Iron in PDB 7owy: Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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 3 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 3 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site, PDB code: 7owy 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) 55.57 / 1.55
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.111, 184.111, 184.111, 90, 90, 90
R / Rfree (%) 15.3 / 17.2

Other elements in 7owy:

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site (pdb code 7owy). 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 3 Minutes Showing A Peroxide Anion As Bridging Species of Iron Ions in the Ferroxidase Site, PDB code: 7owy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7owy

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Iron binding site 1 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:11.9
occ:0.85
 O1 A:PEO210 1.8 16.1 0.5
OE2 A:GLU27 2.0 12.7 1.0
OE1 A:GLU62 2.1 15.6 1.0
ND1 A:HIS65 2.1 13.9 0.8
O A:HOH320 2.2 17.7 1.0
O2 A:PEO210 2.4 16.4 0.5
ND1 A:HIS65 2.5 10.1 0.1
O A:HOH485 2.8 8.9 0.5
CE1 A:HIS65 3.0 15.3 0.8
CD A:GLU62 3.0 14.7 1.0
CD A:GLU27 3.1 12.6 1.0
CG A:HIS65 3.2 13.1 0.8
OE2 A:GLU62 3.4 15.3 1.0
CE1 A:HIS65 3.4 10.1 0.1
OE1 A:GLU27 3.4 13.1 1.0
FE A:FE2203 3.5 17.6 0.5
CG A:HIS65 3.5 10.2 0.1
CB A:HIS65 3.6 11.7 0.8
CB A:HIS65 3.7 10.2 0.1
OE1 A:GLN141 3.8 24.9 1.0
O A:HOH502 4.0 26.6 0.8
NE2 A:HIS65 4.2 15.3 0.8
CG1 A:VAL110 4.3 16.6 1.0
CD2 A:HIS65 4.3 14.0 0.8
CG A:GLU62 4.4 11.9 1.0
CG A:GLU27 4.4 11.3 1.0
O A:HOH302 4.5 5.0 0.2
CA A:GLU62 4.6 10.5 1.0
NE2 A:HIS65 4.6 10.2 0.1
CD2 A:HIS65 4.6 10.1 0.1
CB A:GLU62 4.7 10.2 1.0
CB A:GLU27 4.8 9.9 1.0
CD A:GLN141 4.8 20.2 1.0
OE1 A:GLU107 4.9 16.0 0.5
OE1 A:GLU140 5.0 23.0 0.7

Iron binding site 2 out of 9 in 7owy

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Iron binding site 2 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:16.1
occ:0.25
 O A:HOH490 2.1 22.8 0.2
NE2 A:HIS173 2.2 13.4 0.6
NE2 A:HIS173 2.4 13.5 0.4
CL A:CL213 2.5 18.0 0.2
CE1 A:HIS173 3.1 13.4 0.6
CE1 A:HIS173 3.2 13.9 0.4
CD2 A:HIS173 3.3 13.9 0.6
CD2 A:HIS173 3.5 13.6 0.4
ND1 A:HIS173 4.2 13.7 0.6
CG A:HIS173 4.4 13.5 0.6
ND1 A:HIS173 4.4 13.4 0.4
CG A:HIS173 4.6 13.2 0.4

