Zinc in PDB 4jy6: Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody

The structure of Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody, PDB code: 4jy6 was solved by J.-P.Julien, D.C.Diwanji, D.R.Burton, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.14 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.890, 80.320, 90.430, 90.00, 93.85, 90.00
R / Rfree (%)	20.7 / 26.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody (pdb code 4jy6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody, PDB code: 4jy6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent 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 PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:87.2 occ:1.00 ND1 A:HIS201 2.6 49.9 1.0 O A:HOH412 2.7 54.0 1.0 O A:HOH419 3.1 39.0 1.0 OE2 A:GLU202 3.3 79.6 1.0 CG A:GLU202 3.3 69.6 1.0 CG A:HIS201 3.4 49.9 1.0 CB A:HIS201 3.4 52.3 1.0 CD A:GLU202 3.6 77.0 1.0 CE1 A:HIS201 3.7 43.7 1.0 CA A:ALA116 4.1 39.2 1.0 CB A:ALA116 4.2 40.2 1.0 N A:GLU202 4.3 58.2 1.0 N A:ALA116 4.5 25.5 1.0 CD A:PRO117 4.6 39.3 1.0 CD2 A:HIS201 4.6 45.5 1.0 O A:HOH445 4.6 54.7 1.0 O A:ALA115 4.7 33.0 1.0 CA A:HIS201 4.7 57.8 1.0 CB A:GLU202 4.7 65.1 1.0 NE2 A:HIS201 4.7 42.6 1.0 OE1 A:GLU202 4.7 79.8 1.0 C A:ALA115 4.8 39.9 1.0 OG A:SER204 4.8 84.0 1.0 CB A:SER204 4.8 79.4 1.0 C A:HIS201 4.9 65.5 1.0

Zinc binding site 2 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent 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 PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:0.9 occ:1.00 O A:HOH431 2.6 60.9 1.0 NE2 A:HIS192 2.7 81.3 1.0 CE1 A:HIS192 2.9 83.0 1.0 CD2 A:HIS192 4.1 81.0 1.0 ND1 A:HIS192 4.2 82.9 1.0 CG A:HIS192 4.8 81.4 1.0

Zinc binding site 3 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody


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 Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:0.8 occ:1.00 OE1 A:GLU164 2.6 88.1 1.0 CD A:GLU164 3.7 83.7 1.0 CG A:GLU164 4.2 71.3 1.0 O B:LEU168 4.5 51.1 1.0 N B:SER170 4.7 67.5 1.0 OE2 A:GLU164 4.7 87.5 1.0 CB B:SER170 4.9 72.9 1.0

Zinc binding site 4 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody


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 Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:0.5 occ:1.00 O A:HOH432 2.5 62.8 1.0 OG1 A:THR120 3.4 52.8 1.0 O A:HOH407 3.8 33.0 1.0 OG A:SER118 4.0 36.0 1.0 CG2 B:THR181 4.1 59.3 1.0 OG A:SER141 4.2 44.0 1.0 CB A:THR120 4.5 42.2 1.0 O A:HOH409 4.9 24.4 1.0

Zinc binding site 5 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody


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 Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:89.6 occ:1.00 O A:HOH442 2.5 49.8 1.0 O A:HOH435 2.7 44.1 1.0 OE2 A:GLU26 2.8 63.8 1.0 OE1 A:GLU26 3.3 58.5 1.0 CD A:GLU26 3.4 61.2 1.0 CG A:GLU26 4.8 52.4 1.0

Zinc binding site 6 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody


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 Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:0.6 occ:1.00 O A:ASP92 3.4 31.4 1.0 OG1 A:THR98B 3.9 56.3 1.0 C A:GLY98A 3.9 46.2 1.0 C A:ASP92 4.0 33.2 1.0 CA A:GLY98A 4.0 41.3 1.0 O A:GLY98A 4.2 43.9 1.0 N A:THR98B 4.2 53.0 1.0 N A:ASP92 4.3 39.4 1.0 CA A:ALA96 4.5 30.9 1.0 N A:ALA96 4.5 27.4 1.0 N A:GLY98A 4.6 43.0 1.0 CD2 B:PHE100K 4.6 28.5 1.0 CG B:PHE100K 4.7 25.8 1.0 CA A:ASP92 4.8 39.3 1.0 CA A:THR98B 4.8 51.0 1.0 C A:ALA96 4.9 34.9 1.0 CE2 B:PHE100K 5.0 24.0 1.0 CB B:PHE100K 5.0 25.2 1.0 CD1 B:PHE100K 5.0 23.5 1.0 CB A:THR98B 5.0 52.2 1.0

