Zinc in PDB 5vrf: Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals

The binding sites of Zinc atom in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals (pdb code 5vrf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals, PDB code: 5vrf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.9 occ:1.00 OD2 B:ASP47 2.1 0.3 1.0 OD2 B:ASP51 2.1 0.1 1.0 NE2 B:HIS155 2.2 0.7 1.0 OD2 B:ASP159 2.5 0.3 1.0 OD1 B:ASP51 2.6 0.1 1.0 CG B:ASP51 2.7 0.1 1.0 CG B:ASP47 2.7 0.3 1.0 OD1 B:ASP159 2.8 0.3 1.0 OD1 B:ASP47 2.8 0.3 1.0 CE1 B:HIS155 2.8 0.7 1.0 CG B:ASP159 2.9 0.3 1.0 CD2 B:HIS155 3.2 0.7 1.0 O B:ASP47 3.7 0.3 1.0 ND1 B:HIS155 3.9 0.7 1.0 CB B:ASP47 4.1 0.3 1.0 CG B:HIS155 4.1 0.7 1.0 CB B:ASP51 4.2 0.1 1.0 C B:ASP47 4.3 0.3 1.0 CB B:ASP159 4.3 0.3 1.0 CA B:ASP47 4.6 0.3 1.0 O B:HIS155 4.8 0.7 1.0 N B:ASP51 5.0 0.1 1.0

Zinc binding site 2 out of 8 in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.9 occ:1.00 NE2 B:HIS77 2.2 0.7 1.0 OD2 B:ASP70 2.3 0.8 1.0 ND1 B:HIS73 2.4 0.1 1.0 CE1 B:HIS77 2.8 0.7 1.0 CE1 B:HIS73 2.9 0.1 1.0 CG B:ASP70 3.1 0.8 1.0 CB B:ASP70 3.3 0.8 1.0 CG B:HIS73 3.4 0.1 1.0 CD2 B:HIS77 3.4 0.7 1.0 NE2 B:HIS73 4.0 0.1 1.0 CB B:HIS73 4.0 0.1 1.0 ND1 B:HIS77 4.1 0.7 1.0 CD2 B:HIS73 4.2 0.1 1.0 OD1 B:ASP70 4.3 0.8 1.0 CG B:HIS77 4.4 0.7 1.0 OH B:TYR64 4.8 0.5 1.0 CA B:ASP70 4.9 0.8 1.0 N B:HIS73 4.9 0.1 1.0

Zinc binding site 3 out of 8 in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:0.9 occ:1.00 OD1 B:ASP287 2.1 0.9 1.0 NE2 A:HIS263 2.2 0.6 1.0 NE2 B:HIS285 2.5 0.3 1.0 CE1 A:HIS263 2.8 0.6 1.0 CD2 B:HIS285 3.1 0.3 1.0 CG B:ASP287 3.2 0.9 1.0 CD2 A:HIS263 3.4 0.6 1.0 CE1 B:HIS285 3.5 0.3 1.0 OD2 B:ASP287 3.8 0.9 1.0 ND1 A:HIS263 4.0 0.6 1.0 CG A:HIS263 4.3 0.6 1.0 CG B:HIS285 4.3 0.3 1.0 O B:GLN286 4.3 0.4 1.0 CB B:ASP287 4.4 0.9 1.0 ND1 B:HIS285 4.5 0.3 1.0 CA B:ASP287 4.5 0.9 1.0 C B:GLN286 4.8 0.4 1.0 N B:ASP287 4.9 0.9 1.0

Zinc binding site 4 out of 8 in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:0.9 occ:1.00 OD2 B:ASP287 2.0 0.9 1.0 NE2 B:HIS234 2.2 0.9 1.0 ND1 B:HIS250 2.3 0.1 1.0 CE1 B:HIS234 2.4 0.9 1.0 CB B:HIS250 2.6 0.1 1.0 CG B:HIS250 2.7 0.1 1.0 CG B:ASP287 3.2 0.9 1.0 OD2 B:ASP235 3.3 0.9 1.0 CE1 B:HIS250 3.4 0.1 1.0 CD2 B:HIS234 3.4 0.9 1.0 ND1 B:HIS234 3.6 0.9 1.0 CD2 B:HIS250 3.8 0.1 1.0 OD1 B:ASP287 3.9 0.9 1.0 CA B:HIS250 4.0 0.1 1.0 CG B:HIS234 4.1 0.9 1.0 NE2 B:HIS250 4.2 0.1 1.0 CB B:ASP287 4.2 0.9 1.0 CG B:ASP235 4.2 0.9 1.0 C B:HIS250 4.5 0.1 1.0 O B:HIS285 4.6 0.3 1.0 CB B:ASP235 4.7 0.9 1.0 O B:HIS250 4.9 0.1 1.0

