Atomistry » Iron » PDB 6i95-6j55 » 6iu9
Atomistry »
  Iron »
    PDB 6i95-6j55 »
      6iu9 »

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

Protein crystallography data

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

Other elements in 6iu9:

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

Zinc (Zn) 20 atoms

Iron Binding Sites:

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 6iu9

Go back to Iron Binding Sites List in 6iu9
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 6iu9

Go back to Iron Binding Sites List in 6iu9
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 6iu9

Go back to Iron Binding Sites List in 6iu9
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 6iu9

Go back to Iron Binding Sites List in 6iu9
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 6iu9

Go back to Iron Binding Sites List in 6iu9
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 6iu9

Go back to Iron Binding Sites List in 6iu9
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 6iu9

Go back to Iron Binding Sites List in 6iu9
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

Reference:

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
Page generated: Tue Aug 6 23:10:00 2024

Last articles

Ca in 5VCO
Ca in 5VCN
Ca in 5VC1
Ca in 5VA9
Ca in 5VBJ
Ca in 5VAO
Ca in 5V8K
Ca in 5V6V
Ca in 5V2C
Ca in 5V4D
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy