Sodium in PDB 6vjp: Structure of Staphylococcus Aureus Peptidoglycan O-Acetyltransferase A (Oata) C-Terminal Catalytic Domain

The structure of Structure of Staphylococcus Aureus Peptidoglycan O-Acetyltransferase A (Oata) C-Terminal Catalytic Domain, PDB code: 6vjp was solved by C.J.Jones, D.Sychantha, P.L.Howell, A.J.Clarke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.78 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.347, 61.303, 67.690, 90.00, 100.90, 90.00
R / Rfree (%)	16.6 / 19.5

The binding sites of Sodium atom in the Structure of Staphylococcus Aureus Peptidoglycan O-Acetyltransferase A (Oata) C-Terminal Catalytic Domain (pdb code 6vjp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Staphylococcus Aureus Peptidoglycan O-Acetyltransferase A (Oata) C-Terminal Catalytic Domain, PDB code: 6vjp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Staphylococcus Aureus Peptidoglycan O-Acetyltransferase A (Oata) C-Terminal Catalytic Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Staphylococcus Aureus Peptidoglycan O-Acetyltransferase A (Oata) C-Terminal Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:22.2 occ:1.00 O A:ALA550 2.3 25.9 1.0 O A:HOH852 2.4 27.8 1.0 O A:ARG553 2.4 24.4 1.0 O A:VAL556 2.4 24.6 1.0 O A:HOH899 2.5 28.3 1.0 O A:HOH908 2.5 34.4 1.0 C A:ALA550 3.4 24.3 1.0 C A:ARG553 3.5 24.8 1.0 C A:VAL556 3.6 25.4 1.0 CA A:ALA550 3.9 22.9 1.0 CA A:SER554 4.0 28.7 0.6 CA A:SER554 4.1 28.8 0.4 N A:VAL556 4.1 24.9 1.0 C A:SER554 4.2 27.0 1.0 N A:SER554 4.2 26.1 1.0 O A:SER554 4.2 27.6 1.0 CA A:VAL556 4.3 20.5 1.0 N A:ARG553 4.3 25.0 1.0 O A:HOH873 4.4 27.8 1.0 CA A:ARG553 4.5 23.5 1.0 CB A:VAL556 4.5 22.5 1.0 N A:GLU551 4.5 20.4 1.0 CB A:ALA550 4.5 20.1 1.0 O A:HOH932 4.6 53.9 1.0 N A:HIS557 4.6 24.3 1.0 O A:GLU551 4.7 29.2 1.0 C A:GLU551 4.7 25.5 1.0 CA A:GLU551 4.8 22.0 1.0 N A:ASN555 4.8 23.8 1.0 CA A:HIS557 4.9 22.6 1.0 O A:ALA549 4.9 23.1 1.0 C A:LYS552 4.9 29.3 1.0

Sodium binding site 2 out of 2 in the Structure of Staphylococcus Aureus Peptidoglycan O-Acetyltransferase A (Oata) C-Terminal Catalytic Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Staphylococcus Aureus Peptidoglycan O-Acetyltransferase A (Oata) C-Terminal Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:31.5 occ:1.00 O B:ALA550 2.3 36.5 1.0 O B:VAL556 2.3 28.6 1.0 O B:HOH885 2.3 38.6 1.0 O B:ARG553 2.4 36.0 1.0 O B:HOH881 2.4 47.6 1.0 O B:HOH900 2.5 47.5 1.0 C B:ALA550 3.4 31.8 1.0 C B:ARG553 3.5 36.8 1.0 C B:VAL556 3.5 29.0 1.0 CA B:SER554 4.0 36.5 1.0 N B:VAL556 4.0 31.5 1.0 CA B:ALA550 4.0 25.4 1.0 C B:SER554 4.1 37.6 1.0 O B:SER554 4.1 41.6 1.0 N B:SER554 4.2 37.4 1.0 CA B:VAL556 4.2 27.4 1.0 O B:HOH821 4.2 43.1 1.0 O B:HOH872 4.4 33.8 1.0 N B:ARG553 4.5 36.5 1.0 CB B:VAL556 4.5 25.5 1.0 N B:GLU551 4.5 31.5 1.0 N B:HIS557 4.6 29.0 1.0 CA B:ARG553 4.6 36.5 1.0 C B:GLU551 4.7 37.1 1.0 CB B:ALA550 4.7 30.9 1.0 O B:GLU551 4.7 37.8 1.0 CA B:GLU551 4.8 40.1 1.0 ND1 B:HIS557 4.8 35.6 1.0 N B:ASN555 4.8 33.9 1.0 CA B:HIS557 4.8 28.1 1.0 O B:ALA549 4.8 31.9 1.0

C.S.Jones, D.Sychantha, P.L.Howell, A.J.Clarke. Structural Basis For the O-Acetyltransferase Function of the Extracytoplasmic Domain of Oata From Staphylococcus Aureus J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X