Zinc binding site 5 out of 8 in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:0.5 occ:1.00 NE2 B:HIS263 2.1 0.6 1.0 OD1 A:ASP287 2.2 0.2 1.0 NE2 A:HIS285 2.3 0.7 1.0 CE1 B:HIS263 2.8 0.6 1.0 CD2 B:HIS263 3.1 0.6 1.0 CD2 A:HIS285 3.1 0.7 1.0 CE1 A:HIS285 3.3 0.7 1.0 CG A:ASP287 3.4 0.2 1.0 ND1 B:HIS263 3.9 0.6 1.0 O A:GLN286 4.0 0.4 1.0 CG B:HIS263 4.0 0.6 1.0 OD2 A:ASP287 4.1 0.2 1.0 CG A:HIS285 4.2 0.7 1.0 ND1 A:HIS285 4.2 0.7 1.0 CA A:ASP287 4.4 0.2 1.0 CB A:ASP287 4.5 0.2 1.0 C A:GLN286 4.5 0.4 1.0 N A:ASP287 4.7 0.2 1.0

Zinc binding site 6 out of 8 in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.5 occ:1.00 OD2 A:ASP47 2.1 0.4 1.0 OD2 A:ASP51 2.1 0.9 1.0 NE2 A:HIS155 2.2 1.0 1.0 OD2 A:ASP159 2.5 0.3 1.0 OD1 A:ASP51 2.6 0.9 1.0 CG A:ASP47 2.7 0.4 1.0 CG A:ASP51 2.7 0.9 1.0 OD1 A:ASP47 2.7 0.4 1.0 OD1 A:ASP159 2.8 0.3 1.0 CE1 A:HIS155 2.8 1.0 1.0 CG A:ASP159 2.9 0.3 1.0 CD2 A:HIS155 3.2 1.0 1.0 O A:ASP47 3.6 0.4 1.0 ND1 A:HIS155 3.9 1.0 1.0 CB A:ASP47 4.1 0.4 1.0 CG A:HIS155 4.1 1.0 1.0 CB A:ASP51 4.2 0.9 1.0 C A:ASP47 4.2 0.4 1.0 CB A:ASP159 4.3 0.3 1.0 CA A:ASP47 4.6 0.4 1.0 O A:HIS155 4.9 1.0 1.0 N A:ASP51 5.0 0.9 1.0

Zinc binding site 7 out of 8 in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:0.5 occ:1.00 ND1 A:HIS73 2.3 0.4 1.0 NE2 A:HIS77 2.3 0.1 1.0 OD2 A:ASP70 2.4 0.1 1.0 CE1 A:HIS73 2.6 0.4 1.0 CE1 A:HIS77 3.1 0.1 1.0 CG A:HIS73 3.4 0.4 1.0 CG A:ASP70 3.4 0.1 1.0 CD2 A:HIS77 3.5 0.1 1.0 CB A:ASP70 3.7 0.1 1.0 NE2 A:HIS73 3.7 0.4 1.0 CD2 A:HIS73 4.1 0.4 1.0 CB A:HIS73 4.1 0.4 1.0 ND1 A:HIS77 4.3 0.1 1.0 CG A:HIS77 4.5 0.1 1.0 OH A:TYR64 4.5 0.0 1.0 OD1 A:ASP70 4.6 0.1 1.0 N A:HIS73 5.0 0.4 1.0

Zinc binding site 8 out of 8 in the Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryoem Structure of the Zinc Transporter Yiip From Helical Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:0.5 occ:1.00 OD2 A:ASP287 2.0 0.2 1.0 NE2 A:HIS234 2.2 0.7 1.0 CE1 A:HIS234 2.3 0.7 1.0 ND1 A:HIS250 2.4 0.5 1.0 CB A:HIS250 2.4 0.5 1.0 CG A:HIS250 2.6 0.5 1.0 CG A:ASP287 3.1 0.2 1.0 OD2 A:ASP235 3.5 0.7 1.0 CD2 A:HIS234 3.5 0.7 1.0 CE1 A:HIS250 3.5 0.5 1.0 ND1 A:HIS234 3.5 0.7 1.0 CA A:HIS250 3.7 0.5 1.0 CD2 A:HIS250 3.8 0.5 1.0 OD1 A:ASP287 3.9 0.2 1.0 CB A:ASP287 4.1 0.2 1.0 CG A:HIS234 4.1 0.7 1.0 NE2 A:HIS250 4.2 0.5 1.0 C A:HIS250 4.2 0.5 1.0 O A:HIS285 4.3 0.7 1.0 CG A:ASP235 4.4 0.7 1.0 O A:HIS250 4.6 0.5 1.0 CB A:ASP235 4.7 0.7 1.0 N A:LEU251 4.8 0.2 1.0 N A:HIS250 4.9 0.5 1.0

M.L.Lopez-Redondo, N.Coudray, Z.Zhang, J.Alexopoulos, D.L.Stokes. Structural Basis For the Alternating Access Mechanism of the Cation Diffusion Facilitator Yiip. Proc. Natl. Acad. Sci. V. 115 3042 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29507252
DOI: 10.1073/PNAS.1715051115