Zinc in PDB 8f6f: Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the Yiip-Fab Complex

The binding sites of Zinc atom in the Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the Yiip-Fab Complex (pdb code 8f6f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the Yiip-Fab Complex, PDB code: 8f6f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the 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 D51A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:47.3 occ:1.00 OD2 A:ASP287 2.1 25.9 1.0 NE2 A:HIS234 2.3 29.0 1.0 ND1 A:HIS250 2.3 24.8 1.0 CE1 A:HIS234 2.4 29.0 1.0 CG A:HIS250 3.0 24.8 1.0 CB A:HIS250 3.0 24.8 1.0 CG A:ASP287 3.0 25.9 1.0 CE1 A:HIS250 3.4 24.8 1.0 CD2 A:HIS234 3.6 29.0 1.0 ND1 A:HIS234 3.7 29.0 1.0 CB A:ASP287 3.8 25.9 1.0 OD1 A:ASP287 3.9 25.9 1.0 CD2 A:HIS250 4.2 24.8 1.0 CG A:HIS234 4.2 29.0 1.0 NE2 A:HIS250 4.4 24.8 1.0 CA A:HIS250 4.4 24.8 1.0 ZN A:ZN303 4.4 50.8 1.0 CD2 A:HIS285 4.6 22.8 1.0 C A:HIS250 4.9 24.8 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the 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 D51A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:76.1 occ:1.00 NE2 A:HIS77 2.3 64.3 1.0 ND1 A:HIS73 2.3 64.3 1.0 OD2 A:ASP70 2.4 67.2 1.0 CE1 A:HIS77 2.6 64.3 1.0 CE1 A:HIS73 3.0 64.3 1.0 OD1 A:ASP70 3.0 67.2 1.0 CG A:ASP70 3.1 67.2 1.0 CB A:ASP72 3.4 65.5 1.0 CG A:HIS73 3.5 64.3 1.0 CD2 A:HIS77 3.6 64.3 1.0 OH A:TYR64 3.7 72.5 1.0 ND1 A:HIS77 3.9 64.3 1.0 N A:HIS73 4.0 64.3 1.0 CG A:ASP72 4.0 65.5 1.0 CB A:HIS73 4.0 64.3 1.0 OD1 A:ASP72 4.1 65.5 1.0 NE2 A:HIS73 4.2 64.3 1.0 CA A:ASP72 4.4 65.5 1.0 CG A:HIS77 4.4 64.3 1.0 C A:ASP72 4.4 65.5 1.0 CD2 A:HIS73 4.5 64.3 1.0 CB A:ASP70 4.5 67.2 1.0 CA A:HIS73 4.7 64.3 1.0 N A:ASP72 4.7 65.5 1.0 CZ A:TYR64 4.8 72.5 1.0 OD2 A:ASP72 4.9 65.5 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the 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 D51A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:50.8 occ:1.00 OD1 A:ASP287 2.1 25.9 1.0 NE2 B:HIS263 2.3 24.5 1.0 NE2 A:HIS285 2.3 22.8 1.0 CG A:ASP287 2.9 25.9 1.0 CE1 A:HIS285 3.1 22.8 1.0 OD2 A:ASP287 3.1 25.9 1.0 CD2 A:HIS285 3.2 22.8 1.0 CE1 B:HIS263 3.2 24.5 1.0 CD2 B:HIS263 3.3 24.5 1.0 ND1 A:HIS285 4.1 22.8 1.0 CG A:HIS285 4.2 22.8 1.0 CB A:ASP287 4.3 25.9 1.0 ND1 B:HIS263 4.4 24.5 1.0 CG B:HIS263 4.4 24.5 1.0 ZN A:ZN301 4.4 47.3 1.0 CA A:ASP287 4.8 25.9 1.0 CE1 A:HIS250 4.9 24.8 1.0 ND1 A:HIS250 4.9 24.8 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the 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 D51A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:49.2 occ:1.00 OD1 B:ASP287 2.0 25.8 1.0 NE2 A:HIS263 2.3 23.4 1.0 NE2 B:HIS285 2.3 22.5 1.0 CG B:ASP287 3.0 25.8 1.0 CE1 B:HIS285 3.1 22.5 1.0 CD2 B:HIS285 3.1 22.5 1.0 OD2 B:ASP287 3.2 25.8 1.0 CE1 A:HIS263 3.3 23.4 1.0 CD2 A:HIS263 3.3 23.4 1.0 ND1 B:HIS285 4.1 22.5 1.0 CG B:HIS285 4.1 22.5 1.0 CB B:ASP287 4.4 25.8 1.0 ND1 A:HIS263 4.4 23.4 1.0 CG A:HIS263 4.4 23.4 1.0 ZN B:ZN302 4.5 45.7 1.0 CA B:ASP287 4.7 25.8 1.0 CE1 B:HIS250 4.9 24.8 1.0 ND1 B:HIS250 4.9 24.8 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the 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 D51A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:45.7 occ:1.00 OD2 B:ASP287 2.0 25.8 1.0 NE2 B:HIS234 2.3 30.1 1.0 ND1 B:HIS250 2.3 24.8 1.0 CE1 B:HIS234 2.5 30.1 1.0 CG B:HIS250 3.1 24.8 1.0 CG B:ASP287 3.1 25.8 1.0 CB B:HIS250 3.1 24.8 1.0 CE1 B:HIS250 3.4 24.8 1.0 CD2 B:HIS234 3.6 30.1 1.0 ND1 B:HIS234 3.7 30.1 1.0 CB B:ASP287 3.8 25.8 1.0 OD1 B:ASP287 3.9 25.8 1.0 CG B:HIS234 4.2 30.1 1.0 CD2 B:HIS250 4.3 24.8 1.0 NE2 B:HIS250 4.4 24.8 1.0 ZN B:ZN301 4.5 49.2 1.0 CA B:HIS250 4.6 24.8 1.0 CD2 B:HIS285 4.7 22.5 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of A Zinc-Loaded D51A Mutant of the 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 D51A Mutant of the Yiip-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:75.2 occ:1.00 NE2 B:HIS77 2.3 65.3 1.0 ND1 B:HIS73 2.3 64.5 1.0 OD2 B:ASP70 2.3 67.2 1.0 CE1 B:HIS77 2.5 65.3 1.0 OD1 B:ASP70 2.9 67.2 1.0 CG B:ASP70 2.9 67.2 1.0 CE1 B:HIS73 3.0 64.5 1.0 CB B:ASP72 3.4 66.0 1.0 CG B:HIS73 3.5 64.5 1.0 CD2 B:HIS77 3.6 65.3 1.0 OH B:TYR64 3.8 75.1 1.0 ND1 B:HIS77 3.8 65.3 1.0 N B:HIS73 4.0 64.5 1.0 CB B:HIS73 4.0 64.5 1.0 OD2 B:ASP72 4.1 66.0 1.0 NE2 B:HIS73 4.2 64.5 1.0 CG B:ASP72 4.3 66.0 1.0 CG B:HIS77 4.4 65.3 1.0 CA B:ASP72 4.4 66.0 1.0 CB B:ASP70 4.4 67.2 1.0 C B:ASP72 4.5 66.0 1.0 CD2 B:HIS73 4.5 64.5 1.0 CA B:HIS73 4.7 64.5 1.0 N B:ASP72 4.7 66.0 1.0 CZ B:TYR64 4.8 75.1 1.0

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