Zinc in PDB 5jr1: Crystal Structure of 10E8 Ghv-Maturel Antigen-Binding Fragment.

The structure of Crystal Structure of 10E8 Ghv-Maturel Antigen-Binding Fragment., PDB code: 5jr1 was solved by M.G.Joyce, J.R.Mascola, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.31 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.784, 77.863, 85.003, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.1

The binding sites of Zinc atom in the Crystal Structure of 10E8 Ghv-Maturel Antigen-Binding Fragment. (pdb code 5jr1). 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 10E8 Ghv-Maturel Antigen-Binding Fragment., PDB code: 5jr1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of 10E8 Ghv-Maturel Antigen-Binding Fragment.


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 10E8 Ghv-Maturel Antigen-Binding Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:21.8 occ:1.00 OE2 H:GLU100I 2.0 21.4 1.0 ND1 L:HIS31 2.1 23.3 1.0 OD2 H:ASP100 2.1 23.7 1.0 HG2 H:GLU100I 2.7 28.2 1.0 HB3 L:HIS31 2.8 25.1 1.0 CG H:ASP100 2.9 21.0 1.0 CD H:GLU100I 2.9 25.9 1.0 CG L:HIS31 3.0 22.1 1.0 OD1 H:ASP100 3.0 21.7 1.0 CE1 L:HIS31 3.1 23.3 1.0 HA L:HIS31 3.2 25.5 1.0 CG H:GLU100I 3.2 23.5 1.0 HE1 L:HIS31 3.3 28.0 1.0 CB L:HIS31 3.3 20.9 1.0 HG3 H:GLU100I 3.5 28.2 1.0 HB2 L:ARG91 3.6 34.1 1.0 HB2 H:TRP100B 3.6 30.7 1.0 HB3 L:ARG91 3.7 34.1 1.0 H L:TYR32 3.7 23.0 1.0 CA L:HIS31 3.7 21.3 1.0 HB3 H:TRP100B 3.9 30.7 1.0 CB L:ARG91 4.1 28.4 1.0 OE1 H:GLU100I 4.1 24.5 1.0 HD3 L:ARG91 4.1 37.0 1.0 CD2 L:HIS31 4.1 23.3 1.0 NE2 L:HIS31 4.1 24.1 1.0 HB2 L:HIS31 4.2 25.1 1.0 CB H:TRP100B 4.2 25.6 1.0 CB H:ASP100 4.3 20.3 1.0 N L:TYR32 4.3 19.1 1.0 O H:HOH470 4.3 24.7 1.0 HB3 H:ASP100 4.4 24.4 1.0 H L:ARG91 4.4 30.3 1.0 HE3 H:TRP100B 4.6 34.1 1.0 C L:HIS31 4.6 20.1 1.0 CB H:GLU100I 4.6 23.9 1.0 HA H:GLU100I 4.6 25.1 1.0 H H:TRP100B 4.7 29.3 1.0 H H:ASP100 4.7 26.4 1.0 HB2 H:ASP100 4.7 24.4 1.0 CG H:TRP100B 4.7 27.2 1.0 HG L:SER90 4.7 32.7 1.0 O L:SER30 4.8 27.0 1.0 HG2 L:ARG91 4.8 41.1 1.0 CG L:ARG91 4.9 34.3 1.0 O L:TYR32 4.9 23.9 1.0 N L:HIS31 4.9 22.7 1.0 N H:GLU100I 4.9 21.5 1.0 CD L:ARG91 4.9 30.8 1.0 H H:GLY100H 4.9 32.7 1.0 CE3 H:TRP100B 4.9 28.4 1.0 HE2 L:HIS31 4.9 28.9 1.0 CA H:GLU100I 4.9 20.9 1.0 CD2 H:TRP100B 5.0 27.6 1.0 HD2 L:HIS31 5.0 28.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of 10E8 Ghv-Maturel Antigen-Binding Fragment.


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 10E8 Ghv-Maturel Antigen-Binding Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:14.6 occ:1.00 ND1 L:HIS198 2.0 16.3 1.0 O L:HOH450 2.0 15.8 1.0 O L:HOH568 2.2 25.0 1.0 CE1 L:HIS198 2.9 17.0 1.0 HE1 L:HIS198 3.0 20.4 1.0 HB3 L:HIS198 3.0 18.0 1.0 CG L:HIS198 3.1 15.6 1.0 HA L:ALA112 3.2 17.9 1.0 CB L:HIS198 3.6 15.0 1.0 HB2 L:ALA112 3.8 19.4 1.0 HD2 L:PRO113 3.8 25.8 1.0 O L:HIS198 3.8 16.5 1.0 O L:HOH510 4.0 32.6 1.0 CA L:ALA112 4.0 14.9 1.0 HD3 L:PRO113 4.0 25.8 1.0 NE2 L:HIS198 4.0 16.9 1.0 HB3 L:SER201 4.1 23.6 1.0 CD2 L:HIS198 4.2 15.9 1.0 CB L:ALA112 4.2 16.2 1.0 HB2 L:HIS198 4.2 18.0 1.0 HB1 L:ALA112 4.3 19.4 1.0 HB2 L:GLU199 4.3 29.9 1.0 CD L:PRO113 4.4 21.4 1.0 C L:HIS198 4.4 16.3 1.0 N L:ALA112 4.5 16.3 1.0 O L:ALA111 4.6 15.7 1.0 HG3 L:GLU199 4.6 32.8 1.0 CA L:HIS198 4.6 15.3 1.0 C L:ALA111 4.7 13.2 1.0 HE2 L:HIS198 4.8 20.2 1.0 HB3 L:LYS110 4.9 20.5 1.0 HB2 L:SER201 4.9 23.6 1.0 CB L:SER201 5.0 19.6 1.0 H L:ALA112 5.0 19.6 1.0

C.Soto, G.Ofek, M.G.Joyce, B.Zhang, K.Mckee, N.S.Longo, Y.Yang, J.Huang, R.Parks, J.Eudailey, K.E.Lloyd, S.M.Alam, B.F.Haynes, J.C.Mullikin, M.Connors, J.R.Mascola, L.Shapiro, P.D.Kwong. Developmental Pathway of the Mper-Directed Hiv-1-Neutralizing Antibody 10E8. Plos One V. 11 57409 2016.
ISSN: ESSN 1932-6203
PubMed: 27299673
DOI: 10.1371/JOURNAL.PONE.0157409