Zinc in PDB 8f6e: Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex

The binding sites of Zinc atom in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex (pdb code 8f6e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex, PDB code: 8f6e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:50.8 occ:1.00 OD2 A:ASP287 2.1 10.7 1.0 ND1 A:HIS250 2.3 10.2 1.0 NE2 A:HIS234 2.3 11.8 1.0 CB A:HIS250 2.4 10.2 1.0 CE1 A:HIS234 2.6 11.8 1.0 CG A:HIS250 2.7 10.2 1.0 CG A:ASP287 3.2 10.7 1.0 CD2 A:HIS234 3.4 11.8 1.0 CE1 A:HIS250 3.6 10.2 1.0 ND1 A:HIS234 3.7 11.8 1.0 CB A:ASP287 3.8 10.7 1.0 CA A:HIS250 3.9 10.2 1.0 CD2 A:HIS250 4.0 10.2 1.0 CG A:HIS234 4.1 11.8 1.0 O A:HIS250 4.2 10.2 1.0 OD1 A:ASP287 4.2 10.7 1.0 C A:HIS250 4.4 10.2 1.0 NE2 A:HIS250 4.4 10.2 1.0 N A:HIS250 4.8 10.2 1.0

Zinc binding site 2 out of 8 in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:56.0 occ:1.00 ND1 A:HIS73 2.3 42.6 1.0 NE2 A:HIS77 2.3 38.7 1.0 OD2 A:ASP70 2.5 45.9 1.0 OD1 A:ASP70 2.9 45.9 1.0 CG A:ASP70 3.1 45.9 1.0 CE1 A:HIS77 3.1 38.7 1.0 CG A:HIS73 3.1 42.6 1.0 CE1 A:HIS73 3.2 42.6 1.0 CB A:HIS73 3.4 42.6 1.0 CD2 A:HIS77 3.4 38.7 1.0 CD2 A:HIS73 4.2 42.6 1.0 NE2 A:HIS73 4.2 42.6 1.0 ND1 A:HIS77 4.3 38.7 1.0 OH A:TYR64 4.3 41.1 1.0 N A:HIS73 4.4 42.6 1.0 CG A:HIS77 4.5 38.7 1.0 CA A:HIS73 4.5 42.6 1.0 CB A:ASP70 4.6 45.9 1.0 C A:ASP72 4.8 48.7 1.0 CE1 A:TYR64 4.9 41.1 1.0

Zinc binding site 3 out of 8 in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:63.2 occ:1.00 OD1 A:ASP159 2.1 48.5 1.0 OD1 A:ASP47 2.1 47.1 1.0 OD2 A:ASP51 2.1 45.5 1.0 NE2 A:HIS155 2.3 50.2 1.0 CG A:ASP47 2.7 47.1 1.0 OD2 A:ASP47 2.8 47.1 1.0 CG A:ASP159 2.8 48.5 1.0 CE1 A:HIS155 3.0 50.2 1.0 CG A:ASP51 3.0 45.5 1.0 OD2 A:ASP159 3.1 48.5 1.0 CD2 A:HIS155 3.3 50.2 1.0 OD1 A:ASP51 3.3 45.5 1.0 O A:ASP47 3.6 47.1 1.0 CB A:ASP159 4.0 48.5 1.0 CD1 A:LEU162 4.0 44.5 1.0 ND1 A:HIS155 4.1 50.2 1.0 CB A:ASP47 4.1 47.1 1.0 C A:ASP47 4.2 47.1 1.0 CG A:HIS155 4.3 50.2 1.0 CB A:ASP51 4.4 45.5 1.0 CA A:ASP47 4.5 47.1 1.0 CA A:ASP159 4.7 48.5 1.0 O A:HIS155 4.9 50.2 1.0

Zinc binding site 4 out of 8 in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:46.0 occ:1.00 OD1 A:ASP287 2.1 10.7 1.0 NE2 B:HIS263 2.3 9.9 1.0 NE2 A:HIS285 2.3 7.6 1.0 CD2 A:HIS285 2.9 7.6 1.0 CG A:ASP287 3.1 10.7 1.0 CE1 B:HIS263 3.1 9.9 1.0 CD2 B:HIS263 3.4 9.9 1.0 CE1 A:HIS285 3.4 7.6 1.0 OD2 A:ASP287 3.5 10.7 1.0 CG A:HIS285 4.2 7.6 1.0 ND1 B:HIS263 4.3 9.9 1.0 ND1 A:HIS285 4.4 7.6 1.0 CB A:ASP287 4.4 10.7 1.0 CG B:HIS263 4.5 9.9 1.0 CA A:ASP287 4.6 10.7 1.0 CE1 A:HIS250 4.7 10.2 1.0 ND1 A:HIS250 4.7 10.2 1.0

