Zinc in PDB 5i8e: Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab

The structure of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab, PDB code: 5i8e was solved by K.Xu, T.Zhou, K.Liu, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.31 / 2.66
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	114.606, 114.606, 174.082, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.8

The binding sites of Zinc atom in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab (pdb code 5i8e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab, PDB code: 5i8e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


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 Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.4 occ:1.00 NE1 A:TRP50 3.3 44.3 1.0 CE2 A:TRP50 3.5 36.3 1.0 CD1 A:TRP50 3.8 46.9 1.0 CZ2 A:TRP50 3.9 40.1 1.0 OG1 A:THR58 3.9 45.2 1.0 O A:ASP56 4.0 56.0 1.0 CD2 A:TRP50 4.1 42.3 1.0 CG A:TRP50 4.2 48.0 1.0 CB A:ASP56 4.2 39.7 1.0 N A:ASN52 4.2 57.2 1.0 C A:ASP56 4.3 47.7 1.0 O A:TRP50 4.3 43.0 1.0 N A:THR58 4.4 45.6 1.0 CB A:ASN52 4.5 42.2 1.0 C A:ILE51 4.5 56.4 1.0 N A:THR57 4.6 40.5 1.0 C A:THR57 4.6 53.0 1.0 CA A:THR57 4.6 40.5 1.0 CA A:ILE51 4.7 50.1 1.0 C A:TRP50 4.7 39.6 1.0 CH2 A:TRP50 4.7 35.4 1.0 CB A:THR58 4.8 60.5 1.0 N A:ILE51 4.9 42.7 1.0 CE3 A:TRP50 4.9 41.8 1.0 OH B:TYR94 4.9 57.7 1.0 CA A:ASN52 4.9 44.4 1.0 CA A:ASP56 4.9 42.4 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


