Magnesium in PDB 8acg: Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant

The structure of Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant, PDB code: 8acg was solved by C.J.Harding, C.M.Czekster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.57 / 2.84
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	186.74, 186.74, 84.73, 90, 90, 120
R / Rfree (%)	19.1 / 23.9

The structure of Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant also contains other interesting chemical elements:

Zinc

(Zn)

18 atoms

The binding sites of Magnesium atom in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant (pdb code 8acg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant, PDB code: 8acg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg604 b:88.2 occ:1.00 OE1 F:GLU177 2.2 94.5 1.0 OG1 F:THR173 2.3 97.9 1.0 OD1 F:ASP180 2.4 91.0 1.0 OD2 F:ASP180 2.5 88.4 1.0 OD2 F:ASP163 2.5 90.5 1.0 O F:THR173 2.6 93.0 1.0 CG F:ASP180 2.8 89.0 1.0 CB F:THR173 3.3 98.1 1.0 CD F:GLU177 3.4 96.7 1.0 C F:THR173 3.6 94.7 1.0 CG F:ASP163 3.7 91.1 1.0 CA F:THR173 4.1 97.3 1.0 OE2 F:GLU177 4.1 100.8 1.0 CB F:GLU177 4.2 93.7 1.0 CG F:GLU177 4.3 98.2 1.0 CB F:ASP180 4.3 87.5 1.0 N F:GLU177 4.3 89.8 1.0 CB F:ASP163 4.4 88.7 1.0 CG2 F:THR173 4.5 101.5 1.0 N F:CYS176 4.6 95.0 1.0 OD1 F:ASP163 4.6 94.0 1.0 N F:GLY175 4.7 94.2 1.0 N F:SER174 4.7 94.2 1.0 CA F:GLU177 4.8 90.8 1.0 CB F:CYS176 4.9 97.6 1.0 CA F:SER174 5.0 92.7 1.0

Magnesium binding site 2 out of 3 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg604 b:82.8 occ:1.00 O D:PRO59 2.6 84.0 1.0 O D:LEU62 2.7 82.9 1.0 OD1 D:ASP486 2.8 78.9 1.0 OD2 D:ASP486 3.2 80.0 1.0 CG D:ASP486 3.3 78.5 1.0 C D:PRO59 3.8 84.1 1.0 C D:LEU62 3.8 87.7 1.0 OE2 D:GLU482 4.0 91.0 1.0 O D:ARG60 4.2 98.9 1.0 CA D:ARG60 4.4 94.5 1.0 C D:ARG60 4.5 98.3 1.0 CA D:GLN63 4.6 90.7 1.0 N D:ARG60 4.6 93.9 1.0 N D:GLN63 4.6 91.5 1.0 N D:LEU62 4.7 87.0 1.0 CA D:LEU62 4.7 88.6 1.0 CA D:PRO59 4.7 83.2 1.0 CB D:ASP486 4.8 76.7 1.0 CD D:GLU482 4.8 90.1 1.0 N D:ALA64 4.8 85.8 1.0 CG D:GLU482 4.8 87.0 1.0 CB D:LEU62 5.0 86.8 1.0

Magnesium binding site 3 out of 3 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:105.4 occ:1.00 O A:PRO59 2.6 101.2 1.0 OD1 A:ASP486 2.7 92.8 1.0 O A:LEU62 2.7 104.4 1.0 CG A:ASP486 3.4 93.3 1.0 OD2 A:ASP486 3.4 94.1 1.0 C A:PRO59 3.7 103.7 1.0 OE2 A:GLU482 3.8 99.0 1.0 C A:LEU62 3.9 106.2 1.0 CA A:ARG60 4.5 115.0 1.0 O A:ARG60 4.5 113.8 1.0 N A:ARG60 4.6 116.9 1.0 CA A:PRO59 4.6 105.9 1.0 CD A:GLU482 4.6 100.1 1.0 C A:ARG60 4.6 115.4 1.0 CG A:GLU482 4.7 99.4 1.0 CA A:GLN63 4.8 110.5 1.0 N A:GLN63 4.8 112.3 1.0 CA A:LEU62 4.8 109.1 1.0 CB A:ASP486 4.8 92.8 1.0 N A:LEU62 4.8 109.9 1.0 N A:ALA64 4.9 105.0 1.0 CB A:LEU62 5.0 110.1 1.0

C.J.Harding, M.Bischoff, M.Bergkessel, C.M.Czekster. An Anti-Biofilm Cyclic Peptide Targets A Secreted Aminopeptidase From P. Aeruginosa. Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
PubMed: 37386135
DOI: 10.1038/S41589-023-01373-8