.4 17.9 1.0 OD2 A:ASP367 4.5 30.5 1.0 CA A:ALA428 4.6 17.0 1.0 ND2 A:ASN400 4.7 14.1 1.0 S A:SO4603 4.7 28.8 0.8 CA A:GLY349 4.9 15.6 1.0 NZ A:LYS342 4.9 16.3 1.0 N A:ASP427 5.0 17.8 1.0 CB A:GLU429 5.0 21.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:29.9 occ:1.00 OD2 A:ASP367 2.0 30.5 1.0 OE2 A:GLU429 2.1 29.8 1.0 NZ A:LYS342 2.3 16.3 1.0 O A:HOH701 2.5 30.2 1.0 OD2 A:ASP347 2.7 22.4 1.0 O A:HOH944 2.7 42.1 1.0 CG A:ASP367 3.0 26.4 1.0 MG A:MG601 3.0 9.9 1.0 CE A:LYS342 3.1 15.6 1.0 CD A:GLU429 3.2 26.4 1.0 OD1 A:ASP367 3.3 25.6 1.0 CG A:ASP347 3.4 19.3 1.0 O1 A:SO4603 3.5 33.4 0.8 OE1 A:GLU429 3.5 25.8 1.0 CB A:ASP347 3.8 17.9 1.0 O2 A:SO4603 3.9 30.0 0.8 CB A:ASP367 4.3 21.1 1.0 OD1 A:ASP347 4.4 18.1 1.0 CG A:LEU344 4.4 13.6 1.0 CG A:GLU429 4.5 21.2 1.0 O A:THR454 4.5 19.9 1.0 CD A:LYS342 4.5 14.8 1.0 N A:GLY430 4.6 19.3 1.0 S A:SO4603 4.6 28.8 0.8 CB A:LEU344 4.6 13.2 1.0 CA A:GLY430 4.8 18.0 1.0 O A:ASP427 4.8 17.9 1.0 OD1 A:ASP427 4.9 21.2 1.0

K.Duprez, M.A.Scranton, L.L.Walling, L.Fan. Structure of Tomato Wound-Induced Leucine Aminopeptidase Sheds Light on Substrate Specificity. Acta Crystallogr.,Sect.D V. 70 1649 2014.
ISSN: ISSN 0907-4449
PubMed: 24914976
DOI: 10.1107/S1399004714006245