Calcium in PDB 5t4z: Structure of the Anti-Hiv Antibody DH501 That Binds GP120 V3 Glycan and the Base of V3 with Free MAN9 Glycan

The structure of Structure of the Anti-Hiv Antibody DH501 That Binds GP120 V3 Glycan and the Base of V3 with Free MAN9 Glycan, PDB code: 5t4z was solved by N.I.Nicely, B.F.Haynes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.49 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.757, 115.997, 76.889, 90.00, 97.39, 90.00
R / Rfree (%)	18.7 / 23.9

The binding sites of Calcium atom in the Structure of the Anti-Hiv Antibody DH501 That Binds GP120 V3 Glycan and the Base of V3 with Free MAN9 Glycan (pdb code 5t4z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the Anti-Hiv Antibody DH501 That Binds GP120 V3 Glycan and the Base of V3 with Free MAN9 Glycan, PDB code: 5t4z:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the Anti-Hiv Antibody DH501 That Binds GP120 V3 Glycan and the Base of V3 with Free MAN9 Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Anti-Hiv Antibody DH501 That Binds GP120 V3 Glycan and the Base of V3 with Free MAN9 Glycan within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca304 b:38.9 occ:1.00 O H:GLY218 2.6 67.5 1.0 C H:GLY218 3.4 67.1 1.0 CA H:GLY218 4.8 67.5 1.0

Calcium binding site 2 out of 2 in the Structure of the Anti-Hiv Antibody DH501 That Binds GP120 V3 Glycan and the Base of V3 with Free MAN9 Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Anti-Hiv Antibody DH501 That Binds GP120 V3 Glycan and the Base of V3 with Free MAN9 Glycan within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca301 b:45.6 occ:1.00 O B:HOH358 2.8 45.9 1.0 ND2 L:ASN52 3.3 39.8 1.0 CA L:SER65 3.4 35.6 1.0 ND2 B:ASN51 3.4 35.5 1.0 N L:LYS66 3.4 32.4 1.0 ND2 B:ASN52 3.6 36.0 1.0 CB L:SER65 3.6 42.0 1.0 C L:SER65 3.9 34.8 1.0 O L:LYS66 4.1 45.1 1.0 CB L:ASN52 4.2 32.8 1.0 CG L:ASN52 4.2 39.1 1.0 O L:GLY64 4.3 35.7 1.0 CG B:ASN51 4.4 42.4 1.0 CB B:ASN51 4.4 39.8 1.0 CA L:LYS66 4.4 39.0 1.0 N L:SER65 4.6 35.2 1.0 CG B:ASN52 4.6 34.1 1.0 CB L:LYS66 4.6 43.6 1.0 C L:LYS66 4.7 43.8 1.0 OD1 B:ASN52 4.7 42.8 1.0 O B:GLN50 4.7 39.4 1.0 O L:HOH448 4.7 41.4 1.0 CB L:ASN51 4.8 25.2 1.0 C L:GLY64 4.9 35.5 1.0 OG L:SER65 5.0 39.6 1.0

K.O.Saunders, N.I.Nicely, K.Wiehe, M.Bonsignori, R.R.Meyerhoff, R.Parks, W.E.Walkowicz, B.Aussedat, N.R.Wu, F.Cai, Y.Vohra, P.K.Park, A.Eaton, E.P.Go, L.L.Sutherland, R.M.Scearce, D.H.Barouch, R.Zhang, T.Von Holle, R.G.Overman, K.Anasti, R.W.Sanders, M.A.Moody, T.B.Kepler, B.Korber, H.Desaire, S.Santra, N.L.Letvin, G.J.Nabel, D.C.Montefiori, G.D.Tomaras, H.X.Liao, S.M.Alam, S.J.Danishefsky, B.F.Haynes. Vaccine Elicitation of High Mannose-Dependent Neutralizing Antibodies Against the V3-Glycan Broadly Neutralizing Epitope in Nonhuman Primates. Cell Rep V. 18 2175 2017.
ISSN: ESSN 2211-1247
PubMed: 28249163
DOI: 10.1016/J.CELREP.2017.02.003