Zinc in PDB 1yec: Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3)

The structure of Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3), PDB code: 1yec was solved by B.Golinelli-Pimpaneau, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.180, 78.180, 158.940, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 25.2

The binding sites of Zinc atom in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3) (pdb code 1yec). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3), PDB code: 1yec:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn215 b:28.9 occ:1.00 O L:HOH249 3.7 30.0 1.0 O H:HOH588 4.5 48.8 1.0 NZ L:LYS30 4.6 37.3 1.0 CE L:LYS30 4.9 31.9 1.0

Zinc binding site 2 out of 7 in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn216 b:33.6 occ:1.00 O L:HOH288 1.6 34.0 1.0 O L:HOH300 2.6 39.4 1.0 ZN L:ZN218 3.4 20.4 1.0 O L:HOH280 3.8 53.2 1.0 O L:HOH299 3.8 43.9 1.0 O L:HOH258 4.2 23.1 1.0 ND1 L:HIS93 4.9 18.9 1.0

Zinc binding site 3 out of 7 in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn217 b:26.0 occ:1.00 O L:HOH264 1.6 47.2 1.0 O H:HOH580 1.7 39.1 1.0 OD1 H:ASP100C 2.2 29.1 1.0 NE2 L:HIS49 2.3 19.3 1.0 CG H:ASP100C 2.9 29.3 1.0 OD2 H:ASP100C 3.0 29.4 1.0 CE1 L:HIS49 3.1 16.5 1.0 CD2 L:HIS49 3.3 16.5 1.0 ND1 L:HIS49 4.2 17.9 1.0 N H:TYR100D 4.3 20.1 1.0 CG L:HIS49 4.4 16.0 1.0 CB L:LYS53 4.4 22.4 1.0 CB H:ASP100C 4.4 25.6 1.0 O H:TYR100D 4.6 25.1 1.0 CG L:LYS53 4.7 27.6 1.0 CD1 H:TYR100D 4.9 15.5 1.0 CA H:ASP100C 4.9 23.0 1.0

Zinc binding site 4 out of 7 in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn218 b:20.4 occ:1.00 O L:HOH300 1.7 39.4 1.0 O L:HOH258 2.0 23.1 1.0 ND1 L:HIS93 2.4 18.9 1.0 O L:HOH288 3.2 34.0 1.0 CG L:HIS93 3.2 18.6 1.0 CE1 L:HIS93 3.3 19.8 1.0 ZN L:ZN216 3.4 33.6 1.0 CB L:HIS93 3.5 15.0 1.0 CA L:HIS93 3.9 15.1 1.0 NE2 L:HIS93 4.3 21.6 1.0 CD2 L:HIS93 4.4 19.8 1.0 O L:HOH235 4.7 24.1 1.0 O L:THR92 4.7 16.7 1.0 N L:PHE94 4.8 19.4 1.0 C L:HIS93 4.9 17.5 1.0 N L:HIS93 4.9 14.2 1.0

Zinc binding site 5 out of 7 in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn219 b:26.4 occ:1.00 O L:HOH256 1.7 17.6 1.0 OD2 L:ASP151 1.9 23.2 1.0 O L:HOH270 2.3 30.3 1.0 ND1 L:HIS189 2.4 29.0 1.0 CG L:ASP151 2.9 19.9 1.0 ZN L:ZN220 3.2 27.9 1.0 CG L:HIS189 3.2 28.6 1.0 CE1 L:HIS189 3.3 28.2 1.0 CB L:ASP151 3.3 18.9 1.0 CB L:HIS189 3.5 26.6 1.0 O L:HOH231 3.7 32.2 1.0 CA L:HIS189 3.7 26.0 1.0 O L:HOH272 3.9 26.0 1.0 O L:HOH281 3.9 42.0 1.0 OD1 L:ASP151 4.1 22.7 1.0 O L:ARG188 4.1 31.8 1.0 O L:HOH271 4.2 17.7 1.0 NE2 L:HIS189 4.3 28.9 1.0 CD2 L:HIS189 4.3 29.7 1.0 CG2 L:ILE150 4.5 20.8 1.0 N L:HIS189 4.6 25.9 1.0 N L:ASN190 4.7 26.8 1.0 O L:HOH283 4.7 36.1 1.0 CA L:ASP151 4.7 19.4 1.0 C L:ARG188 4.7 29.6 1.0 C L:HIS189 4.8 24.9 1.0 O L:ILE150 4.8 18.4 1.0 O L:HOH242 4.8 26.8 1.0 ZN L:ZN221 4.9 28.4 1.0

Zinc binding site 6 out of 7 in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn220 b:27.9 occ:1.00 O L:HOH283 1.6 36.1 1.0 O L:HOH256 1.7 17.6 1.0 O L:HOH272 1.7 26.0 1.0 O L:HOH281 2.1 42.0 1.0 ZN L:ZN219 3.2 26.4 1.0 O L:HOH231 3.3 32.2 1.0 O L:HOH242 3.4 26.8 1.0 ZN L:ZN221 3.4 28.4 1.0 O L:HOH270 4.0 30.3 1.0 O L:HOH271 4.0 17.7 1.0 O L:HOH274 4.0 22.8 1.0 CB L:ASP151 4.2 18.9 1.0 OD2 L:ASP151 4.6 23.2 1.0 OG L:SER153 4.8 35.6 1.0 O L:ASP151 4.9 20.1 1.0 CG L:ASP151 4.9 19.9 1.0 ND1 L:HIS189 5.0 29.0 1.0

Zinc binding site 7 out of 7 in the Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Catalytic Antibody IGG2A Fab Fragment (D2.3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn221 b:28.4 occ:1.00 O L:HOH272 1.8 26.0 1.0 O L:HOH271 1.8 17.7 1.0 O L:HOH274 2.0 22.8 1.0 ZN L:ZN220 3.4 27.9 1.0 O L:HOH281 3.6 42.0 1.0 O L:HOH242 3.7 26.8 1.0 O L:HOH270 4.1 30.3 1.0 O L:HOH283 4.2 36.1 1.0 O L:HOH256 4.3 17.6 1.0 ZN L:ZN219 4.9 26.4 1.0

J.B.Charbonnier, B.Golinelli-Pimpaneau, B.Gigant, D.S.Tawfik, R.Chap, D.G.Schindler, S.H.Kim, B.S.Green, Z.Eshhar, M.Knossow. Structural Convergence in the Active Sites of A Family of Catalytic Antibodies. Science V. 275 1140 1997.
ISSN: ISSN 0036-8075
PubMed: 9027317
DOI: 10.1126/SCIENCE.275.5303.1140