Sodium in PDB 6vh9: Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form

All present enzymatic activity of Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form:
3.1.2.12;

The structure of Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form, PDB code: 6vh9 was solved by M.Fellner, S.A.Jamieson, J.L.Brewster, P.D.Mace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.57 / 1.71
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.145, 87.145, 453.600, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.1

The binding sites of Sodium atom in the Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form (pdb code 6vh9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form, PDB code: 6vh9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:47.4 occ:0.79 O A:HOH701 1.9 55.0 0.8 O A:HOH607 2.3 49.3 0.8 OG A:SER121 2.3 49.2 1.0 N A:MET122 2.8 24.8 1.0 N A:LEU48 2.9 24.7 1.0 CB A:SER121 3.1 38.2 1.0 CB A:MET122 3.3 27.2 1.0 CB A:LEU48 3.4 29.4 1.0 CA A:MET122 3.6 28.3 1.0 C A:SER121 3.7 30.4 1.0 CA A:LEU48 3.7 28.6 1.0 O A:HOH712 3.8 44.9 1.0 CA A:GLY47 3.9 27.5 1.0 C A:GLY47 3.9 26.7 1.0 CA A:SER121 3.9 33.1 1.0 O A:LEU48 4.6 31.7 1.0 NE2 A:HIS234 4.7 36.7 1.0 CG A:MET122 4.7 27.4 1.0 C A:LEU48 4.7 29.8 1.0 O A:HIS120 4.7 28.7 1.0 CG A:LEU48 4.8 31.1 1.0 CD1 A:LEU153 4.8 41.8 1.0 C A:MET122 4.9 30.2 1.0 O A:SER121 4.9 28.2 1.0 CD2 A:LEU48 5.0 35.1 1.0

Sodium binding site 2 out of 4 in the Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:40.5 occ:0.76 O B:HOH609 2.2 40.4 0.8 O B:HOH660 2.2 50.7 0.8 OG B:SER121 2.4 56.2 1.0 N B:LEU48 2.9 24.2 1.0 N B:MET122 2.9 25.8 1.0 CB B:SER121 3.1 45.5 1.0 CB B:LEU48 3.3 30.1 1.0 CB B:MET122 3.4 26.2 1.0 O B:HOH697 3.4 48.8 1.0 CA B:LEU48 3.7 27.3 1.0 CA B:MET122 3.7 25.0 1.0 C B:GLY47 3.8 26.3 1.0 CA B:GLY47 3.8 24.1 1.0 C B:SER121 3.9 27.1 1.0 CA B:SER121 4.0 36.9 1.0 O B:LEU48 4.4 31.6 1.0 C B:LEU48 4.6 31.2 1.0 NE2 B:HIS234 4.6 39.0 1.0 CG B:LEU48 4.7 32.0 1.0 O B:HIS120 4.7 29.0 1.0 CG B:MET122 4.8 22.8 1.0 CD1 B:LEU153 4.9 48.9 1.0 CD2 B:LEU48 4.9 36.7 1.0 O B:SER121 5.0 29.9 1.0 O B:GLY47 5.0 25.4 1.0

Sodium binding site 3 out of 4 in the Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:44.3 occ:0.77 O C:HOH692 2.2 46.4 0.8 O C:HOH607 2.3 64.0 0.8 OG C:SER121 2.5 52.0 1.0 N C:LEU48 2.9 29.0 1.0 N C:MET122 3.0 26.1 1.0 CB C:SER121 3.2 37.8 1.0 CB C:LEU48 3.3 28.7 1.0 CB C:MET122 3.4 29.1 1.0 CA C:LEU48 3.7 28.5 1.0 O C:HOH697 3.7 50.2 1.0 CA C:MET122 3.8 29.8 1.0 C C:GLY47 3.9 24.5 1.0 CA C:GLY47 3.9 26.6 1.0 C C:SER121 4.0 24.5 1.0 CA C:SER121 4.1 32.5 1.0 O C:LEU48 4.4 43.1 1.0 C C:LEU48 4.6 34.8 1.0 CG C:LEU48 4.6 37.9 1.0 NE2 C:HIS234 4.7 37.4 1.0 CG C:MET122 4.7 35.3 1.0 CD1 C:LEU153 4.8 47.2 1.0 O C:HIS120 4.8 26.6 1.0 CD2 C:LEU48 4.9 46.9 1.0

Sodium binding site 4 out of 4 in the Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Fphf, Staphylococcus Aureus Fluorophosphonate-Binding Serine Hydrolases F, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:37.2 occ:0.70 O D:HOH601 2.0 39.7 0.7 O D:HOH659 2.2 61.2 0.7 OG D:SER121 2.5 52.2 1.0 N D:LEU48 2.7 27.3 1.0 N D:MET122 2.8 28.1 1.0 CB D:MET122 3.1 31.0 1.0 CB D:LEU48 3.3 33.7 1.0 CB D:SER121 3.3 40.5 1.0 CA D:MET122 3.5 27.8 1.0 CA D:LEU48 3.6 31.2 1.0 O D:HOH713 3.6 52.0 1.0 C D:GLY47 3.7 25.6 1.0 CA D:GLY47 3.7 27.0 1.0 C D:SER121 3.8 26.0 1.0 CA D:SER121 4.1 30.9 1.0 O D:LEU48 4.4 42.6 1.0 CD1 D:LEU153 4.4 67.8 1.0 C D:LEU48 4.5 36.8 1.0 CG D:MET122 4.5 30.6 1.0 CG D:LEU48 4.7 37.6 1.0 O D:HIS120 4.8 26.1 1.0 C D:MET122 4.8 23.0 1.0 O D:GLY47 4.9 27.4 1.0 O D:SER121 4.9 25.6 1.0 CD2 D:LEU48 5.0 43.5 1.0 N D:GLY123 5.0 27.0 1.0 NE2 D:HIS234 5.0 33.2 1.0 O D:HOH653 5.0 45.2 1.0

M.Fellner, C.S.Lentz, S.A.Jamieson, J.L.Brewster, L.Chen, M.Bogyo, P.D.Mace. Structural Basis For the Inhibitor and Substrate Specificity of the Unique Fph Serine Hydrolases of Staphylococcus Aureus . Acs Infect Dis. V. 6 2771 2020.
ISSN: ESSN 2373-8227
PubMed: 32865965
DOI: 10.1021/ACSINFECDIS.0C00503