Zinc in PDB 2qsc: Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide

The structure of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide, PDB code: 2qsc was solved by C.H.Bell, A.Schiefner, R.L.Stanfield, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.912, 39.858, 97.960, 90.00, 108.50, 90.00
R / Rfree (%)	21.9 / 26.4

The structure of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide (pdb code 2qsc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide, PDB code: 2qsc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn215 b:60.7 occ:1.00 NE2 H:HIS172 2.0 47.7 1.0 OD1 L:ASN137 2.1 51.8 1.0 CL L:CL217 2.3 63.0 1.0 OD1 L:ASN138 2.3 51.8 1.0 CD2 H:HIS172 2.8 48.0 1.0 CG L:ASN137 3.0 51.3 1.0 CE1 H:HIS172 3.2 47.9 1.0 ND2 L:ASN137 3.3 51.8 1.0 CG L:ASN138 3.4 51.5 1.0 OG1 H:THR192 3.6 55.3 1.0 O H:GLY169 3.9 49.3 1.0 ND2 L:ASN138 4.0 51.8 1.0 CG H:HIS172 4.1 48.2 1.0 ND1 H:HIS172 4.2 47.8 1.0 CG2 H:THR192 4.2 55.2 1.0 OG L:SER174 4.2 47.9 1.0 CB L:ASN137 4.4 51.1 1.0 CB L:ASN138 4.4 51.2 1.0 N L:ASN138 4.5 51.1 1.0 CB H:THR192 4.5 55.2 1.0 C H:GLY169 4.7 49.3 1.0 CA H:GLY169 4.8 49.3 1.0 O L:HOH225 4.8 43.3 1.0 CA L:ASN137 4.9 51.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn216 b:54.0 occ:1.00 ND1 L:HIS70 2.1 50.6 1.0 O L:HOH219 2.6 30.8 1.0 CG L:HIS70 3.0 49.9 1.0 CE1 L:HIS70 3.0 50.8 1.0 NE2 L:GLN24 3.3 53.4 1.0 CB L:HIS70 3.3 49.1 1.0 NE2 L:HIS70 4.1 50.8 1.0 CD2 L:HIS70 4.1 50.3 1.0 CD L:GLN24 4.4 53.3 1.0 CA L:HIS70 4.5 49.0 1.0 CG L:GLN24 4.7 53.1 1.0 OG1 L:THR69 4.7 48.8 1.0 N L:HIS70 5.0 49.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn230 b:42.6 occ:1.00 OD2 H:ASP53 1.9 49.3 1.0 OE2 H:GLU55 2.2 50.3 1.0 CL H:CL234 2.7 52.9 1.0 CG H:ASP53 2.8 49.0 1.0 OD1 H:ASP53 3.1 49.1 1.0 CD H:GLU55 3.2 49.8 1.0 CG H:GLU55 3.5 49.1 1.0 OG1 H:THR56 3.9 48.9 1.0 CB H:ASP53 4.2 48.8 1.0 OE1 H:GLU55 4.4 49.6 1.0 OG H:SER52 4.5 48.2 1.0 CB H:GLU55 4.9 48.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn231 b:49.5 occ:1.00 OE1 H:GLU85 2.3 48.3 1.0 CL H:CL232 2.6 50.4 1.0 CL H:CL233 2.7 55.7 1.0 OE2 H:GLU85 2.9 47.7 1.0 CD H:GLU85 2.9 48.2 1.0 OG1 H:THR84 3.8 48.4 1.0 CB H:THR84 4.0 48.5 1.0 N H:THR84 4.0 48.6 1.0 CB H:ARG83 4.2 48.6 1.0 N H:GLU85 4.4 48.7 1.0 CG H:GLU85 4.4 48.6 1.0 CA H:THR84 4.5 48.5 1.0 C H:THR84 4.9 48.6 1.0 C H:ARG83 5.0 48.5 1.0

C.H.Bell, R.Pantophlet, A.Schiefner, L.A.Cavacini, R.L.Stanfield, D.R.Burton, I.A.Wilson. Structure of Antibody F425-B4E8 in Complex with A V3 Peptide Reveals A New Binding Mode For Hiv-1 Neutralization. J.Mol.Biol. V. 375 969 2008.
ISSN: ISSN 0022-2836
PubMed: 18068724
DOI: 10.1016/J.JMB.2007.11.013