Iron binding site 3 out of 9 in 7owy

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Iron binding site 3 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:17.6
occ:0.50
 O1 A:PEO210 2.0 16.1 0.5
O2 A:PEO210 2.0 16.4 0.5
OE2 A:GLU62 2.0 15.3 1.0
OE1 A:GLU107 2.0 16.0 0.5
OE2 A:GLU107 2.1 11.9 0.5
OE1 A:GLU107 2.1 12.0 0.5
OE2 A:GLU107 2.2 17.5 0.5
CD A:GLU107 2.4 16.4 0.5
CD A:GLU107 2.4 12.5 0.5
O A:HOH485 2.4 8.9 0.5
O A:HOH316 2.5 18.8 0.4
O A:HOH302 2.6 5.0 0.2
CD A:GLU62 3.0 14.7 1.0
OE1 A:GLU62 3.4 15.6 1.0
FE A:FE2201 3.5 11.9 0.8
OE1 A:GLN141 3.7 24.9 1.0
O A:HOH404 3.8 21.6 1.0
O A:HOH330 3.8 7.2 0.2
CG A:GLU107 3.9 14.5 0.5
CG A:GLU107 3.9 11.9 0.5
NE2 A:GLN141 4.1 20.7 1.0
O A:HOH322 4.2 20.9 0.5
CE1 A:HIS65 4.3 15.3 0.8
FE A:FE2207 4.3 18.1 0.2
CD A:GLN141 4.3 20.2 1.0
CG A:GLU62 4.3 11.9 1.0
CE2 A:TYR34 4.5 14.0 1.0
ND1 A:HIS65 4.5 13.9 0.8
O A:HOH330 4.5 18.4 0.4
OE1 A:GLU140 4.5 23.0 0.7
O A:HOH320 4.6 17.7 1.0
OH A:TYR34 4.7 21.5 1.0
CB A:GLU107 4.7 12.2 0.5
CB A:GLU107 4.8 10.9 0.5
O A:HOH308 4.8 11.7 0.2
CA A:GLU107 5.0 11.5 0.5
CA A:GLU107 5.0 11.0 0.5
OG A:SER144 5.0 17.7 1.0

Iron binding site 4 out of 9 in 7owy

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Iron binding site 4 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:20.8
occ:0.40
 O A:HOH329 2.0 24.7 0.4
O A:HOH422 2.0 24.7 0.4
OE2 A:GLU61 2.0 29.0 1.0
O A:HOH509 2.1 18.4 0.4
NE2 A:HIS57 2.1 25.0 1.0
O A:HOH516 2.3 20.5 0.4
CE1 A:HIS57 2.8 25.8 1.0
CD A:GLU61 3.1 22.8 1.0
CD2 A:HIS57 3.4 22.5 1.0
CG A:GLU61 3.8 17.6 1.0
O A:HOH515 3.9 30.8 1.0
ND1 A:HIS57 4.0 23.5 1.0
OE1 A:GLU61 4.1 27.6 1.0
CG A:HIS57 4.3 19.4 1.0
O A:HOH382 4.4 32.4 1.0
O A:HOH434 4.8 17.1 0.4

Iron binding site 5 out of 9 in 7owy

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Iron binding site 5 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:14.4
occ:0.20
 O A:HOH353 2.0 15.3 1.0
O A:HOH540 2.1 18.4 1.0
OE2 A:GLU134 3.9 16.0 1.0
O A:HOH344 4.0 17.4 0.5
O A:HOH433 4.2 25.1 1.0
O A:HOH610 4.2 15.8 1.0
OE1 A:GLU134 4.3 20.0 1.0
CD A:GLU134 4.5 16.6 1.0

Iron binding site 6 out of 9 in 7owy

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Iron binding site 6 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:24.4
occ:0.40
 O A:HOH434 1.8 12.0 0.2
OE1 A:GLU61 2.1 27.6 1.0
OE1 A:GLN58 2.2 22.0 1.0
O A:HOH434 2.2 17.1 0.4
O A:HOH330 2.2 18.4 0.4
O A:HOH511 2.3 29.3 1.0
O A:HOH515 2.4 30.8 1.0
O A:HOH308 2.9 11.7 0.2
CD A:GLN58 3.1 19.0 1.0
CD A:GLU61 3.1 22.8 1.0
FE A:FE2207 3.2 18.1 0.2
O A:HOH330 3.3 7.2 0.2
NE2 A:GLN58 3.4 21.8 1.0
OE2 A:GLU61 3.5 29.0 1.0
O A:HOH331 3.7 41.2 1.0
O A:HOH404 4.1 21.6 1.0
O A:HOH503 4.1 29.2 1.0
OE2 A:GLU140 4.2 24.9 0.7
O A:HOH563 4.2 38.0 1.0
OG A:SER144 4.3 17.7 1.0
O A:HOH422 4.4 24.7 0.4
CG A:GLU61 4.5 17.6 1.0
O A:HOH316 4.5 18.8 0.4
O A:HOH352 4.5 36.4 1.0
O A:HOH322 4.5 20.9 0.5
CG A:GLN58 4.5 15.9 1.0
CD2 A:HIS57 4.7 22.5 1.0
CB A:GLU61 4.8 13.0 1.0
CA A:GLN58 4.9 11.2 1.0
OE1 A:GLU147 4.9 20.5 1.0

