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Iron in PDB 7o69: Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site

Enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site

All present enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site, PDB code: 7o69 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) 91.94 / 1.35
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.873, 183.873, 183.873, 90, 90, 90
R / Rfree (%) 13.4 / 15.3

Other elements in 7o69:

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site (pdb code 7o69). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site, PDB code: 7o69:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 7o69

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Iron binding site 1 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:11.1
occ:0.85
 O1 A:PEO210 1.9 15.2 0.5
OE1 A:GLU62 2.0 15.8 1.0
OE1 A:GLU27 2.0 11.2 1.0
O A:HOH373 2.1 14.9 0.8
ND1 A:HIS65 2.2 14.2 0.8
ND1 A:HIS65 2.3 8.4 0.1
O2 A:PEO210 2.5 15.5 0.5
O A:HOH495 2.8 8.9 0.5
CD A:GLU62 3.0 12.5 1.0
CD A:GLU27 3.1 10.0 1.0
CE1 A:HIS65 3.1 15.0 0.8
CE1 A:HIS65 3.3 8.4 0.1
CG A:HIS65 3.3 13.7 0.8
CG A:HIS65 3.3 8.4 0.1
OE2 A:GLU62 3.4 14.6 1.0
FE A:FE2202 3.4 14.7 0.5
OE2 A:GLU27 3.4 11.7 1.0
CB A:HIS65 3.6 9.8 0.1
CB A:HIS65 3.7 11.7 0.8
OE1 A:GLN141 3.8 24.2 1.0
O A:HOH517 4.0 22.5 0.8
CG1 A:VAL110 4.2 17.9 1.0
NE2 A:HIS65 4.2 14.8 0.8
CG A:GLU62 4.4 10.9 1.0
CD2 A:HIS65 4.4 14.2 0.8
CG A:GLU27 4.4 9.7 1.0
NE2 A:HIS65 4.4 8.4 0.1
CD2 A:HIS65 4.4 8.4 0.1
O A:HOH466 4.5 5.0 0.2
CA A:GLU62 4.6 8.8 1.0
CB A:GLU62 4.7 9.3 1.0
CB A:GLU27 4.7 8.8 1.0
CD A:GLN141 4.8 15.7 1.0
OE1 A:GLU107 4.9 11.7 0.5
OE1 A:GLU140 4.9 21.6 0.7
CA A:GLU27 5.0 7.8 1.0

Iron binding site 2 out of 10 in 7o69

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Iron binding site 2 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:14.7
occ:0.50
 O1 A:PEO210 1.8 15.2 0.5
OE2 A:GLU62 2.0 14.6 1.0
O2 A:PEO210 2.0 15.5 0.5
OE1 A:GLU107 2.0 11.7 0.5
OE2 A:GLU107 2.1 11.4 0.5
OE1 A:GLU107 2.2 15.5 0.5
O A:HOH466 2.3 17.9 0.5
OE2 A:GLU107 2.3 16.9 0.5
CD A:GLU107 2.3 11.0 0.5
O A:HOH495 2.4 8.9 0.5
CD A:GLU107 2.4 15.7 0.5
O A:HOH466 2.6 5.0 0.2
CD A:GLU62 3.0 12.5 1.0
OE1 A:GLU62 3.4 15.8 1.0
FE A:FE2201 3.4 11.1 0.8
OE1 A:GLN141 3.6 24.2 1.0
O A:HOH335 3.8 9.1 0.2
O A:HOH386 3.8 21.4 1.0
CG A:GLU107 3.8 15.2 0.5
CG A:GLU107 3.8 10.9 0.5
NE2 A:GLN141 4.0 21.7 1.0
CD A:GLN141 4.3 15.7 1.0
CE1 A:HIS65 4.3 15.0 0.8
CG A:GLU62 4.3 10.9 1.0
FE A:FE2203 4.3 14.6 0.2
O A:HOH303 4.4 35.8 1.0
CE2 A:TYR34 4.4 5.7 0.2
ND1 A:HIS65 4.5 14.2 0.8
OE1 A:GLU140 4.5 21.6 0.7
OH A:TYR34 4.5 5.9 0.2
CE2 A:TYR34 4.5 12.3 0.8
OG A:SER144 4.5 9.9 0.2
O A:HOH373 4.5 14.9 0.8
CB A:GLU107 4.6 14.1 0.5
OH A:TYR34 4.7 15.2 0.8
CB A:GLU107 4.7 10.1 0.5
O A:HOH313 4.7 9.9 0.2
O A:HOH335 4.7 17.6 0.4
CA A:GLU107 4.9 13.8 0.5
CA A:GLU107 4.9 10.1 0.5
OG A:SER144 5.0 15.6 0.8
CZ A:TYR34 5.0 5.7 0.2

