Iron in PDB 6iu9: Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions

The structure of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions, PDB code: 6iu9 was solved by T.Kato, T.Nishizawa, K.Yamashita, 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)	42.66 / 3.00
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	85.321, 85.321, 97.573, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 26.5

The structure of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions also contains other interesting chemical elements:

Zinc

(Zn)

20 atoms

The binding sites of Iron atom in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions (pdb code 6iu9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions, PDB code: 6iu9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:84.6 occ:1.00 OE2 A:GLU153 1.7 81.9 1.0 OE1 A:GLU102 1.8 0.9 1.0 OE2 A:GLU113 2.0 66.8 1.0 OE1 A:GLU116 2.2 56.6 1.0 O A:HOH301 2.4 43.5 1.0 CD A:GLU102 2.8 0.6 1.0 CD A:GLU153 2.9 75.4 1.0 SD A:MET149 2.9 86.0 1.0 CD A:GLU113 3.1 66.9 1.0 OE2 A:GLU102 3.3 0.2 1.0 OE1 A:GLU153 3.4 74.1 1.0 CD A:GLU116 3.4 64.6 1.0 ZN A:ZN203 3.4 73.6 1.0 OE1 A:GLU113 3.5 52.6 1.0 ZN A:ZN201 3.6 87.1 1.0 CG A:MET149 3.8 79.0 1.0 CB A:MET149 3.8 71.5 1.0 OE2 A:GLU116 4.1 62.2 1.0 CG A:GLU153 4.1 63.4 1.0 CG A:GLU102 4.1 100.0 1.0 CE A:MET149 4.2 95.1 1.0 OE2 A:GLU105 4.2 84.3 1.0 CG A:GLU113 4.4 59.4 1.0 CB A:GLU153 4.5 68.5 1.0 CB A:GLU116 4.5 53.0 1.0 CG A:GLU116 4.5 62.9 1.0 O D:GLY87 4.8 61.1 1.0 CB A:GLU113 4.8 61.2 1.0 CA A:GLU113 4.9 64.5 1.0 CA A:MET149 4.9 72.1 1.0

Iron binding site 2 out of 7 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:88.2 occ:1.00 OE1 B:GLU153 1.7 0.0 1.0 OE1 B:GLU113 1.8 0.6 1.0 OE2 B:GLU116 1.9 72.3 1.0 OE2 B:GLU102 2.1 93.7 1.0 O B:HOH301 2.3 54.4 1.0 CD B:GLU153 2.7 0.0 1.0 CD B:GLU113 2.7 0.6 1.0 CD B:GLU116 3.0 77.2 1.0 OE2 B:GLU113 3.0 0.1 1.0 OE2 B:GLU153 3.2 0.7 1.0 CD B:GLU102 3.2 0.6 1.0 OE1 B:GLU116 3.5 74.2 1.0 ZN B:ZN201 3.6 86.5 1.0 ZN B:ZN203 3.6 95.8 1.0 OE1 B:GLU102 3.8 0.6 1.0 SD B:MET149 4.0 0.3 1.0 CG B:GLU153 4.1 0.4 1.0 CG B:MET149 4.1 0.3 1.0 CG B:GLU113 4.2 97.9 1.0 CG B:GLU116 4.3 79.9 1.0 CB B:MET149 4.3 0.1 1.0 OE2 B:GLU105 4.4 74.4 1.0 CG B:GLU102 4.4 0.9 1.0 CB B:GLU116 4.5 83.0 1.0 CB B:GLU153 4.5 0.9 1.0 CB B:GLU113 4.7 95.2 1.0 OE1 B:GLU105 4.7 61.4 1.0 CD B:GLU105 4.7 76.7 1.0 NE2 C:HIS89 4.8 1.0 1.0 O C:GLY87 4.9 0.4 1.0 CA B:GLU113 4.9 92.7 1.0

Iron binding site 3 out of 7 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:0.2 occ:1.00 OE2 C:GLU153 1.9 0.1 1.0 O C:HOH301 2.0 55.8 1.0 OE1 C:GLU102 2.2 81.4 1.0 OE2 C:GLU113 2.3 0.6 1.0 OE1 C:GLU116 2.4 83.5 1.0 SD C:MET149 2.6 0.5 1.0 CD C:GLU153 2.7 0.3 1.0 OE1 C:GLU153 3.0 0.1 1.0 CD C:GLU102 3.1 85.8 1.0 ZN B:ZN205 3.2 90.5 1.0 CD C:GLU113 3.4 0.3 1.0 OE2 C:GLU102 3.4 81.5 1.0 ZN B:ZN206 3.6 0.5 1.0 CD C:GLU116 3.6 91.7 1.0 OE1 C:GLU113 3.8 99.3 1.0 CB C:MET149 3.8 98.0 1.0 CG C:MET149 3.9 0.4 1.0 CG C:GLU153 4.2 0.2 1.0 CE C:MET149 4.2 0.0 1.0 OE2 C:GLU116 4.2 81.6 1.0 OE2 C:GLU105 4.3 88.5 1.0 O B:GLY87 4.3 82.6 1.0 CG C:GLU102 4.5 0.6 1.0 CG C:GLU113 4.6 95.3 1.0 CB C:GLU153 4.7 0.9 1.0 CG C:GLU116 4.7 90.4 1.0 CB C:GLU116 4.8 93.8 1.0 CD C:GLU105 4.9 0.5 1.0

Iron binding site 4 out of 7 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:66.6 occ:1.00 O D:HOH301 1.9 35.9 1.0 OE2 D:GLU102 1.9 82.0 1.0 OE2 D:GLU153 2.0 59.8 1.0 OE2 D:GLU116 2.0 56.0 1.0 OE1 D:GLU113 2.0 59.8 1.0 CD D:GLU153 2.8 65.1 1.0 SD D:MET149 2.8 84.8 1.0 OE1 D:GLU153 2.9 68.2 1.0 CD D:GLU113 3.0 57.1 1.0 CD D:GLU102 3.0 88.5 1.0 CD D:GLU116 3.1 75.0 1.0 OE2 D:GLU113 3.3 53.8 1.0 ZN A:ZN205 3.3 72.6 1.0 ZN A:ZN204 3.5 95.5 1.0 OE1 D:GLU102 3.6 0.8 1.0 OE1 D:GLU116 3.6 88.6 1.0 CE D:MET149 3.7 73.5 1.0 CG D:MET149 4.1 84.6 1.0 OE1 D:GLU105 4.1 95.7 1.0 CG D:GLU153 4.2 71.7 1.0 CG D:GLU102 4.3 85.1 1.0 CB D:MET149 4.3 70.0 1.0 CG D:GLU113 4.3 59.7 1.0 CG D:GLU116 4.4 66.9 1.0 CB D:GLU116 4.5 67.0 1.0 CB D:GLU113 4.7 70.2 1.0 O A:GLY87 4.8 73.5 1.0 CA D:GLU113 4.8 83.5 1.0 CB D:GLU153 4.8 70.9 1.0 NE2 A:HIS89 4.9 94.2 1.0

Iron binding site 5 out of 7 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe202 b:0.6 occ:1.00 OE2 E:GLU113 1.9 94.7 1.0 O E:HOH301 1.9 63.1 1.0 OE1 E:GLU102 2.0 92.8 1.0 OE2 E:GLU153 2.1 0.9 1.0 OE1 E:GLU116 2.3 94.5 1.0 CD E:GLU102 2.9 87.2 1.0 CD E:GLU113 3.0 82.4 1.0 CD E:GLU153 3.0 89.0 1.0 OE2 E:GLU102 3.1 73.7 1.0 SD E:MET149 3.1 1.0 1.0 OE1 E:GLU153 3.3 76.1 1.0 CD E:GLU116 3.5 86.9 1.0 OE1 E:GLU113 3.5 76.4 1.0 ZN E:ZN203 3.7 80.3 1.0 ZN E:ZN201 3.7 0.3 1.0 CB E:MET149 3.9 85.3 1.0 CG E:MET149 4.0 93.4 1.0 OE2 E:GLU116 4.1 74.6 1.0 CG E:GLU102 4.2 81.7 1.0 CG E:GLU113 4.3 73.8 1.0 OE1 E:GLU105 4.4 82.8 1.0 CE E:MET149 4.4 0.0 1.0 CG E:GLU153 4.4 94.7 1.0 CB E:GLU113 4.6 77.0 1.0 CG E:GLU116 4.6 79.8 1.0 CB E:GLU116 4.8 73.6 1.0 CA E:GLU113 4.8 78.9 1.0 CB E:GLU153 4.9 89.5 1.0

