Sodium in PDB 8cwp: X-Ray Crystal Structure of Nthi Protein D Bound to A Putative Glycerol Moiety

The structure of X-Ray Crystal Structure of Nthi Protein D Bound to A Putative Glycerol Moiety, PDB code: 8cwp was solved by S.P.Jones, K.H.Cook, M.L.Holmquist, L.Almekinder, A.Delaney, N.Labbe, J.Perdue, N.Jackson, R.Charles, M.Pichichero, R.Kaur, L.Michel, M.L.Gleghorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.00 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.09, 73.09, 162.859, 90, 90, 90
R / Rfree (%)	15.5 / 18.8

The binding sites of Sodium atom in the X-Ray Crystal Structure of Nthi Protein D Bound to A Putative Glycerol Moiety (pdb code 8cwp). 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 X-Ray Crystal Structure of Nthi Protein D Bound to A Putative Glycerol Moiety, PDB code: 8cwp:

Sodium binding site 1 out of 1 in the X-Ray Crystal Structure of Nthi Protein D Bound to A Putative Glycerol Moiety


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Nthi Protein D Bound to A Putative Glycerol Moiety within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:31.2 occ:1.00 O1 A:GOL402 2.1 30.9 0.4 H12 A:GOL402 2.2 45.2 0.4 H11 A:GOL402 2.2 45.4 0.6 OE2 A:GLU49 2.3 35.3 1.0 OE1 A:GLU157 2.3 32.8 1.0 OD1 A:ASP51 2.3 30.1 1.0 H12 A:GOL402 2.5 45.4 0.6 O A:HOH568 2.5 34.5 1.0 C1 A:GOL402 2.5 37.7 0.4 O3 A:GOL402 2.7 39.8 0.6 C1 A:GOL402 2.8 37.8 0.6 O3 A:GOL402 2.9 40.6 0.4 HO3 A:GOL402 3.0 47.7 0.6 H2 A:GOL402 3.1 50.7 0.4 C2 A:GOL402 3.2 42.2 0.4 HZ1 A:LYS159 3.3 50.9 1.0 CG A:ASP51 3.3 30.3 1.0 CD A:GLU49 3.3 34.7 1.0 H11 A:GOL402 3.4 45.2 0.4 HO3 A:GOL402 3.5 48.7 0.4 HE21 A:GLN194 3.5 38.6 1.0 CD A:GLU157 3.5 35.5 1.0 C2 A:GOL402 3.5 42.6 0.6 H2 A:GOL402 3.6 51.1 0.6 C3 A:GOL402 3.6 45.8 0.4 OD2 A:ASP51 3.6 28.1 1.0 C3 A:GOL402 3.6 46.4 0.6 HB2 A:GLU157 3.7 36.8 1.0 HB3 A:GLU157 3.7 36.8 1.0 HD2 A:HIS64 3.8 45.6 1.0 HE2 A:HIS22 3.8 41.7 1.0 OE1 A:GLU49 3.9 35.5 1.0 H32 A:GOL402 3.9 54.9 0.4 H32 A:GOL402 3.9 55.6 0.6 NE2 A:GLN194 3.9 32.2 1.0 O1 A:GOL402 4.0 35.2 0.6 CB A:GLU157 4.1 30.7 1.0 NZ A:LYS159 4.1 42.4 1.0 HZ3 A:LYS159 4.3 50.9 1.0 HE22 A:GLN194 4.3 38.6 1.0 OE2 A:GLU157 4.4 32.4 1.0 HD3 A:LYS159 4.4 42.9 1.0 CG A:GLU157 4.4 31.2 1.0 HD2 A:HIS22 4.4 43.4 1.0 HO1 A:GOL402 4.4 42.2 0.6 NE2 A:HIS22 4.4 34.8 1.0 H31 A:GOL402 4.5 55.6 0.6 CG A:GLU49 4.5 35.9 1.0 H31 A:GOL402 4.5 54.9 0.4 HZ2 A:LYS159 4.5 50.9 1.0 CD A:GLN194 4.5 32.1 1.0 HG2 A:GLU49 4.5 43.1 1.0 OE1 A:GLN194 4.5 33.3 1.0 O2 A:GOL402 4.5 43.4 0.4 HG3 A:GLU49 4.6 43.1 1.0 HE A:ARG23 4.6 40.6 1.0 CD2 A:HIS64 4.6 38.0 1.0 CB A:ASP51 4.7 26.2 1.0 HD11 A:LEU221 4.7 39.2 1.0 CD2 A:HIS22 4.7 36.2 1.0 HD13 A:LEU221 4.8 39.2 1.0 HA A:ASP51 4.8 33.0 1.0 O2 A:GOL402 4.9 43.4 0.6 HG3 A:GLU157 4.9 37.4 1.0 HB3 A:ASP51 4.9 31.5 1.0

S.P.Jones, K.H.Cook, M.L.Holmquist, L.J.Almekinder, A.M.Delaney, R.Charles, N.Labbe, J.Perdue, N.Jackson, M.E.Pichichero, R.Kaur, L.V.Michel, M.L.Gleghorn. Vaccine Target and Carrier Molecule Nontypeable Haemophilus Influenzae Protein D Dimerizes Like the Close Escherichia Coli Glpq Homolog But Unlike Other Known Homolog Dimers. Proteins 2022.
ISSN: ESSN 1097-0134
PubMed: 36065600
DOI: 10.1002/PROT.26418