Sodium in PDB 6dw2: Structure of the 6078 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog

The structure of Structure of the 6078 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog, PDB code: 6dw2 was solved by R.Fong, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.55 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.287, 90.254, 105.527, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20.8

The binding sites of Sodium atom in the Structure of the 6078 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog (pdb code 6dw2). 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 the 6078 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog, PDB code: 6dw2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the 6078 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the 6078 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:35.5 occ:1.00 O A:HOH432 2.6 37.1 1.0 O A:HOH343 2.8 29.0 1.0 O B:HOH542 2.8 26.9 1.0 CD1 B:LEU102 3.5 28.9 1.0 O B:ALA106 3.6 44.2 1.0 O B:HOH423 3.7 42.3 1.0 CE1 A:PHE96 3.9 28.0 1.0 CZ A:PHE96 4.1 26.1 1.0 CA B:LEU107 4.3 36.2 1.0 CD2 B:LEU107 4.3 42.8 1.0 O B:HOH411 4.4 30.6 1.0 O A:TYR91 4.5 29.8 1.0 C B:ALA106 4.6 45.2 1.0 O34 B:HD4304 4.7 32.2 1.0 N B:GLY108 4.7 30.4 1.0 CG B:LEU107 4.8 41.9 1.0 CB B:ARG109 4.8 22.5 1.0 CB B:LEU107 4.9 36.2 1.0 NE B:ARG109 4.9 25.9 1.0 O B:HOH615 4.9 45.0 1.0 N B:LEU107 5.0 38.9 1.0 C33 B:HD4304 5.0 28.5 1.0 CG B:LEU102 5.0 29.1 1.0

Sodium binding site 2 out of 2 in the Structure of the 6078 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the 6078 Antibody Fab Fragment Bound to A Staphylococcus Aureus Wall Techoic Acid Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:36.6 occ:1.00 O B:HOH440 2.3 36.6 1.0 O B:HOH603 2.3 39.8 1.0 O B:HOH534 2.5 35.6 1.0 O B:TYR60 2.5 25.9 1.0 O B:HOH618 3.1 59.7 1.0 C B:TYR60 3.6 26.4 1.0 N B:TYR60 3.7 22.1 1.0 CA B:TYR60 4.1 22.0 1.0 O B:HOH562 4.2 28.7 1.0 O B:HOH624 4.5 51.2 1.0 CB B:TYR60 4.5 23.6 1.0 CE1 A:TYR94 4.5 25.4 1.0 C B:GLY59 4.7 28.0 1.0 O29 B:HD4304 4.7 35.8 1.0 N B:ALA61 4.8 22.4 1.0 OH A:TYR94 4.9 28.3 1.0 CA B:GLY59 5.0 25.4 1.0

R.Fong, K.Kajihara, M.Chen, I.Hotzel, S.Mariathasan, W.L.W.Hazenbos, P.J.Lupardus. Structural Investigation of Human S. Aureus-Targeting Antibodies That Bind Wall Teichoic Acid. Mabs V. 10 979 2018.
ISSN: ESSN 1942-0870
PubMed: 30102105
DOI: 10.1080/19420862.2018.1501252