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Iron in PDB 7o67: Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site

Enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site

All present enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site, PDB code: 7o67 was solved by C.Pozzi, S.Ciambellotti, G.Tassone, P.Turano, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.09 / 1.86
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.184, 184.184, 184.184, 90, 90, 90
R / Rfree (%) 17.1 / 22.4

Other elements in 7o67:

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site (pdb code 7o67). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site, PDB code: 7o67:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7o67

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Iron binding site 1 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


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 Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:31.5
occ:0.25
 NE2 A:HIS173 2.2 31.6 1.0
O A:HOH456 2.4 53.3 0.2
CL A:CL211 2.6 41.9 0.2
CE1 A:HIS173 3.1 33.7 1.0
CD2 A:HIS173 3.4 32.9 1.0
ND1 A:HIS173 4.3 34.0 1.0
CG A:HIS173 4.4 31.8 1.0

Iron binding site 2 out of 9 in 7o67

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Iron binding site 2 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


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 Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:29.1
occ:0.85
 OE2 A:GLU27 2.0 30.9 1.0
OE1 A:GLU62 2.0 32.6 1.0
O A:HOH309 2.1 22.0 0.6
ND1 A:HIS65 2.2 35.6 1.0
O A:HOH355 2.3 34.9 1.0
O1 A:OXY201 2.6 27.3 0.6
CD A:GLU62 3.0 31.5 1.0
CD A:GLU27 3.0 27.0 1.0
CE1 A:HIS65 3.1 36.5 1.0
OE2 A:GLU62 3.3 31.2 1.0
CG A:HIS65 3.3 32.8 1.0
FE A:FE2205 3.4 34.7 0.6
OE1 A:GLU27 3.4 26.3 1.0
O2 A:OXY201 3.7 31.2 0.6
CB A:HIS65 3.7 23.6 1.0
OE1 A:GLN141 3.8 42.7 1.0
O A:HOH448 3.9 23.5 0.4
NE2 A:HIS65 4.3 36.8 1.0
CG1 A:VAL110 4.3 26.9 1.0
CG A:GLU27 4.4 24.7 1.0
CG A:GLU62 4.4 23.8 1.0
CD2 A:HIS65 4.4 31.3 1.0
CA A:GLU62 4.6 22.3 1.0
O A:HOH424 4.8 28.0 0.4
CB A:GLU62 4.8 23.6 1.0
CD A:GLN141 4.8 36.7 1.0
CB A:GLU27 4.8 21.9 1.0

Iron binding site 3 out of 9 in 7o67

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Iron binding site 3 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


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 Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:42.3
occ:0.25
 O A:HOH304 2.1 47.5 1.0
O A:HOH340 2.2 38.1 1.0
OD1 A:ASP131 3.4 36.5 1.0
O A:HOH509 3.8 42.5 0.3
OE1 A:GLU134 4.0 42.7 1.0
OG1 A:THR135 4.3 28.9 1.0
CG A:ASP131 4.6 39.5 1.0
CB A:GLU134 4.9 26.6 1.0

Iron binding site 4 out of 9 in 7o67

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Iron binding site 4 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


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 Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:34.7
occ:0.60
 O A:HOH309 1.9 22.0 0.6
OE2 A:GLU62 2.0 31.2 1.0
OE1 A:GLU107 2.1 37.0 1.0
OE2 A:GLU107 2.3 42.9 1.0
O2 A:OXY201 2.4 31.2 0.6
O1 A:OXY201 2.4 27.3 0.6
O A:HOH424 2.4 30.8 0.6
CD A:GLU107 2.5 39.2 1.0
O A:HOH424 2.6 28.0 0.4
CD A:GLU62 3.0 31.5 1.0
FE A:FE2203 3.4 29.1 0.8
OE1 A:GLU62 3.4 32.6 1.0
OE1 A:GLN141 3.6 42.7 1.0
O A:HOH401 3.7 41.8 1.0
CG A:GLU107 4.0 29.4 1.0
NE2 A:GLN141 4.1 38.2 1.0
CD A:GLN141 4.3 36.7 1.0
CE1 A:HIS65 4.3 36.5 1.0
CG A:GLU62 4.3 23.8 1.0
ND1 A:HIS65 4.5 35.6 1.0
CE2 A:TYR34 4.6 30.5 1.0
OH A:TYR34 4.6 41.5 1.0
O A:HOH355 4.7 34.9 1.0
O A:HOH366 4.8 29.7 0.4
CB A:GLU107 4.9 27.1 1.0
OG A:SER144 4.9 35.0 1.0

Iron binding site 5 out of 9 in 7o67

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Iron binding site 5 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


