Nickel in PDB 6iu6: Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions

The structure of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions, PDB code: 6iu6 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)	42.37 / 2.90
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	84.744, 84.744, 97.398, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 21.1

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

Zinc

(Zn)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Nickel atom in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions (pdb code 6iu6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 22 binding sites of Nickel where determined in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions, PDB code: 6iu6:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:61.8 occ:1.00 OE2 A:GLU113 1.7 45.6 1.0 OE2 A:GLU153 1.9 59.3 1.0 OE1 A:GLU116 1.9 57.5 1.0 O A:HOH301 2.0 47.1 1.0 OE1 A:GLU102 2.1 47.2 1.0 CD A:GLU113 2.7 40.9 1.0 CD A:GLU153 2.9 65.7 1.0 CE A:MET149 3.0 71.1 1.0 CD A:GLU102 3.0 55.4 1.0 OE1 A:GLU113 3.1 38.0 1.0 SD A:MET149 3.1 60.6 1.0 CD A:GLU116 3.1 59.6 1.0 OE1 A:GLU153 3.3 55.6 1.0 ZN A:ZN201 3.3 78.4 1.0 NI A:NI203 3.3 61.9 1.0 OE2 A:GLU102 3.4 50.7 1.0 OE2 A:GLU116 3.6 58.8 1.0 CG A:GLU113 4.0 45.9 1.0 CG A:GLU153 4.2 69.0 1.0 CG A:GLU116 4.3 59.8 1.0 CB A:MET149 4.3 71.6 1.0 CG A:MET149 4.4 73.0 1.0 CG A:GLU102 4.4 55.0 1.0 CB A:GLU116 4.4 55.5 1.0 OE2 A:GLU105 4.5 70.2 1.0 CB A:GLU113 4.5 51.5 1.0 CB A:GLU153 4.7 68.8 1.0 O D:GLY87 4.7 77.2 1.0 CA A:GLU113 4.8 55.7 1.0 NE2 D:HIS89 5.0 72.7 1.0

Nickel binding site 2 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:61.9 occ:1.00 OE1 A:GLU113 1.9 38.0 1.0 OE2 A:GLU116 2.0 58.8 1.0 O A:HOH301 2.1 47.1 1.0 O D:GLY87 2.1 77.2 1.0 N D:GLY87 2.4 93.4 1.0 CD A:GLU116 2.8 59.6 1.0 OE1 A:GLU105 2.8 65.7 1.0 C D:GLY87 2.9 86.4 1.0 OE1 A:GLU116 2.9 57.5 1.0 CD A:GLU113 3.0 40.9 1.0 CA D:GLY87 3.0 82.8 1.0 NI A:NI202 3.3 61.8 1.0 CD A:GLU105 3.4 70.0 1.0 OE2 A:GLU113 3.4 45.6 1.0 ZN A:ZN201 3.5 78.4 1.0 OE2 A:GLU105 3.5 70.2 1.0 OE1 A:GLU153 4.1 55.6 1.0 CG A:GLU116 4.2 59.8 1.0 N D:SER88 4.2 95.5 1.0 CG A:GLU113 4.2 45.9 1.0 CG A:GLU105 4.5 67.5 1.0 OE2 A:GLU153 4.5 59.3 1.0 NE2 D:HIS89 4.6 72.7 1.0 CB A:GLU105 4.6 62.5 1.0 OE2 A:GLU102 4.7 50.7 1.0 CD A:GLU153 4.7 65.7 1.0 CD2 D:HIS89 4.7 68.0 1.0 OE1 A:GLU102 4.8 47.2 1.0

Nickel binding site 3 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni204 b:98.8 occ:1.00 NE2 A:HIS129 2.0 89.9 1.0 OE2 A:GLU127 2.4 0.2 1.0 CE1 A:HIS129 2.6 82.4 1.0 CD2 A:HIS129 3.2 81.9 1.0 OE1 A:GLU130 3.5 73.3 1.0 CD A:GLU127 3.6 0.2 1.0 ND1 A:HIS129 3.8 81.4 1.0 CG A:GLU127 4.1 0.4 1.0 CG A:HIS129 4.2 71.7 1.0 CD A:GLU130 4.2 73.5 1.0 OE1 A:GLU127 4.6 0.7 1.0 CB A:GLU127 4.6 0.4 1.0 CG A:GLU130 4.8 68.6 1.0 OE2 A:GLU130 4.9 62.4 1.0

