Sodium in PDB 4jan: Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120

The structure of Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120, PDB code: 4jan was solved by T.Zhou, S.Moquin, A.Zheng, S.Srivatsan, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 3.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.943, 208.651, 69.422, 90.00, 107.21, 90.00
R / Rfree (%)	19.6 / 25.6

The binding sites of Sodium atom in the Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120 (pdb code 4jan). 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 Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120, PDB code: 4jan:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 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 Neutralizing Antibody CH103 in Complex with Hiv-1 GP120 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:40.4 occ:1.00 O L:GLY41 2.9 79.7 1.0 O H:GLY106 3.1 69.0 1.0 HB2 B:ARG189 3.1 0.1 1.0 HA2 L:GLY41 3.2 92.8 1.0 HA3 H:GLY106 3.3 80.9 1.0 HG11 H:VAL89 3.4 71.0 1.0 C L:GLY41 3.7 80.8 1.0 HG13 H:VAL89 3.8 71.0 1.0 C H:GLY106 3.8 68.1 1.0 CA L:GLY41 3.9 77.4 1.0 CA H:GLY106 4.0 67.4 1.0 CB B:ARG189 4.0 0.9 1.0 CG1 H:VAL89 4.1 59.2 1.0 HD2 B:ARG189 4.1 0.4 1.0 HA B:ARG189 4.2 0.2 1.0 HG21 H:VAL89 4.3 73.2 1.0 HG3 B:ARG189 4.3 0.3 1.0 O L:HOH402 4.4 44.7 1.0 HA2 H:GLY106 4.5 80.9 1.0 HB2 H:LEU108 4.5 80.2 1.0 CA B:ARG189 4.5 0.8 1.0 HA3 L:GLY41 4.5 92.8 1.0 HG22 H:VAL89 4.6 73.2 1.0 CG B:ARG189 4.6 0.1 1.0 H L:GLY41 4.6 85.5 1.0 N B:ARG189 4.7 0.5 1.0 HB3 B:ARG189 4.7 0.1 1.0 H B:ARG189 4.7 0.9 1.0 HG12 H:VAL89 4.7 71.0 1.0 O H:ARG105 4.8 85.8 1.0 CG2 H:VAL89 4.8 61.0 1.0 N L:GLY41 4.8 71.3 1.0 CD B:ARG189 4.8 0.4 1.0 HZ H:PHE91 4.9 76.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 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 Neutralizing Antibody CH103 in Complex with Hiv-1 GP120 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:65.5 occ:1.00 OE2 L:GLU3 2.3 87.0 1.0 HA3 H:GLY44 3.0 66.8 1.0 O L:GLY99 3.0 49.9 1.0 O H:LEU45 3.2 56.4 1.0 O H:LYS43 3.2 64.3 1.0 CD L:GLU3 3.4 84.6 1.0 H H:LEU45 3.5 63.0 1.0 HB2 L:PHE98 3.5 58.3 1.0 HA L:SER100 3.6 64.5 1.0 N H:LEU45 3.7 52.5 1.0 CA H:GLY44 3.7 55.6 1.0 C H:GLY44 3.8 53.0 1.0 C H:LEU45 4.0 54.8 1.0 HE2 L:TYR87 4.0 73.0 1.0 OE1 L:GLU3 4.0 86.4 1.0 C L:GLY99 4.1 49.7 1.0 C H:LYS43 4.1 62.5 1.0 O L:PHE98 4.2 44.4 1.0 HD2 L:TYR87 4.3 72.5 1.0 HB3 H:GLU46 4.3 68.3 1.0 N H:GLY44 4.3 60.2 1.0 HG2 L:GLU3 4.3 96.6 1.0 HB3 L:PHE98 4.4 58.3 1.0 CB L:PHE98 4.4 48.5 1.0 CA H:LEU45 4.4 53.6 1.0 CA L:SER100 4.4 53.7 1.0 HA2 H:GLY44 4.5 66.8 1.0 CG L:GLU3 4.5 80.5 1.0 C L:PHE98 4.5 45.4 1.0 O H:GLY44 4.6 49.5 1.0 HB3 H:LEU45 4.6 64.4 1.0 HB3 L:GLU3 4.6 91.1 1.0 N L:SER100 4.7 51.4 1.0 CE2 L:TYR87 4.7 60.8 1.0 CD2 L:TYR87 4.9 60.4 1.0 HA H:GLU46 4.9 65.9 1.0 N L:GLY99 4.9 47.1 1.0 N H:GLU46 4.9 53.8 1.0 H L:PHE98 5.0 53.8 1.0

H.X.Liao, R.Lynch, T.Zhou, F.Gao, S.M.Alam, S.D.Boyd, A.Z.Fire, K.M.Roskin, C.A.Schramm, Z.Zhang, J.Zhu, L.Shapiro, J.C.Mullikin, S.Gnanakaran, P.Hraber, K.Wiehe, G.Kelsoe, G.Yang, S.M.Xia, D.C.Montefiori, R.Parks, K.E.Lloyd, R.M.Scearce, K.A.Soderberg, M.Cohen, G.Kamanga, M.K.Louder, L.M.Tran, Y.Chen, F.Cai, S.Chen, S.Moquin, X.Du, M.G.Joyce, S.Srivatsan, B.Zhang, A.Zheng, G.M.Shaw, B.H.Hahn, T.B.Kepler, B.T.Korber, P.D.Kwong, J.R.Mascola, B.F.Haynes. Co-Evolution of A Broadly Neutralizing Hiv-1 Antibody and Founder Virus. Nature V. 496 469 2013.
ISSN: ISSN 0028-0836
PubMed: 23552890
DOI: 10.1038/NATURE12053