Magnesium in PDB 8t87: Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1

The structure of Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1, PDB code: 8t87 was solved by M.Fellner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.73 / 1.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.787, 74.082, 71.424, 90, 91.28, 90
R / Rfree (%)	18.7 / 21.9

The binding sites of Magnesium atom in the Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1 (pdb code 8t87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1, PDB code: 8t87:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:39.3 occ:0.76 O A:HOH483 2.0 43.6 0.8 OE1 A:GLN7 2.1 34.5 1.0 O A:HOH485 2.3 44.1 0.8 CD A:GLN7 3.2 34.4 1.0 HE22 A:GLN7 3.4 43.6 1.0 O A:HOH474 3.6 39.5 1.0 NE2 A:GLN7 3.7 36.4 1.0 HB2 A:GLN7 4.0 44.1 1.0 HA A:GLN7 4.4 40.2 1.0 O A:HOH479 4.5 39.7 1.0 CG A:GLN7 4.5 37.6 1.0 HE21 A:GLN7 4.6 43.6 1.0 CB A:GLN7 4.7 36.7 1.0

Magnesium binding site 2 out of 6 in the Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:41.0 occ:0.91 NE2 B:HIS149 1.9 41.6 1.0 O B:HOH490 2.1 44.8 0.9 O B:HOH446 2.3 39.8 0.9 O B:HOH401 2.3 47.7 0.9 CE1 B:HIS149 2.9 45.3 1.0 CD2 B:HIS149 3.0 44.5 1.0 HE1 B:HIS149 3.1 54.4 1.0 HD2 B:HIS149 3.2 53.4 1.0 OG1 B:THR153 4.0 43.4 1.0 ND1 B:HIS149 4.0 46.7 1.0 OE2 B:GLU157 4.1 65.4 1.0 CG B:HIS149 4.1 37.7 1.0 HG3 B:GLU154 4.1 55.2 1.0 HH B:TYR191 4.3 88.9 1.0 OE2 B:GLU154 4.3 47.6 1.0 HG1 B:THR153 4.5 52.1 1.0 HG2 B:GLU154 4.5 55.2 1.0 HE2 B:TYR191 4.6 70.4 1.0 CG B:GLU154 4.7 46.0 1.0 HB B:THR153 4.8 57.6 1.0 HD1 B:HIS149 4.8 56.0 1.0 OH B:TYR191 4.9 74.1 1.0 CB B:THR153 5.0 48.0 1.0

Magnesium binding site 3 out of 6 in the Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:39.0 occ:0.83 O B:MET274 1.9 38.8 1.0 O B:HOH448 2.0 37.5 0.8 O B:HOH461 2.1 40.0 0.8 O B:HOH476 2.1 41.5 0.8 O B:HOH456 2.1 41.1 0.8 C B:MET274 3.1 43.9 1.0 HA B:MET274 3.4 42.7 1.0 HD1 B:TRP275 3.6 43.0 1.0 HA B:TRP275 3.8 47.3 1.0 CA B:MET274 3.8 35.6 1.0 N B:TRP275 4.1 40.4 1.0 O B:ASN273 4.2 42.8 1.0 HE3 A:LYS122 4.2 54.0 1.0 CA B:TRP275 4.5 39.5 1.0 CD1 B:TRP275 4.5 35.8 1.0 HB3 B:MET274 4.7 44.4 1.0 N B:MET274 4.9 40.0 1.0 CB B:MET274 4.9 37.0 1.0 H B:TRP275 4.9 48.5 1.0 C B:ASN273 5.0 42.3 1.0

Magnesium binding site 4 out of 6 in the Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:51.4 occ:0.98 O B:HOH443 1.8 42.4 1.0 OD1 B:ASN273 2.1 41.7 1.0 O B:HOH473 2.3 42.9 1.0 CG B:ASN273 3.2 41.0 1.0 HD21 B:ASN273 3.5 55.3 1.0 ND2 B:ASN273 3.8 46.1 1.0 HA B:ASN273 4.1 51.2 1.0 CB B:ASN273 4.5 40.2 1.0 HD22 B:ASN273 4.6 55.3 1.0 O B:ASP269 4.6 35.3 1.0 CA B:ASN273 4.7 42.7 1.0 H B:ASN273 4.7 43.6 1.0 N B:ASN273 4.8 36.3 1.0 HB3 B:ASN273 4.8 48.2 1.0

Magnesium binding site 5 out of 6 in the Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:41.4 occ:0.89 O B:HOH465 2.0 39.5 0.9 O B:HOH464 2.0 39.0 0.9 OD2 B:ASP237 2.1 42.8 1.0 O B:HOH493 2.2 36.1 0.9 O B:HOH498 2.5 46.5 0.9 CG B:ASP237 3.2 37.7 1.0 OD1 B:ASP237 3.6 36.9 1.0 O B:GLY232 3.8 34.7 1.0 O B:HOH483 4.1 42.4 1.0 HA B:PHE234 4.2 31.6 1.0 CB B:ASP237 4.5 30.6 1.0 HB2 B:ASP237 4.5 36.7 1.0 C B:GLY232 4.6 35.0 1.0 HA2 B:GLY232 4.6 41.3 1.0 O B:SER233 4.7 30.2 1.0 HB3 B:ASP237 4.8 36.7 1.0 C B:SER233 4.9 28.7 1.0

Magnesium binding site 6 out of 6 in the Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Fphe, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases E, Unbound Dimer Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:34.8 occ:0.92 O A:HOH508 1.9 40.6 0.9 O A:HOH433 2.0 38.4 0.9 O B:HOH415 2.0 34.2 0.9 O B:HOH503 2.1 40.3 0.9 O B:HOH499 2.1 41.1 0.9 O B:HIS207 3.9 26.0 1.0 HA B:SER208 3.9 26.8 1.0 HB2 A:ASP73 4.0 41.3 1.0 HB2 B:ASN209 4.0 31.9 1.0 O B:HOH441 4.1 31.4 0.9 O A:ASP73 4.3 29.7 1.0 O B:HOH507 4.4 40.5 1.0 O A:HOH506 4.4 40.0 1.0 HB3 A:ASP75 4.6 34.8 1.0 HA A:ASP73 4.7 37.0 1.0 H B:ASN209 4.8 32.0 1.0 CA B:SER208 4.8 22.3 1.0 N B:ASN209 4.8 26.7 1.0 HD2 B:HIS207 4.8 36.4 1.0 CB A:ASP73 4.9 34.4 1.0 O B:HOH495 4.9 23.4 1.0 CB B:ASN209 5.0 26.6 1.0 C B:HIS207 5.0 24.1 1.0

J.Jo, T.Upadhyay, E.C.Woods, K.W.Park, N.J.Pedowitz, J.Jaworek-Korjakowska, S.Wang, T.A.Valdez, M.Fellner, M.Bogyo. Development of Oxadiazolone Activity-Based Probes Targeting Fphe For Specific Detection of Staphylococcus Aureus Infections. J.Am.Chem.Soc. 2024.
ISSN: ESSN 1520-5126
PubMed: 38411555
DOI: 10.1021/JACS.3C13974