Nickel binding site 4 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni206 b:64.3 occ:1.00 OE1 D:GLU116 1.8 73.8 1.0 OE2 D:GLU113 1.9 45.0 1.0 O D:HOH301 1.9 44.6 1.0 N A:GLY87 2.1 74.3 1.0 O A:GLY87 2.3 85.7 1.0 OE1 D:GLU105 2.5 56.5 1.0 CD D:GLU116 2.6 71.1 1.0 CA A:GLY87 2.7 78.1 1.0 CD D:GLU113 2.8 50.2 1.0 OE2 D:GLU116 2.9 61.5 1.0 C A:GLY87 2.9 83.2 1.0 OE1 D:GLU113 3.1 64.4 1.0 NI D:NI201 3.2 58.5 1.0 ZN A:ZN205 3.3 63.9 1.0 OE1 D:GLU153 3.6 60.1 1.0 CD D:GLU105 3.6 67.7 1.0 CG D:GLU116 4.0 64.1 1.0 N A:SER88 4.2 85.4 1.0 CG D:GLU113 4.2 42.6 1.0 NE2 A:HIS89 4.2 79.8 1.0 CG D:GLU105 4.4 71.8 1.0 CD D:GLU153 4.5 65.3 1.0 CD2 A:HIS89 4.5 87.2 1.0 OE2 D:GLU102 4.5 64.2 1.0 OE2 D:GLU153 4.6 66.9 1.0 OE2 D:GLU105 4.6 73.5 1.0 CB D:GLU105 4.8 62.3 1.0 CA D:GLU113 5.0 59.7 1.0

Nickel binding site 5 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni203 b:61.0 occ:1.00 O C:HOH301 1.7 64.7 1.0 OE2 B:GLU113 1.9 62.2 1.0 N C:GLY87 2.0 67.5 1.0 OE1 B:GLU116 2.1 83.4 1.0 O C:GLY87 2.3 53.5 1.0 OE1 B:GLU105 2.6 55.4 1.0 CA C:GLY87 2.9 70.0 1.0 C C:GLY87 3.0 62.0 1.0 CD B:GLU116 3.0 71.0 1.0 CD B:GLU113 3.0 72.1 1.0 CD B:GLU105 3.1 69.7 1.0 OE2 B:GLU116 3.1 66.8 1.0 ZN B:ZN202 3.2 69.9 1.0 ZN B:ZN201 3.4 70.7 1.0 OE1 B:GLU113 3.6 70.7 1.0 OE2 B:GLU105 3.7 71.9 1.0 CG B:GLU105 3.9 66.6 1.0 OE2 B:GLU153 4.0 87.1 1.0 CB B:GLU105 4.2 69.9 1.0 CG B:GLU113 4.2 71.6 1.0 N C:SER88 4.3 64.2 1.0 OE2 B:GLU102 4.4 73.0 1.0 CG B:GLU116 4.4 64.2 1.0 NE2 C:HIS89 4.5 70.9 1.0 CD2 C:HIS89 4.6 81.0 1.0 OE1 B:GLU153 4.6 70.0 1.0 CG2 B:THR112 4.7 80.9 1.0 CD B:GLU153 4.8 69.5 1.0

Nickel binding site 6 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni205 b:86.3 occ:1.00 NE2 B:HIS129 2.2 91.7 1.0 CE1 B:HIS129 2.8 90.8 1.0 OE1 B:GLU130 3.4 70.7 1.0 CD2 B:HIS129 3.4 91.4 1.0 ND1 B:HIS129 4.1 93.7 1.0 CD B:GLU130 4.3 70.0 1.0 CG B:HIS129 4.4 91.1 1.0 CG B:GLU130 4.7 61.8 1.0 CB B:GLU127 4.9 67.2 1.0 CG B:GLU127 5.0 78.8 1.0

Nickel binding site 7 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni208 b:69.0 occ:1.00 O C:HOH302 1.8 40.2 1.0 OE1 C:GLU113 1.9 58.5 1.0 N B:GLY87 2.1 70.9 1.0 OE2 C:GLU116 2.2 56.6 1.0 O B:GLY87 2.2 58.8 1.0 CA B:GLY87 2.6 63.0 1.0 C B:GLY87 2.7 73.0 1.0 OE1 C:GLU116 2.7 44.1 1.0 CD C:GLU116 2.7 56.2 1.0 CD C:GLU113 2.9 64.1 1.0 NI C:NI201 3.1 54.5 1.0 ZN B:ZN207 3.1 70.8 1.0 OE1 C:GLU105 3.2 83.8 1.0 OE2 C:GLU113 3.4 67.2 1.0 OE1 C:GLU153 3.4 60.5 1.0 CD C:GLU105 3.8 85.4 1.0 NE2 B:HIS89 3.8 64.9 1.0 N B:SER88 3.8 99.0 1.0 CG C:GLU116 4.2 55.5 1.0 OE2 C:GLU105 4.2 86.1 1.0 CD2 B:HIS89 4.2 79.2 1.0 CG C:GLU113 4.3 52.3 1.0 CD C:GLU153 4.4 77.9 1.0 OE2 C:GLU153 4.4 81.8 1.0 OE2 C:GLU102 4.5 55.0 1.0 CG C:GLU105 4.6 65.9 1.0 CB C:GLU105 4.6 72.8 1.0 CG2 C:THR112 4.7 75.6 1.0 OE1 C:GLU102 4.7 57.9 1.0 CA C:GLU113 4.8 55.6 1.0 CA B:SER88 4.9 99.5 1.0