Iron binding site 7 out of 9 in 7owy

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Iron binding site 7 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:18.1
occ:0.20
 O A:HOH330 1.6 18.4 0.4
OE2 A:GLU140 1.8 24.9 0.7
O A:HOH308 1.9 11.7 0.2
O A:HOH330 2.1 7.2 0.2
OG A:SER144 2.1 17.7 1.0
O A:HOH302 2.1 5.0 0.2
O A:HOH316 2.2 18.8 0.4
O A:HOH434 2.2 12.0 0.2
CD A:GLU140 2.7 21.9 0.7
O A:HOH434 3.0 17.1 0.4
OE1 A:GLU140 3.0 23.0 0.7
FE A:FE2206 3.2 24.4 0.4
CB A:SER144 3.3 13.3 1.0
O A:HOH352 3.4 36.4 1.0
O A:HOH511 3.6 29.3 1.0
O A:HOH404 3.6 21.6 1.0
OE1 A:GLU61 3.8 27.6 1.0
O2 A:PEO210 4.1 16.4 0.5
CG A:GLU140 4.1 19.9 0.7
O A:HOH322 4.1 20.9 0.5
OE1 A:GLN58 4.1 22.0 1.0
O A:GLU140 4.2 13.9 1.0
CE1 A:HIS65 4.3 15.3 0.8
FE A:FE2203 4.3 17.6 0.5
OE1 A:GLU107 4.3 12.0 0.5
O A:HOH453 4.4 37.7 1.0
OE2 A:GLU107 4.4 17.5 0.5
CA A:SER144 4.4 11.9 1.0
O A:HOH503 4.6 29.2 1.0
O A:HOH563 4.6 38.0 1.0
NE2 A:HIS65 4.7 15.3 0.8
CD A:GLU61 4.8 22.8 1.0
OE1 A:GLU140 4.8 18.8 0.3
OE2 A:GLU62 4.8 15.3 1.0
N A:SER144 4.9 11.3 1.0
C A:GLU140 4.9 14.3 1.0

Iron binding site 8 out of 9 in 7owy

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Iron binding site 8 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:19.2
occ:0.35
 O A:HOH607 2.1 13.1 0.5
O A:HOH541 2.2 14.0 1.0
O A:HOH399 4.2 12.3 1.0
CD A:LYS86 4.3 11.1 0.5
NZ A:LYS86 4.5 11.0 0.5
O A:HOH597 4.5 20.3 1.0
CE A:LYS87 4.5 13.7 0.5
CE A:LYS86 4.5 11.8 0.5
O A:HOH546 4.7 23.7 1.0
CE A:LYS87 4.9 13.6 0.5

Iron binding site 9 out of 9 in 7owy

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Iron binding site 9 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 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:26.0
occ:0.10
 O A:HOH307 1.9 18.8 1.0
O A:HOH315 1.9 24.4 0.6
OD1 A:ASP131 3.3 18.8 1.0
O A:HOH593 3.6 36.4 0.3
O A:HOH424 4.2 20.0 0.5
OG1 A:THR135 4.4 18.3 1.0
OE1 A:GLU134 4.4 20.0 1.0
CG A:ASP131 4.5 15.9 1.0
CB A:GLU134 5.0 13.7 1.0

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: Fri Nov 5 14:06:36 2021

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