Zinc in PDB 6iu4: Crystal Structure of Iron Transporter VIT1 with Cobalt Ion

The structure of Crystal Structure of Iron Transporter VIT1 with Cobalt Ion, PDB code: 6iu4 was solved by T.Kato, T.Nishizawa, K.Yamashita, R.Taniguchi, K.Kumazaki, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.57 / 3.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.830, 290.770, 45.670, 90.00, 90.00, 90.00
R / Rfree (%)	30.6 / 35.6

The structure of Crystal Structure of Iron Transporter VIT1 with Cobalt Ion also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Iron Transporter VIT1 with Cobalt Ion (pdb code 6iu4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Iron Transporter VIT1 with Cobalt Ion, PDB code: 6iu4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Iron Transporter VIT1 with Cobalt Ion


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 Iron Transporter VIT1 with Cobalt Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.4 occ:1.00 OE1 A:GLU102 2.3 0.6 1.0 CD A:GLU102 3.2 0.3 1.0 OE1 A:GLU105 3.2 0.7 1.0 OE2 A:GLU98 3.5 0.8 1.0 OE2 A:GLU102 3.6 0.1 1.0 ZN A:ZN302 3.7 0.1 1.0 CG A:GLU102 4.3 0.9 1.0 CB A:GLU102 4.4 0.5 1.0 CD A:GLU105 4.4 0.1 1.0 OE2 A:GLU116 4.4 0.1 1.0 CD A:GLU98 4.5 0.0 1.0 OE1 A:GLU116 4.7 0.2 1.0 CA A:GLU102 4.7 0.4 1.0 OE2 A:GLU105 4.8 0.8 1.0 CD A:GLU116 5.0 0.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Iron Transporter VIT1 with Cobalt Ion


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 Iron Transporter VIT1 with Cobalt Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:0.1 occ:1.00 OE2 A:GLU105 2.2 0.8 1.0 CD A:GLU105 2.3 0.1 1.0 OE1 A:GLU105 2.3 0.7 1.0 OE1 A:GLU113 2.5 0.2 1.0 ZN A:ZN303 2.8 0.1 1.0 OE1 A:GLU102 2.9 0.6 1.0 OE2 A:GLU102 3.1 0.1 1.0 CD A:GLU102 3.3 0.3 1.0 OE2 A:GLU116 3.3 0.1 1.0 CG A:GLU105 3.4 0.9 1.0 CD A:GLU113 3.6 0.1 1.0 ZN A:ZN301 3.7 0.4 1.0 CD A:GLU116 3.7 0.8 1.0 OE1 A:GLU116 3.8 0.2 1.0 CB A:GLU105 4.1 0.8 1.0 OE2 A:GLU113 4.3 0.4 1.0 CA A:GLU113 4.4 1.0 1.0 CB A:GLU113 4.5 0.5 1.0 CG A:GLU113 4.6 0.5 1.0 CG A:GLU102 4.6 0.9 1.0 CB A:GLU116 4.7 0.7 1.0 CG A:GLU116 4.8 0.5 1.0 N A:GLU113 4.9 0.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Iron Transporter VIT1 with Cobalt Ion


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 Iron Transporter VIT1 with Cobalt Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:0.1 occ:1.00 OE1 A:GLU116 2.0 0.2 1.0 CE A:MET149 2.3 0.4 1.0 OE2 A:GLU102 2.4 0.1 1.0 CD A:GLU116 2.4 0.8 1.0 ZN A:ZN302 2.8 0.1 1.0 OE1 A:GLU113 2.9 0.2 1.0 CB A:GLU116 3.0 0.7 1.0 CD A:GLU113 3.1 0.1 1.0 OE2 A:GLU116 3.1 0.1 1.0 CG A:GLU116 3.1 0.5 1.0 OE2 A:GLU113 3.2 0.4 1.0 CD A:GLU102 3.4 0.3 1.0 SD A:MET149 3.6 0.4 1.0 O A:GLU113 3.8 0.9 1.0 OE1 A:GLU102 4.0 0.6 1.0 CG A:GLU113 4.0 0.5 1.0 CA A:GLU113 4.1 1.0 1.0 CA A:GLU116 4.4 0.9 1.0 C A:GLU113 4.5 0.6 1.0 CB A:GLU113 4.5 0.5 1.0 CG A:GLU102 4.6 0.9 1.0 OE1 A:GLU153 4.6 0.3 1.0 CG A:MET149 4.7 0.9 1.0 C A:GLU116 4.7 0.2 1.0 OE2 A:GLU105 4.8 0.8 1.0 N A:VAL117 4.8 0.8 1.0 N A:GLU116 5.0 0.1 1.0

T.Kato, K.Kumazaki, M.Wada, R.Taniguchi, T.Nakane, K.Yamashita, K.Hirata, R.Ishitani, K.Ito, T.Nishizawa, O.Nureki. Crystal Structure of Plant Vacuolar Iron Transporter VIT1. Nat Plants V. 5 308 2019.
ISSN: ESSN 2055-0278
PubMed: 30742036
DOI: 10.1038/S41477-019-0367-2