Zinc binding site 5 out of 8 in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:45.3 occ:1.00 OD1 B:ASP287 2.1 9.8 1.0 NE2 A:HIS263 2.3 10.5 1.0 NE2 B:HIS285 2.3 7.5 1.0 CD2 B:HIS285 2.9 7.5 1.0 CG B:ASP287 3.1 9.8 1.0 CE1 A:HIS263 3.1 10.5 1.0 CD2 A:HIS263 3.4 10.5 1.0 CE1 B:HIS285 3.4 7.5 1.0 OD2 B:ASP287 3.5 9.8 1.0 CG B:HIS285 4.2 7.5 1.0 ND1 A:HIS263 4.3 10.5 1.0 ND1 B:HIS285 4.4 7.5 1.0 CB B:ASP287 4.4 9.8 1.0 CG A:HIS263 4.5 10.5 1.0 CA B:ASP287 4.6 9.8 1.0 CE1 B:HIS250 4.7 11.3 1.0 ND1 B:HIS250 4.7 11.3 1.0

Zinc binding site 6 out of 8 in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:43.5 occ:1.00 OD2 B:ASP287 2.1 9.8 1.0 ND1 B:HIS250 2.3 11.3 1.0 NE2 B:HIS234 2.3 13.7 1.0 CB B:HIS250 2.4 11.3 1.0 CE1 B:HIS234 2.4 13.7 1.0 CG B:HIS250 2.6 11.3 1.0 CG B:ASP287 3.2 9.8 1.0 CD2 B:HIS234 3.4 13.7 1.0 ND1 B:HIS234 3.4 13.7 1.0 CE1 B:HIS250 3.6 11.3 1.0 CB B:ASP287 3.8 9.8 1.0 CA B:HIS250 3.8 11.3 1.0 CG B:HIS234 4.0 13.7 1.0 CD2 B:HIS250 4.0 11.3 1.0 O B:HIS250 4.2 11.3 1.0 OD1 B:ASP287 4.2 9.8 1.0 C B:HIS250 4.3 11.3 1.0 NE2 B:HIS250 4.4 11.3 1.0 O B:HIS234 4.7 13.7 1.0 N B:HIS250 4.8 11.3 1.0 CB B:ASP235 4.9 19.1 1.0

Zinc binding site 7 out of 8 in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:62.1 occ:1.00 OD1 B:ASP70 2.1 44.6 1.0 ND1 B:HIS73 2.3 40.3 1.0 NE2 B:HIS77 2.3 38.3 1.0 CE1 B:HIS77 2.8 38.3 1.0 CG B:ASP70 3.0 44.6 1.0 CE1 B:HIS73 3.1 40.3 1.0 OD2 B:ASP70 3.2 44.6 1.0 CG B:HIS73 3.2 40.3 1.0 CD2 B:HIS77 3.6 38.3 1.0 CB B:HIS73 3.6 40.3 1.0 ND1 B:HIS77 4.1 38.3 1.0 NE2 B:HIS73 4.2 40.3 1.0 OH B:TYR64 4.2 40.9 1.0 CD2 B:HIS73 4.3 40.3 1.0 CB B:ASP70 4.4 44.6 1.0 CG B:HIS77 4.5 38.3 1.0 N B:HIS73 4.6 40.3 1.0 CE1 B:TYR64 4.7 40.9 1.0 CA B:HIS73 4.7 40.3 1.0 CZ B:TYR64 4.9 40.9 1.0

Zinc binding site 8 out of 8 in the Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of A Zinc-Loaded Wild-Type Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:63.1 occ:1.00 OD1 B:ASP159 2.1 49.3 1.0 OD1 B:ASP47 2.1 49.4 1.0 OD2 B:ASP51 2.1 45.1 1.0 NE2 B:HIS155 2.3 50.5 1.0 CG B:ASP159 2.8 49.3 1.0 CG B:ASP47 2.8 49.4 1.0 OD2 B:ASP47 2.9 49.4 1.0 CE1 B:HIS155 3.1 50.5 1.0 OD2 B:ASP159 3.2 49.3 1.0 CG B:ASP51 3.3 45.1 1.0 CD2 B:HIS155 3.3 50.5 1.0 OD1 B:ASP51 3.8 45.1 1.0 O B:ASP47 3.8 49.4 1.0 CD1 B:LEU162 3.9 43.6 1.0 CB B:ASP159 4.0 49.3 1.0 ND1 B:HIS155 4.2 50.5 1.0 CB B:ASP47 4.2 49.4 1.0 CG B:HIS155 4.3 50.5 1.0 C B:ASP47 4.4 49.4 1.0 CB B:ASP51 4.5 45.1 1.0 CA B:ASP159 4.6 49.3 1.0 CA B:ASP47 4.7 49.4 1.0 O B:HIS155 4.9 50.5 1.0

M.L.Lopez-Redondo, A.K.Hussein, D.L.Stokes. Characterization of Individual ZN2+ Binding Sites of Yiip To Be Published.