Iron binding site 3 out of 10 in 7o69

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Iron binding site 3 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:14.6
occ:0.20
 O A:HOH335 1.5 17.6 0.4
OE2 A:GLU140 1.8 23.1 0.7
O A:HOH313 2.0 9.9 0.2
O A:HOH335 2.0 9.1 0.2
OG A:SER144 2.0 15.6 0.8
O A:HOH416 2.1 18.1 0.2
O A:HOH466 2.1 5.0 0.2
O A:HOH466 2.3 17.9 0.5
CD A:GLU140 2.8 21.3 0.7
O A:HOH416 3.0 14.1 0.4
OE1 A:GLU140 3.1 21.6 0.7
FE A:FE2204 3.2 17.9 0.4
CB A:SER144 3.2 9.7 0.2
CB A:SER144 3.2 13.7 0.8
O A:HOH323 3.3 29.1 1.0
O A:HOH510 3.5 29.6 1.0
OG A:SER144 3.5 9.9 0.2
O A:HOH386 3.6 21.4 1.0
OE1 A:GLU61 3.9 26.2 0.8
O2 A:PEO210 4.0 15.5 0.5
OE1 A:GLN58 4.1 20.3 1.0
CG A:GLU140 4.1 20.6 0.7
O A:GLU140 4.2 12.0 1.0
O A:HOH303 4.2 35.8 1.0
O A:HOH461 4.3 38.8 1.0
OE2 A:GLU107 4.3 16.9 0.5
FE A:FE2202 4.3 14.7 0.5
CE1 A:HIS65 4.3 15.0 0.8
CA A:SER144 4.4 9.7 0.2
CA A:SER144 4.4 13.1 0.8
OE1 A:GLU107 4.4 15.5 0.5
O A:HOH562 4.5 35.2 1.0
O A:HOH454 4.6 29.0 1.0
CD A:GLU107 4.7 15.7 0.5
NE2 A:HIS65 4.8 14.8 0.8
OE2 A:GLU62 4.9 14.6 1.0
N A:SER144 4.9 10.0 1.0
CD A:GLU61 4.9 25.4 0.8
O A:HOH427 4.9 18.5 0.4
C A:GLU140 4.9 11.8 1.0
OE1 A:GLU107 5.0 11.7 0.5

Iron binding site 4 out of 10 in 7o69

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Iron binding site 4 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:17.9
occ:0.40
 O A:HOH427 1.9 18.5 0.4
O A:HOH416 2.0 18.1 0.2
O A:HOH335 2.0 17.6 0.4
OE1 A:GLN58 2.1 20.3 1.0
OE1 A:GLU61 2.1 26.2 0.8
O A:HOH416 2.2 14.1 0.4
O A:HOH510 2.2 29.6 1.0
O A:HOH313 3.0 9.9 0.2
O A:HOH427 3.0 17.1 0.4
CD A:GLN58 3.0 17.8 1.0
CD A:GLU61 3.2 25.4 0.8
FE A:FE2203 3.2 14.6 0.2
O A:HOH334 3.3 23.0 0.4
O A:HOH335 3.3 9.1 0.2
NE2 A:GLN58 3.3 22.9 1.0
OE2 A:GLU61 3.5 26.7 0.8
O A:HOH386 4.1 21.4 1.0
O A:HOH334 4.1 21.1 0.4
O A:HOH454 4.2 29.0 1.0
OE2 A:GLU140 4.2 23.1 0.7
O A:HOH562 4.2 35.2 1.0
OG A:SER144 4.3 15.6 0.8
CG A:GLN58 4.4 14.8 1.0
CG A:GLU61 4.5 13.4 1.0
O A:HOH323 4.5 29.1 1.0
O A:HOH303 4.6 35.8 1.0
O A:HOH466 4.6 17.9 0.5
O A:HOH481 4.6 26.4 0.4
CD2 A:HIS57 4.8 20.3 1.0
CB A:GLU61 4.8 12.0 1.0
OE1 A:GLU147 4.8 19.4 1.0
CA A:GLN58 4.9 9.4 1.0
CB A:GLN58 5.0 11.2 1.0