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 Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:81.2 occ:1.00 O A:HOH414 1.9 43.1 1.0 NE2 A:HIS53 2.7 52.4 1.0 O A:HOH418 3.2 87.0 1.0 CD2 A:HIS53 3.5 55.0 1.0 CE1 A:HIS53 3.8 54.4 1.0 CG A:HIS53 4.7 66.2 1.0 ND1 A:HIS53 4.9 73.1 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:51.2 occ:1.00 OE2 B:GLU32 1.8 41.8 1.0 OE2 A:GLU100A 2.2 83.8 1.0 OE1 A:GLU100A 2.4 60.2 1.0 CD A:GLU100A 2.6 71.3 1.0 CD B:GLU32 2.7 53.6 1.0 OE1 B:GLU32 3.0 59.4 1.0 CG A:GLU100A 4.0 64.9 1.0 CG B:GLU32 4.1 40.8 1.0 CE1 B:TYR50 4.5 52.7 1.0 NH1 B:ARG30 4.7 72.5 1.0 CB A:GLU100A 4.9 46.7 1.0 OH B:TYR50 4.9 68.0 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:0.6 occ:1.00 OD1 B:ASN137 2.1 63.4 1.0 ND2 B:ASN138 2.2 85.6 1.0 NE2 A:HIS164 2.6 0.3 1.0 CD2 A:HIS164 2.7 0.9 1.0 CG B:ASN137 2.8 72.0 1.0 ND2 B:ASN137 3.0 66.8 1.0 CG B:ASN138 3.4 90.1 1.0 CE1 A:HIS164 3.7 0.4 1.0 CG A:HIS164 3.9 0.2 1.0 OD1 B:ASN138 3.9 97.3 1.0 CG2 A:THR183 4.1 0.6 1.0 ND1 A:HIS164 4.3 0.6 1.0 CB B:ASN137 4.3 84.4 1.0 O A:GLY162 4.4 87.7 1.0 OG B:SER174 4.4 95.2 1.0 OG1 A:THR183 4.4 0.5 1.0 N B:ASN138 4.5 78.1 1.0 CB B:ASN138 4.5 83.9 1.0 CA B:ASN137 4.9 89.6 1.0 CB A:THR183 5.0 0.0 1.0 CB A:HIS164 5.0 91.1 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:94.9 occ:1.00 N B:ILE2 2.2 49.8 1.0 ZN D:ZN301 2.4 58.6 1.0 O B:HOH420 2.8 47.3 1.0 CA B:ILE2 3.6 51.3 1.0 CB B:ILE2 4.4 58.0 1.0 N D:ILE2 4.5 42.1 1.0 C B:ILE2 4.5 68.3 1.0 CG2 B:ILE2 4.6 95.3 1.0 O D:HOH417 4.9 41.4 1.0 N B:GLN3 4.9 62.9 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:1.0 occ:1.00 NE1 C:TRP50 3.5 59.6 1.0 CE2 C:TRP50 3.7 53.7 1.0 OG1 C:THR58 3.7 50.7 1.0 CD1 C:TRP50 4.0 47.4 1.0 CZ2 C:TRP50 4.0 54.2 1.0 O C:ASP56 4.1 62.3 1.0 N C:THR58 4.2 51.0 1.0 O C:TRP50 4.3 48.9 1.0 C C:ASP56 4.3 66.2 1.0 CB C:ASP56 4.3 53.5 1.0 CD2 C:TRP50 4.3 46.0 1.0 CG C:TRP50 4.4 46.4 1.0 C C:THR57 4.5 52.1 1.0 O D:HOH413 4.5 62.9 1.0 N C:THR57 4.5 56.5 1.0 CA C:THR57 4.5 52.2 1.0 N C:ASN52 4.5 53.7 1.0 CB C:THR58 4.6 62.2 1.0 OH D:TYR94 4.7 52.2 1.0 CB C:ASN52 4.8 63.6 1.0 C C:TRP50 4.8 47.9 1.0 C C:ILE51 4.8 55.6 1.0 CA C:ILE51 4.9 51.2 1.0 CH2 C:TRP50 4.9 45.8 1.0 O C:HOH415 5.0 41.3 1.0 CA C:ASP56 5.0 53.9 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:72.4 occ:1.00 O C:HOH424 2.5 58.1 1.0 NE2 C:HIS53 2.5 54.3 1.0 CD2 C:HIS53 3.4 54.7 1.0 CE1 C:HIS53 3.6 65.5 1.0 CG C:HIS53 4.6 61.3 1.0 ND1 C:HIS53 4.6 67.6 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:49.7 occ:1.00 OE2 D:GLU32 2.0 51.0 1.0 OE2 C:GLU100A 2.0 88.5 1.0 OE1 C:GLU100A 2.5 75.7 1.0 CD C:GLU100A 2.6 81.7 1.0 O C:HOH411 2.8 71.4 1.0 CD D:GLU32 2.9 46.9 1.0 OE1 D:GLU32 3.1 45.3 1.0 CG C:GLU100A 4.0 82.1 1.0 NH1 D:ARG30 4.1 63.1 1.0 CG D:GLU32 4.3 36.6 1.0 CE1 D:TYR50 4.4 42.2 1.0 OH D:TYR50 4.8 70.5 1.0 CB C:GLU100A 5.0 46.5 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn304 b:0.2 occ:1.00 ND2 D:ASN137 2.3 68.1 1.0 OD1 D:ASN138 2.3 0.8 1.0 NE2 C:HIS164 2.5 0.5 1.0 CD2 C:HIS164 2.8 0.2 1.0 O D:HOH419 2.9 63.7 1.0 OD1 D:ASN137 2.9 83.1 1.0 CG D:ASN137 3.0 78.5 1.0 CG D:ASN138 3.4 0.7 1.0 CE1 C:HIS164 3.6 0.6 1.0 CG2 C:THR183 3.7 0.9 1.0 ND2 D:ASN138 4.0 0.6 1.0 CG C:HIS164 4.0 0.5 1.0 O C:GLY162 4.0 92.2 1.0 ND1 C:HIS164 4.3 0.5 1.0 CB D:ASN137 4.5 74.6 1.0 OG D:SER174 4.5 81.7 1.0 CB D:ASN138 4.6 87.6 1.0 OG1 C:THR183 4.6 85.7 1.0 N D:ASN138 4.6 74.2 1.0 C C:GLY162 4.7 89.9 1.0 CB C:THR183 4.8 87.1 1.0 CA C:GLY162 4.8 93.4 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Broadly Neutralizing Hiv-1 Fusion Peptide- Targeting Antibody VRC34.01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:58.6 occ:1.00 ZN B:ZN301 2.4 94.9 1.0 N D:ILE2 2.9 42.1 1.0 O B:HOH420 3.2 47.3 1.0 O D:HOH417 3.3 41.4 1.0 N B:ILE2 3.6 49.8 1.0 CA D:ILE2 4.1 55.9 1.0 CA B:ILE2 4.6 51.3 1.0 C D:ILE2 4.7 60.0 1.0 N D:GLN3 4.9 54.8 1.0

R.Kong, K.Xu, T.Zhou, P.Acharya, T.Lemmin, K.Liu, G.Ozorowski, C.Soto, J.D.Taft, R.T.Bailer, E.M.Cale, L.Chen, C.W.Choi, G.Y.Chuang, N.A.Doria-Rose, A.Druz, I.S.Georgiev, J.Gorman, J.Huang, M.G.Joyce, M.K.Louder, X.Ma, K.Mckee, S.O'dell, M.Pancera, Y.Yang, S.C.Blanchard, W.Mothes, D.R.Burton, W.C.Koff, M.Connors, A.B.Ward, P.D.Kwong, J.R.Mascola. Fusion Peptide of Hiv-1 As A Site of Vulnerability to Neutralizing Antibody. Science V. 352 828 2016.
ISSN: ESSN 1095-9203
PubMed: 27174988
DOI: 10.1126/SCIENCE.AAE0474