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 Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:39.1
occ:0.40
 O A:HOH432 1.9 22.4 0.5
OE1 A:GLU61 2.0 47.2 0.7
O A:HOH324 2.0 18.0 0.3
O A:HOH408 2.2 39.0 0.5
OE1 A:GLN58 2.3 41.7 1.0
CD A:GLU61 3.1 44.0 0.7
CD A:GLN58 3.2 36.7 1.0
NE2 A:GLN58 3.4 42.2 1.0
OE2 A:GLU61 3.5 50.7 0.7
O A:HOH425 4.1 45.2 1.0
O A:HOH401 4.1 41.8 1.0
OG A:SER144 4.2 35.0 1.0
O A:HOH515 4.3 33.6 0.3
CG A:GLU61 4.4 36.2 0.7
O A:HOH424 4.4 30.8 0.6
O A:HOH428 4.5 56.8 1.0
CG A:GLN58 4.6 30.6 1.0
OE1 A:GLU147 4.6 38.2 1.0
CD2 A:HIS57 4.6 46.2 1.0
O A:HOH366 4.7 29.7 0.4
CG A:GLU61 4.7 24.4 0.3
NE2 A:HIS57 4.8 50.9 1.0
CB A:GLU61 4.8 23.5 0.3
CB A:GLU61 4.9 27.9 0.7
O A:HOH424 4.9 28.0 0.4

Iron binding site 6 out of 9 in 7o67

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Iron binding site 6 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


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 Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:45.8
occ:0.20
 O A:HOH368 2.2 39.1 1.0
O A:HOH449 2.3 51.2 1.0
OE2 A:GLU134 3.7 35.3 1.0
OE1 A:GLU134 4.0 42.7 1.0
O A:HOH519 4.1 38.7 1.0
CD A:GLU134 4.3 34.0 1.0
O A:HOH416 4.4 52.1 1.0

Iron binding site 7 out of 9 in 7o67

Go back to Iron Binding Sites List in 7o67
Iron binding site 7 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


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 Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:85.3
occ:0.30
 OE2 A:GLU61 2.5 50.7 0.7
NE2 A:HIS57 2.5 50.9 1.0
CE1 A:HIS57 3.0 46.6 1.0
O A:HOH455 3.2 38.2 0.4
OE2 A:GLU61 3.3 26.6 0.3
CD A:GLU61 3.4 44.0 0.7
O A:HOH408 3.5 39.0 0.5
CD A:GLU61 3.6 26.2 0.3
CD2 A:HIS57 3.8 46.2 1.0
O A:HOH454 3.9 34.8 0.4
CG A:GLU61 3.9 24.4 0.3
CG A:GLU61 4.0 36.2 0.7
O A:HOH515 4.2 33.6 0.3
OE1 A:GLU61 4.3 47.2 0.7
ND1 A:HIS57 4.3 44.4 1.0
OE1 A:GLU61 4.4 29.0 0.3
O A:HOH526 4.4 32.4 0.4
FE A:FE2210 4.4 62.1 0.3
O A:HOH324 4.6 18.0 0.3
CG A:HIS57 4.7 38.8 1.0

Iron binding site 8 out of 9 in 7o67

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Iron binding site 8 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe209

b:56.0
occ:0.40
 O A:HOH326 2.1 28.2 1.0
O A:HOH314 2.3 26.4 0.5
OD2 A:ASP84 4.1 24.2 1.0
OD1 A:ASP84 4.1 20.1 1.0
CG A:ASP84 4.5 24.2 1.0
O A:HOH378 4.8 20.3 1.0

Iron binding site 9 out of 9 in 7o67

Go back to Iron Binding Sites List in 7o67
Iron binding site 9 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Showing Either A Dioxygen or A Superoxide Anion Coordinated to Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:62.1
occ:0.30
 OE1 A:GLU64 2.1 36.9 0.6
OE1 A:GLU61 2.1 29.0 0.3
O A:HOH526 2.1 32.4 0.4
O A:HOH455 2.3 38.2 0.4
OE2 A:GLU61 2.5 26.6 0.3
CD A:GLU61 2.6 26.2 0.3
CD A:GLU64 3.1 35.8 0.6
O A:HOH454 3.3 34.8 0.4
OE2 A:GLU64 3.5 43.6 0.6
OE2 A:GLU61 4.1 50.7 0.7
CG A:GLU61 4.1 24.4 0.3
CG A:GLU61 4.3 36.2 0.7
FE A:FE2208 4.4 85.3 0.3
CG A:GLU64 4.5 31.0 0.6
O A:HOH532 4.5 34.6 0.6
CD A:GLU61 4.7 44.0 0.7
CB A:GLU64 4.8 26.6 1.0
CB A:GLU61 4.8 23.5 0.3
CA A:GLU61 5.0 24.6 0.7

Reference:

S.Ciambellotti, A.Pratesi, G.Tassone, P.Turano, S.Mangani, C.Pozzi. Iron Binding in the Ferroxidase Site of Human Mitochondrial Ferritin. Chemistry 2021.
ISSN: ISSN 0947-6539
PubMed: 34343376
DOI: 10.1002/CHEM.202102270
Page generated: Thu Aug 8 14:00:33 2024

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