Nickel binding site 8 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni201 b:54.5 occ:1.00 OE2 C:GLU113 2.0 67.2 1.0 OE2 C:GLU153 2.1 81.8 1.0 OE1 C:GLU102 2.2 57.9 1.0 OE1 C:GLU116 2.3 44.1 1.0 O C:HOH302 2.4 40.2 1.0 SD C:MET149 2.4 79.7 1.0 CD C:GLU153 2.8 77.9 1.0 CD C:GLU113 2.9 64.1 1.0 OE1 C:GLU153 2.9 60.5 1.0 ZN B:ZN207 3.0 70.8 1.0 NI B:NI208 3.1 69.0 1.0 CD C:GLU102 3.1 63.5 1.0 OE1 C:GLU113 3.1 58.5 1.0 OE2 C:GLU102 3.3 55.0 1.0 CD C:GLU116 3.5 56.2 1.0 CE C:MET149 3.8 99.4 1.0 CG C:MET149 3.9 82.2 1.0 OE2 C:GLU116 4.0 56.6 1.0 CB C:MET149 4.1 74.6 1.0 CG C:GLU153 4.2 84.9 1.0 CG C:GLU113 4.3 52.3 1.0 OE2 C:GLU105 4.5 86.1 1.0 NE2 B:HIS89 4.5 64.9 1.0 CG C:GLU102 4.5 69.0 1.0 O B:GLY87 4.6 58.8 1.0 CG C:GLU116 4.7 55.5 1.0 CB C:GLU153 4.8 79.7 1.0 CB C:GLU113 4.8 54.5 1.0 CB C:GLU116 4.8 50.5 1.0 CA C:GLU113 4.8 55.6 1.0 CD C:GLU105 4.9 85.4 1.0 OE1 C:GLU105 5.0 83.8 1.0 N B:GLY87 5.0 70.9 1.0

Nickel binding site 9 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni202 b:81.2 occ:1.00 OE2 C:GLU127 1.6 72.3 1.0 NE2 C:HIS129 2.0 87.7 1.0 CD C:GLU127 2.8 81.5 1.0 CE1 C:HIS129 2.8 80.6 1.0 CD2 C:HIS129 3.2 82.9 1.0 OE1 C:GLU127 3.4 75.7 1.0 CG C:GLU127 4.0 81.2 1.0 ND1 C:HIS129 4.0 76.4 1.0 OE1 C:GLU130 4.0 70.5 1.0 CG C:HIS129 4.2 72.7 1.0 CD C:GLU130 4.7 63.1 1.0

Nickel binding site 10 out of 22 in the Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of Cytoplasmic Metal Binding Domain with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni201 b:58.5 occ:1.00 OE1 D:GLU113 1.8 64.4 1.0 OE2 D:GLU102 1.9 64.2 1.0 OE2 D:GLU153 2.0 66.9 1.0 OE2 D:GLU116 2.1 61.5 1.0 O D:HOH301 2.2 44.6 1.0 SD D:MET149 2.6 77.4 1.0 CD D:GLU153 2.7 65.3 1.0 CD D:GLU113 2.8 50.2 1.0 OE1 D:GLU153 2.8 60.1 1.0 CD D:GLU102 3.0 72.1 1.0 ZN A:ZN205 3.0 63.9 1.0 NI A:NI206 3.2 64.3 1.0 CD D:GLU116 3.2 71.1 1.0 OE2 D:GLU113 3.3 45.0 1.0 CE D:MET149 3.4 67.7 1.0 OE1 D:GLU102 3.6 65.4 1.0 OE1 D:GLU116 3.7 73.8 1.0 OE1 D:GLU105 3.7 56.5 1.0 CG D:MET149 3.9 60.8 1.0 CG D:GLU113 4.1 42.6 1.0 CB D:MET149 4.1 57.9 1.0 CG D:GLU102 4.2 68.3 1.0 CG D:GLU153 4.2 67.5 1.0 NE2 A:HIS89 4.5 79.8 1.0 CG D:GLU116 4.5 64.1 1.0 O A:GLY87 4.6 85.7 1.0 CB D:GLU116 4.6 65.4 1.0 CB D:GLU113 4.7 48.3 1.0 CD D:GLU105 4.7 67.7 1.0 CB D:GLU153 4.8 63.9 1.0 CA D:GLU113 4.9 59.7 1.0 CD2 A:HIS89 4.9 87.2 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