Iron binding site 5 out of 10 in 7o69

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Iron binding site 5 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:19.5
occ:0.40
 OE2 A:GLU61 2.0 26.7 0.8
O A:HOH496 2.1 22.0 0.4
NE2 A:HIS57 2.1 24.5 1.0
O A:HOH358 2.1 23.5 0.4
O A:HOH507 2.1 23.2 0.4
O A:HOH481 2.2 26.4 0.4
CE1 A:HIS57 2.9 26.4 1.0
CD A:GLU61 3.1 25.4 0.8
CD2 A:HIS57 3.2 20.3 1.0
CG A:GLU61 3.7 13.4 1.0
O A:HOH427 3.9 18.5 0.4
O A:HOH427 4.0 17.1 0.4
OE1 A:GLU61 4.1 26.2 0.8
O A:HOH600 4.1 42.4 0.7
ND1 A:HIS57 4.1 22.9 1.0
CG A:HIS57 4.3 17.4 1.0
O A:HOH371 4.4 36.2 1.0
O A:HOH541 4.4 30.6 0.5
O A:HOH416 4.8 14.1 0.4
O A:HOH310 4.8 46.0 1.0

Iron binding site 6 out of 10 in 7o69

Go back to Iron Binding Sites List in 7o69
Iron binding site 6 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:13.8
occ:0.25
 O A:HOH500 1.9 19.8 0.2
NE2 A:HIS173 2.2 12.0 1.0
CL A:CL218 2.6 120.3 0.2
CE1 A:HIS173 3.1 14.2 1.0
CD2 A:HIS173 3.3 12.1 1.0
ND1 A:HIS173 4.3 12.6 1.0
CG A:HIS173 4.4 11.6 1.0

Iron binding site 7 out of 10 in 7o69

Go back to Iron Binding Sites List in 7o69
Iron binding site 7 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:15.1
occ:0.30
 O A:HOH620 2.0 13.8 0.5
O A:HOH606 2.0 11.9 1.0
O A:HOH555 2.2 14.4 1.0
O A:HOH366 4.2 12.6 1.0
CD A:LYS86 4.4 10.3 0.4
O A:HOH601 4.5 17.5 1.0
NZ A:LYS86 4.5 11.6 0.6
CE A:LYS87 4.5 7.0 0.2
CE A:LYS86 4.7 10.8 0.4
CE A:LYS87 4.7 15.6 0.8
O A:HOH515 4.7 26.3 1.0
CD A:LYS86 5.0 10.9 0.6

Iron binding site 8 out of 10 in 7o69

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Iron binding site 8 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:13.4
occ:0.20
 O A:HOH336 2.1 13.6 1.0
O A:HOH657 2.1 15.5 1.0
OE2 A:GLU134 3.8 15.2 0.4
OE2 A:GLU134 3.9 11.2 0.6
O A:HOH308 4.0 19.2 0.5
O A:HOH628 4.2 15.5 1.0
O A:HOH411 4.2 26.6 1.0
OE1 A:GLU134 4.3 11.2 0.6
OE1 A:GLU134 4.4 15.3 0.4
CD A:GLU134 4.5 11.3 0.6
CD A:GLU134 4.5 15.3 0.4

Iron binding site 9 out of 10 in 7o69

Go back to Iron Binding Sites List in 7o69
Iron binding site 9 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe209

b:77.7
occ:0.20
 O A:HOH304 2.0 21.8 1.0
O A:HOH328 2.1 26.4 0.6
OD1 A:ASP131 3.3 19.2 1.0
O A:HOH602 3.4 26.4 0.2
OE1 A:GLU134 4.0 15.3 0.4
O A:HOH462 4.1 22.0 0.5
OG1 A:THR135 4.3 20.3 1.0
CG A:ASP131 4.5 16.2 1.0
OE1 A:GLU134 4.6 11.2 0.6

Iron binding site 10 out of 10 in 7o69

Go back to Iron Binding Sites List in 7o69
Iron binding site 10 out of 10 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of 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 10 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe211

b:12.8
occ:0.20
 O A:HOH390 1.9 17.4 0.5
O A:HOH588 2.0 17.9 0.5
O A:HOH658 2.0 23.8 0.5
O A:HOH655 2.1 20.6 0.5
O A:HOH580 2.1 18.8 0.5
O A:HOH397 2.3 17.6 1.0
O A:HOH637 4.2 32.3 0.5
O A:HOH626 4.2 26.4 0.5
OD1 A:ASN25 4.3 8.7 1.0
O A:HOH587 4.3 25.5 1.0
O A:HOH665 4.3 31.3 0.5
O A:HOH646 4.4 31.6 1.0
O A:ARG22 4.4 8.1 1.0
O A:HOH609 4.4 19.3 1.0
O A:HOH661 4.5 33.0 0.5
O A:HOH394 4.6 24.3 1.0
CB A:LEU26 4.9 8.6 1.0
O A:HOH636 5.0 22.2 1.0
CB A:ARG22 5.0 19.9 0.4

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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