Sodium in PDB 4lss: Crystal Structure of Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120

The structure of Crystal Structure of Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120, PDB code: 4lss was solved by T.Zhou, S.Moquin, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.39 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.639, 65.267, 259.146, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 26.3

The binding sites of Sodium atom in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120 (pdb code 4lss). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120, PDB code: 4lss:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120


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 Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na515 b:42.2 occ:1.00 CG G:LYS62 3.3 54.5 1.0 N G:THR63 3.6 48.9 1.0 CG2 G:THR63 3.6 60.9 1.0 N G:GLU64 3.8 34.1 1.0 CB G:LYS62 4.1 49.5 1.0 CB G:GLU64 4.1 29.1 1.0 CA G:LYS62 4.2 53.9 1.0 CE G:LYS62 4.2 76.3 1.0 CD G:LYS62 4.3 66.3 1.0 C G:LYS62 4.3 53.8 1.0 CA G:THR63 4.4 39.0 1.0 NZ G:LYS62 4.4 90.2 1.0 C G:THR63 4.5 31.0 1.0 CA G:GLU64 4.5 33.3 1.0 CB G:THR63 4.5 52.7 1.0 CG2 G:THR209 4.7 33.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120


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 Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na516 b:54.7 occ:1.00 O G:HOH665 2.5 63.5 1.0 NE2 G:GLN203 2.8 0.2 1.0 O G:ALA204 2.9 68.4 1.0 O G:PRO118 3.1 36.0 1.0 CB G:GLN203 3.1 70.0 1.0 C G:LYS117 3.4 38.4 1.0 CA G:LYS117 3.5 41.8 1.0 CB G:LYS117 3.5 46.2 1.0 CD G:GLN203 3.6 0.2 1.0 N G:PRO118 3.7 30.9 1.0 O G:LYS117 3.9 34.8 1.0 CG G:GLN203 3.9 93.3 1.0 C G:PRO118 4.0 35.3 1.0 C G:ALA204 4.0 66.3 1.0 CD G:PRO118 4.1 29.7 1.0 N G:ALA204 4.1 63.5 1.0 C G:GLN203 4.2 53.6 1.0 CA G:GLN203 4.3 56.8 1.0 CG G:LYS117 4.4 43.4 1.0 NZ G:LYS117 4.5 82.1 1.0 CA G:PRO118 4.5 32.6 1.0 OE1 G:GLN203 4.5 0.4 1.0 CA G:ALA204 4.7 66.4 1.0 CE G:LYS117 4.7 74.2 1.0 O G:GLN203 4.8 54.0 1.0 N G:LYS117 4.9 37.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Broadly and Potently Neutralizing Antibody VRC01 in Complex with Hiv-1 Clade A Strain KER_2018_11 GP120 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na601 b:39.7 occ:1.00 O H:HOH625 2.5 37.0 1.0 O L:SER30 2.5 37.6 1.0 OH H:TYR100 2.6 28.9 1.0 N L:TYR91 2.9 29.2 1.0 C L:SER30 3.6 30.4 1.0 CZ H:TYR100 3.7 35.4 1.0 CA L:TYR91 3.7 26.2 1.0 CB H:TRP100B 3.8 32.2 1.0 C L:GLN90 3.8 32.3 1.0 CA L:GLN90 3.9 25.3 1.0 CE2 H:TYR100 4.0 31.2 1.0 OG L:SER30 4.0 52.5 1.0 CB L:SER30 4.1 32.8 1.0 O L:HOH704 4.2 32.3 1.0 CD1 L:TYR91 4.2 42.2 1.0 CA L:SER30 4.2 24.9 1.0 N L:SER30 4.4 53.5 1.0 O L:GLN89 4.4 40.9 1.0 OD1 H:ASP100C 4.5 42.6 1.0 CG H:TRP100B 4.5 28.6 1.0 N L:LEU33 4.5 30.0 1.0 CG L:TYR91 4.5 33.8 1.0 O L:TYR91 4.7 23.2 1.0 N L:GLN90 4.7 27.9 1.0 CB L:TYR91 4.7 33.0 1.0 CE1 L:TYR91 4.7 36.9 1.0 C L:TYR91 4.7 37.7 1.0 OE1 L:GLN89 4.8 32.4 1.0 CD1 H:TRP100B 4.8 29.6 1.0 CA L:LEU33 4.8 31.2 1.0 CG L:GLN90 4.8 38.8 1.0 C L:GLN89 4.8 35.6 1.0 CE1 H:TYR100 4.9 36.9 1.0 CD L:GLN89 4.9 36.5 1.0 CB L:GLN90 4.9 22.8 1.0 C L:GLY29 4.9 26.4 1.0

T.Zhou, J.Zhu, X.Wu, S.Moquin, B.Zhang, P.Acharya, I.S.Georgiev, H.R.Altae-Tran, G.Y.Chuang, M.G.Joyce, Y.Do Kwon, N.S.Longo, M.K.Louder, T.Luongo, K.Mckee, C.A.Schramm, J.Skinner, Y.Yang, Z.Yang, Z.Zhang, A.Zheng, M.Bonsignori, B.F.Haynes, J.F.Scheid, M.C.Nussenzweig, M.Simek, D.R.Burton, W.C.Koff, J.C.Mullikin, M.Connors, L.Shapiro, G.J.Nabel, J.R.Mascola, P.D.Kwong. Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway For Hiv-1 Neutralization By VRC01-Class Antibodies. Immunity V. 39 245 2013.
ISSN: ISSN 1074-7613
PubMed: 23911655
DOI: 10.1016/J.IMMUNI.2013.04.012