Sodium in PDB 5tpp: Crystal Structure of DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage

The structure of Crystal Structure of DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage, PDB code: 5tpp was solved by D.Fera, S.C.Harrison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.96 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.114, 68.798, 59.463, 90.00, 113.21, 90.00
R / Rfree (%)	17.9 / 21.2

The binding sites of Sodium atom in the Crystal Structure of DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage (pdb code 5tpp). 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 DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage, PDB code: 5tpp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage


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 DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:79.5 occ:1.00 O L:ASP28 2.4 30.7 1.0 N L:PHE32 2.4 36.6 1.0 O L:HOH428 2.6 33.8 1.0 O L:HOH444 2.8 75.7 1.0 CB L:PHE32 2.9 39.8 1.0 CA L:PHE32 3.0 37.2 1.0 O L:PHE32 3.3 33.9 1.0 C L:PHE32 3.4 38.4 1.0 CD2 L:PHE32 3.5 45.7 1.0 CB L:LYS31 3.5 37.2 1.0 C L:LYS31 3.5 35.8 1.0 C L:ASP28 3.5 30.7 1.0 CG L:PHE32 3.6 44.0 1.0 CB L:PHE93 3.8 27.5 1.0 CA L:LYS31 3.8 37.5 1.0 O L:PHE93 3.9 26.9 1.0 N L:LYS31 4.0 38.4 1.0 OG L:SER92 4.1 23.8 1.0 O L:VAL29 4.1 39.1 1.0 CD1 L:PHE93 4.2 37.9 1.0 CA L:ASP28 4.3 29.6 1.0 CG L:PHE93 4.4 33.5 1.0 C L:VAL29 4.4 36.2 1.0 N L:VAL29 4.5 30.1 1.0 O L:HOH520 4.5 69.3 1.0 N L:ASP33 4.5 34.8 1.0 N L:LEU34 4.5 26.2 1.0 CG L:LYS31 4.6 39.6 1.0 CA L:VAL29 4.6 31.2 1.0 O L:LYS31 4.6 36.8 1.0 C L:PHE93 4.6 27.1 1.0 CB L:LEU34 4.6 24.1 1.0 CA L:PHE93 4.7 24.7 1.0 CE2 L:PHE32 4.7 46.5 1.0 N L:PHE93 4.8 23.6 1.0 C L:GLY30 4.9 44.4 1.0 CD1 L:PHE32 5.0 46.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage


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 DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage within 5.0Å range: probe atom residue distance (Å) B Occ L:Na302 b:72.7 occ:1.00 NE2 L:GLN171 2.3 34.1 1.0 CG L:ASP142 2.4 37.1 1.0 OD2 L:ASP142 2.4 40.3 1.0 OD1 L:ASP142 2.5 41.5 1.0 ND2 L:ASN173 2.5 33.0 1.0 CA L:ASP142 3.2 25.0 1.0 CG L:ASN173 3.3 32.8 1.0 OD1 L:ASN173 3.3 32.3 1.0 CD L:GLN171 3.3 32.5 1.0 CB L:ASP142 3.3 29.5 1.0 OE1 L:GLN171 3.6 31.9 1.0 N L:ASP142 3.8 24.1 1.0 CB L:LYS175 3.9 28.6 1.0 CG L:LYS175 4.4 29.4 1.0 CD L:LYS175 4.4 30.5 1.0 C L:ASP142 4.4 25.0 1.0 CG L:GLN171 4.6 32.4 1.0 CB L:ASN173 4.7 32.8 1.0 CB L:GLN171 4.8 31.5 1.0 O L:ASP142 4.9 25.6 1.0 C L:SER141 4.9 17.3 1.0 CA L:LYS175 5.0 28.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage


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 DH270.5 (Unliganded) From the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage within 5.0Å range: probe atom residue distance (Å) B Occ L:Na303 b:70.9 occ:1.00 O L:HOH485 2.2 37.9 1.0 O L:PRO212 2.2 37.5 1.0 C L:PRO212 3.0 33.5 1.0 CA L:PRO212 3.2 28.4 1.0 O L:HOH540 3.4 46.7 1.0 NE1 L:TRP189 3.9 19.2 1.0 CB L:PRO212 4.0 29.4 1.0 CZ2 L:TRP189 4.1 20.5 1.0 N L:GLU214 4.1 50.3 1.0 O L:ALA211 4.2 27.3 1.0 N L:THR213 4.2 47.4 1.0 CE2 L:TRP189 4.4 18.9 1.0 N L:PRO212 4.5 25.1 1.0 CB L:GLU214 4.7 52.2 1.0 C L:ALA211 4.8 26.7 1.0 C L:THR213 4.8 52.3 1.0 CA L:THR213 4.8 52.5 1.0 CA L:GLU214 4.8 51.9 1.0

M.Bonsignori, E.F.Kreider, D.Fera, R.R.Meyerhoff, T.Bradley, K.Wiehe, S.M.Alam, B.Aussedat, W.E.Walkowicz, K.K.Hwang, K.O.Saunders, R.Zhang, M.A.Gladden, A.Monroe, A.Kumar, S.M.Xia, M.Cooper, M.K.Louder, K.Mckee, R.T.Bailer, B.W.Pier, C.A.Jette, G.Kelsoe, W.B.Williams, L.Morris, J.Kappes, K.Wagh, G.Kamanga, M.S.Cohen, P.T.Hraber, D.C.Montefiori, A.Trama, H.X.Liao, T.B.Kepler, M.A.Moody, F.Gao, S.J.Danishefsky, J.R.Mascola, G.M.Shaw, B.H.Hahn, S.C.Harrison, B.T.Korber, B.F.Haynes. Staged Induction of Hiv-1 Glycan-Dependent Broadly Neutralizing Antibodies. Sci Transl Med V. 9 2017.
ISSN: ESSN 1946-6242
PubMed: 28298420
DOI: 10.1126/SCITRANSLMED.AAI7514