Sodium in PDB 8duz: Protective Antibody Against Gonococcal Lipooligosaccharide Bound to Peptide Mimetic

The structure of Protective Antibody Against Gonococcal Lipooligosaccharide Bound to Peptide Mimetic, PDB code: 8duz was solved by P.T.Beernink, B.P.Beernink, P.A.Rice, S.Ram, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.16 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.61, 64.19, 110.81, 90, 97.12, 90
R / Rfree (%)	18.9 / 23.4

The structure of Protective Antibody Against Gonococcal Lipooligosaccharide Bound to Peptide Mimetic also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Protective Antibody Against Gonococcal Lipooligosaccharide Bound to Peptide Mimetic (pdb code 8duz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Protective Antibody Against Gonococcal Lipooligosaccharide Bound to Peptide Mimetic, PDB code: 8duz:

Sodium binding site 1 out of 1 in the Protective Antibody Against Gonococcal Lipooligosaccharide Bound to Peptide Mimetic


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Protective Antibody Against Gonococcal Lipooligosaccharide Bound to Peptide Mimetic within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:28.6 occ:1.00 HE21 B:GLN26 2.0 27.9 1.0 HB3 B:LEU40 2.5 21.8 1.0 HB3 B:GLN26 2.6 31.1 1.0 OG1 B:THR124 2.7 22.0 1.0 O B:THR41 2.8 23.5 1.0 HZ3 B:TRP57 2.9 23.9 1.0 NE2 B:GLN26 2.9 23.3 1.0 HH2 B:TRP57 3.0 20.7 1.0 HG2 B:GLN26 3.0 27.2 1.0 H B:THR41 3.1 26.1 1.0 HG1 B:THR124 3.2 26.4 1.0 OE1 B:GLU27 3.2 26.0 1.0 HD23 B:LEU40 3.2 28.7 1.0 CB B:GLN26 3.4 25.9 1.0 HE22 B:GLN26 3.4 27.9 1.0 CB B:LEU40 3.4 18.2 1.0 N B:THR41 3.5 21.8 1.0 CG B:GLN26 3.5 22.6 1.0 H B:GLU27 3.5 32.0 1.0 CZ3 B:TRP57 3.5 19.9 1.0 HB B:THR124 3.6 23.1 1.0 CH2 B:TRP57 3.6 17.2 1.0 CD B:GLN26 3.7 23.2 1.0 C B:THR41 3.7 22.1 1.0 CB B:THR124 3.7 19.3 1.0 HA B:GLN26 3.8 30.6 1.0 HG B:LEU40 3.8 26.9 1.0 C B:LEU40 4.0 19.0 1.0 CG B:LEU40 4.0 22.4 1.0 CD2 B:LEU40 4.0 23.9 1.0 HA B:LEU40 4.0 25.8 1.0 HB2 B:LEU40 4.0 21.8 1.0 CA B:LEU40 4.1 21.5 1.0 CA B:GLN26 4.1 25.5 1.0 N B:GLU27 4.1 26.7 1.0 HB2 B:GLN26 4.1 31.1 1.0 HG21 B:THR124 4.1 29.6 1.0 CA B:THR41 4.2 19.5 1.0 HB2 B:GLU27 4.3 26.4 1.0 HG3 B:GLN26 4.4 27.2 1.0 CD B:GLU27 4.4 30.6 1.0 HD22 B:LEU40 4.5 28.7 1.0 CG2 B:THR124 4.5 24.7 1.0 HB2 B:CYS42 4.6 24.9 1.0 C B:GLN26 4.6 26.0 1.0 HD21 B:LEU40 4.7 28.7 1.0 HA B:THR41 4.7 23.4 1.0 O B:GLU27 4.7 24.9 1.0 HA B:CYS42 4.8 29.7 1.0 N B:CYS42 4.8 24.4 1.0 CE3 B:TRP57 4.8 18.9 1.0 O B:TYR108 4.8 20.9 1.0 O B:LEU40 4.8 20.1 1.0 H B:THR124 4.9 25.0 1.0 HB3 B:CYS110 4.9 24.4 0.6 OE1 B:GLN26 4.9 24.6 1.0 CA B:THR124 4.9 18.3 1.0 HB2 B:CYS110 4.9 24.3 0.4 N B:THR124 4.9 20.9 1.0 CZ2 B:TRP57 5.0 22.0 1.0 HB2 B:TYR108 5.0 19.7 1.0

P.T.Beernink, B.P.Beernink, S.Ram. Protective Antibody Against Gonococcal Lipooligosaccharide Bound to Peptide Mimetic To Be Published.