Sodium in PDB 4fqq: Crystal Structure of Germline Antibody PGT121-Gl Fab

The structure of Crystal Structure of Germline Antibody PGT121-Gl Fab, PDB code: 4fqq was solved by L.Scharf, P.J.Bjorkman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.44 / 2.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.934, 344.743, 55.230, 90.00, 91.95, 90.00
R / Rfree (%)	19.4 / 23.7

The binding sites of Sodium atom in the Crystal Structure of Germline Antibody PGT121-Gl Fab (pdb code 4fqq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Germline Antibody PGT121-Gl Fab, PDB code: 4fqq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Germline Antibody PGT121-Gl Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Germline Antibody PGT121-Gl Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Na400 b:44.9 occ:1.00 O L:HOH524 3.7 47.5 1.0 OG H:SER177 3.7 44.8 1.0 CD H:GLN171 3.8 60.9 1.0 CB H:SER177 3.8 36.4 1.0 NE2 H:GLN171 3.8 52.4 1.0 CB L:TYR178 3.8 27.8 1.0 OE1 L:GLU161 3.9 71.7 1.0 CG H:GLN171 3.9 51.4 1.0 CG L:TYR178 3.9 36.3 1.0 CD2 L:TYR178 4.2 37.7 1.0 OE1 H:GLN171 4.2 74.5 1.0 CG1 H:VAL169 4.3 38.1 1.0 CD1 L:TYR178 4.4 31.3 1.0 OG L:SER180 4.6 43.0 1.0 CE2 L:TYR178 4.9 31.5 1.0 CG2 L:THR132 5.0 28.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Germline Antibody PGT121-Gl Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Germline Antibody PGT121-Gl Fab within 5.0Å range: probe atom residue distance (Å) B Occ D:Na400 b:47.7 occ:1.00 O D:HOH525 3.1 32.2 1.0 OG D:SER177 3.7 34.6 1.0 OE1 D:GLN171 3.9 40.4 1.0 CB D:SER177 4.0 29.9 1.0 CD D:GLN171 4.1 31.9 1.0 CG2 C:THR132 4.2 24.0 1.0 OG C:SER180 4.4 42.5 1.0 O C:HOH334 4.4 36.6 1.0 OE1 C:GLU161 4.4 59.5 1.0 OG1 C:THR132 4.4 37.6 1.0 NE2 D:GLN171 4.5 35.7 1.0 CB C:TYR178 4.5 30.7 1.0 O C:HOH304 4.5 30.5 1.0 CD1 C:TYR178 4.5 27.5 1.0 CG C:TYR178 4.6 31.3 1.0 CG D:GLN171 4.7 29.0 1.0 OD1 D:ASP144 4.8 34.9 1.0 CE D:LYS143 4.9 40.0 1.0 O D:HOH570 4.9 44.2 1.0 CB D:LYS143 4.9 32.1 1.0 CB C:THR132 5.0 31.5 1.0

H.Mouquet, L.Scharf, Z.Euler, Y.Liu, C.Eden, J.F.Scheid, A.Halper-Stromberg, P.N.Gnanapragasam, D.I.Spencer, M.S.Seaman, H.Schuitemaker, T.Feizi, M.C.Nussenzweig, P.J.Bjorkman. Complex-Type N-Glycan Recognition By Potent Broadly Neutralizing Hiv Antibodies. Proc.Natl.Acad.Sci.Usa V. 109 E3268 2012.
ISSN: ISSN 0027-8424
PubMed: 23115339
DOI: 10.1073/PNAS.1217207109