Iron binding site 6 out of 7 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe202 b:73.8 occ:1.00 OE2 F:GLU102 1.8 0.8 1.0 OE1 F:GLU153 1.9 87.1 1.0 SD F:MET149 1.9 0.7 1.0 OE1 F:GLU113 2.1 70.7 1.0 O F:HOH301 2.1 24.9 1.0 OE2 F:GLU116 2.3 34.8 1.0 CD F:GLU153 2.7 83.8 1.0 CE F:MET149 2.8 0.2 1.0 OE2 F:GLU153 2.9 81.2 1.0 CG F:MET149 2.9 0.6 1.0 CD F:GLU113 3.0 68.5 1.0 CD F:GLU102 3.0 90.4 1.0 OE2 F:GLU113 3.2 56.0 1.0 CD F:GLU116 3.4 57.8 1.0 ZN F:ZN201 3.5 0.3 1.0 OE1 F:GLU102 3.6 77.4 1.0 ZN F:ZN203 3.7 89.9 1.0 OE1 F:GLU116 3.9 56.5 1.0 CG F:GLU153 4.1 91.9 1.0 CG F:GLU102 4.1 0.6 1.0 CB F:MET149 4.2 0.6 1.0 CG F:GLU113 4.3 80.1 1.0 OE2 F:GLU105 4.5 82.5 1.0 CB F:GLU153 4.6 81.1 1.0 CG F:GLU116 4.6 57.0 1.0 O I:GLY87 4.7 0.5 1.0 OE1 F:GLU105 4.7 98.5 1.0 CB F:GLU116 4.7 61.8 1.0 CB F:GLU113 4.7 92.3 1.0 CD F:GLU105 4.8 98.0 1.0 CA F:GLU113 4.8 99.6 1.0

Iron binding site 7 out of 7 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Cytoplasmic Metal Binding Domain with Iron Ions within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe201 b:89.3 occ:1.00 O H:HOH301 1.9 62.6 1.0 OE1 H:GLU102 2.0 76.7 1.0 OE2 H:GLU113 2.0 79.9 1.0 OE2 H:GLU153 2.1 80.1 1.0 OE1 H:GLU116 2.2 61.3 1.0 SD H:MET149 2.9 95.5 1.0 CD H:GLU102 3.0 92.8 1.0 CD H:GLU113 3.1 75.7 1.0 CD H:GLU153 3.1 92.3 1.0 CD H:GLU116 3.4 58.6 1.0 ZN E:ZN204 3.4 95.1 1.0 CG H:MET149 3.4 88.8 1.0 OE1 H:GLU153 3.4 95.7 1.0 OE2 H:GLU102 3.5 0.2 1.0 OE1 H:GLU113 3.5 77.6 1.0 CB H:MET149 3.7 83.5 1.0 ZN H:ZN202 3.9 77.3 1.0 OE2 H:GLU116 4.0 54.4 1.0 CE H:MET149 4.0 0.2 1.0 CG H:GLU102 4.3 0.6 1.0 CG H:GLU113 4.3 64.0 1.0 CG H:GLU153 4.4 91.1 1.0 CG H:GLU116 4.6 58.0 1.0 CB H:GLU113 4.7 55.7 1.0 CB H:GLU116 4.7 55.1 1.0 CB H:GLU153 4.8 87.2 1.0 OE2 H:GLU105 4.8 58.4 1.0 CA H:GLU113 4.8 67.0 1.0 CA H:MET149 4.8 73.4 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