Zinc binding site 7 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody


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 Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:98.1 occ:1.00 O A:HOH434 2.8 46.8 1.0 ND2 A:ASN51 3.7 21.8 1.0 NE B:ARG100 3.8 43.3 1.0 OD1 A:ASN50 3.8 32.8 1.0 CZ B:ARG100 3.9 39.6 1.0 CD B:ARG100 4.2 37.4 1.0 NH2 B:ARG100 4.2 20.7 1.0 NH1 B:ARG100 4.2 31.5 1.0 O A:ASN50 4.3 19.1 1.0 OE1 A:GLN52 4.5 46.7 1.0 NE2 A:GLN52 4.5 43.8 1.0 CG A:ASN50 4.5 34.2 1.0 ND2 A:ASN50 4.5 24.5 1.0 CG A:ASN51 4.8 27.7 1.0 CD A:GLN52 4.9 45.2 1.0 CB A:ASN51 5.0 19.3 1.0

Zinc binding site 8 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody


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 Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:93.9 occ:1.00 OD2 A:ASP102 2.5 50.7 1.0 CG A:ASP102 3.3 46.2 1.0 OD1 A:ASP102 3.5 44.5 1.0 CD A:LYS25 4.2 55.1 1.0 ND2 A:ASN98C 4.4 47.4 1.0 CG A:LYS25 4.6 44.3 1.0 CB A:ASP102 4.7 36.8 1.0 CA A:GLY24 4.9 32.5 1.0 N A:LYS25 5.0 38.8 1.0

Zinc binding site 9 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody


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 Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.7 occ:1.00 O B:HOH414 2.5 27.3 1.0 O A:HOH441 2.5 48.7 1.0 NE2 B:HIS162 2.7 57.6 1.0 O A:HOH409 3.1 24.4 1.0 CD2 B:HIS162 3.3 56.8 1.0 CE1 B:HIS162 3.3 57.3 1.0 O A:HOH407 4.1 33.0 1.0 CG B:HIS162 4.1 61.6 1.0 ND1 B:HIS162 4.1 59.4 1.0 O B:GLY160 4.2 61.4 1.0 C B:GLY160 4.3 62.2 1.0 CA B:GLY160 4.4 65.0 1.0 OD1 A:ASP142 4.7 56.9 1.0 O B:VAL161 5.0 55.0 1.0

Zinc binding site 10 out of 18 in the Crystal Structure of Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody


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 Human Fab PGT123, A Broadly Reactive and Potent Hiv-1 Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.6 occ:1.00 O B:HOH415 2.8 43.4 1.0 CE1 B:HIS97 3.2 70.3 1.0 ND1 B:HIS97 3.5 66.5 1.0 O B:HOH428 3.8 60.0 1.0 NE2 B:HIS97 4.2 69.5 1.0 CE B:LYS99 4.4 35.1 1.0 OH B:TYR33 4.5 37.4 1.0 NZ B:LYS99 4.6 35.2 1.0 CG B:HIS97 4.7 57.8 1.0

J.P.Julien, D.Sok, R.Khayat, J.H.Lee, K.J.Doores, L.M.Walker, A.Ramos, D.C.Diwanji, R.Pejchal, A.Cupo, U.Katpally, R.S.Depetris, R.L.Stanfield, R.Mcbride, A.J.Marozsan, J.C.Paulson, R.W.Sanders, J.P.Moore, D.R.Burton, P.Poignard, A.B.Ward, I.A.Wilson. Broadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding Via Recognition of the Hiv-1 GP120 V3 Base and Multiple Surrounding Glycans. Plos Pathog. V. 9 03342 2013.
ISSN: ISSN 1553-7366
PubMed: 23658524
DOI: 10.1371/JOURNAL.PPAT.1003342