Zinc in PDB 4od3: Crystal Structure of Human Fab CAP256-VRC26.07, A Potent V1V2-Directed Hiv-1 Neutralizing Antibody

The structure of Crystal Structure of Human Fab CAP256-VRC26.07, A Potent V1V2-Directed Hiv-1 Neutralizing Antibody, PDB code: 4od3 was solved by J.Gorman, N.A.Doria-Rose, C.A.Schramm, P.L.Moore, J.R.Mascola, L.Shapiro, L.Morris, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.90 / 2.62
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	70.550, 87.268, 224.351, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 24.5

The binding sites of Zinc atom in the Crystal Structure of Human Fab CAP256-VRC26.07, A Potent V1V2-Directed Hiv-1 Neutralizing Antibody (pdb code 4od3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Fab CAP256-VRC26.07, A Potent V1V2-Directed Hiv-1 Neutralizing Antibody, PDB code: 4od3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Fab CAP256-VRC26.07, A Potent V1V2-Directed Hiv-1 Neutralizing Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Fab CAP256-VRC26.07, A Potent V1V2-Directed Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:0.9 occ:1.00 NE2 H:HIS164 2.4 80.3 1.0 OD2 L:ASP138 2.5 83.8 1.0 HD2 H:HIS164 2.9 93.8 1.0 CD2 H:HIS164 3.0 78.2 1.0 CG L:ASP138 3.2 77.0 1.0 OD1 L:ASP138 3.3 77.2 1.0 CE1 H:HIS164 3.6 80.9 1.0 HE1 H:HIS164 3.9 97.1 1.0 HG L:SER137 4.0 73.6 1.0 HB2 L:SER137 4.0 72.5 1.0 CG H:HIS164 4.3 77.5 1.0 OG L:SER137 4.4 61.4 1.0 ND1 H:HIS164 4.5 79.3 1.0 CB L:ASP138 4.6 74.4 1.0 CB L:SER137 4.7 60.4 1.0 HB2 L:ASP138 4.7 89.3 1.0 HE22 L:GLN167 4.9 0.7 1.0 HD21 L:ASN169 4.9 0.1 1.0 HG1 H:THR183 4.9 84.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Fab CAP256-VRC26.07, A Potent V1V2-Directed Hiv-1 Neutralizing Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Fab CAP256-VRC26.07, A Potent V1V2-Directed Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:40.7 occ:0.50 ND1 L:HIS188 2.3 59.0 1.0 OD2 L:ASP151 2.4 59.7 1.0 HB2 L:ASP151 2.9 73.4 1.0 HA L:HIS188 2.9 71.0 1.0 CG L:HIS188 3.2 59.1 1.0 CG L:ASP151 3.2 61.5 1.0 CE1 L:HIS188 3.2 59.5 1.0 HB3 L:HIS188 3.3 70.6 1.0 HE1 L:HIS188 3.4 71.4 1.0 CB L:ASP151 3.5 61.2 1.0 CB L:HIS188 3.5 58.8 1.0 H L:ARG189 3.6 70.2 1.0 CA L:HIS188 3.6 59.2 1.0 HB3 L:ASP151 3.9 73.4 1.0 NE2 L:HIS188 4.2 59.7 1.0 CD2 L:HIS188 4.2 59.7 1.0 OD1 L:ASP151 4.3 63.7 1.0 N L:ARG189 4.3 58.5 1.0 O L:ALA150 4.3 57.7 1.0 HB2 L:HIS188 4.5 70.6 1.0 O L:SER187 4.5 59.1 1.0 C L:HIS188 4.5 58.7 1.0 HG3 L:ARG189 4.7 70.6 1.0 N L:HIS188 4.7 59.3 1.0 C L:ALA150 4.7 57.5 1.0 CA L:ASP151 4.8 59.8 1.0 HB1 L:ALA150 4.8 71.0 1.0 N L:ASP151 4.8 58.1 1.0 H L:SER152 4.9 72.0 1.0 HE2 L:HIS188 5.0 71.6 1.0 C L:SER187 5.0 58.9 1.0

N.A.Doria-Rose, C.A.Schramm, J.Gorman, P.L.Moore, J.N.Bhiman, B.J.Dekosky, M.J.Ernandes, I.S.Georgiev, H.J.Kim, M.Pancera, R.P.Staupe, H.R.Altae-Tran, R.T.Bailer, E.T.Crooks, A.Cupo, A.Druz, N.J.Garrett, K.H.Hoi, R.Kong, M.K.Louder, N.S.Longo, K.Mckee, M.Nonyane, S.O'dell, R.S.Roark, R.S.Rudicell, S.D.Schmidt, D.J.Sheward, C.Soto, C.K.Wibmer, Y.Yang, Z.Zhang, Nisc Comparative Sequencing, J.C.Mullikin, J.M.Binley, R.W.Sanders, I.A.Wilson, J.P.Moore, A.B.Ward, G.Georgiou, C.Williamson, S.S.Abdool Karim, L.Morris, P.D.Kwong, L.Shapiro, J.R.Mascola. Developmental Pathway For Potent V1V2-Directed Hiv-Neutralizing Antibodies. Nature V. 509 55 2014.
ISSN: ISSN 0028-0836
PubMed: 24590074
DOI: 10.1038/NATURE13036