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Iron in PDB 7o6a: Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment

Enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment

All present enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment, PDB code: 7o6a 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) 106.04 / 1.40
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.675, 183.675, 183.675, 90, 90, 90
R / Rfree (%) 13.2 / 16.3

Other elements in 7o6a:

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Magnesium (Mg) 3 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 Under Anaerobic Environment (pdb code 7o6a). 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 5 Minutes Under Anaerobic Environment, PDB code: 7o6a:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7o6a

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Iron binding site 1 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:19.2
occ:0.25
 O A:HOH498 2.1 25.8 0.2
NE2 A:HIS173 2.2 17.5 0.7
NE2 A:HIS173 2.3 16.1 0.3
O A:HOH517 2.5 10.7 0.2
CE1 A:HIS173 3.0 18.9 0.7
CE1 A:HIS173 3.2 16.7 0.3
CD2 A:HIS173 3.3 18.3 0.7
CD2 A:HIS173 3.4 16.2 0.3
ND1 A:HIS173 4.2 18.8 0.7
CG A:HIS173 4.4 17.8 0.7
ND1 A:HIS173 4.4 16.0 0.3
CG A:HIS173 4.5 15.9 0.3

Iron binding site 2 out of 9 in 7o6a

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Iron binding site 2 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:15.7
occ:0.80
 OE1 A:GLU62 2.0 20.9 1.0
OE2 A:GLU27 2.0 16.4 1.0
O A:HOH314 2.1 22.5 1.0
ND1 A:HIS65 2.2 18.4 0.8
O A:HOH307 2.2 30.7 1.0
ND1 A:HIS65 2.4 13.2 0.2
O A:HOH484 2.7 24.0 1.0
CD A:GLU62 3.0 19.1 1.0
CE1 A:HIS65 3.0 19.9 0.8
CD A:GLU27 3.1 14.4 1.0
CG A:HIS65 3.3 17.8 0.8
CE1 A:HIS65 3.4 13.3 0.2
OE2 A:GLU62 3.4 21.4 1.0
CG A:HIS65 3.4 13.3 0.2
FE A:FE2203 3.5 19.6 0.4
OE1 A:GLU27 3.5 16.8 1.0
CB A:HIS65 3.6 13.3 0.2
CB A:HIS65 3.7 16.3 0.8
OE1 A:GLN141 3.7 31.0 1.0
O A:HOH499 4.0 25.4 0.8
CG1 A:VAL110 4.2 23.4 1.0
NE2 A:HIS65 4.2 19.8 0.8
CD2 A:HIS65 4.3 19.0 0.8
CG A:GLU62 4.4 17.2 1.0
CG A:GLU27 4.4 14.4 1.0
NE2 A:HIS65 4.5 13.3 0.2
O A:HOH316 4.5 11.1 0.2
CD2 A:HIS65 4.5 13.2 0.2
CA A:GLU62 4.6 13.8 1.0
CB A:GLU62 4.7 14.6 1.0
CD A:GLN141 4.7 20.6 1.0
CB A:GLU27 4.8 13.4 1.0
OE1 A:GLU140 4.8 26.1 0.7
OE1 A:GLU107 4.8 21.0 0.5

Iron binding site 3 out of 9 in 7o6a

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Iron binding site 3 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:19.6
occ:0.40
 O A:HOH307 1.8 30.7 1.0
OE1 A:GLU107 1.9 21.0 0.5
OE2 A:GLU62 2.0 21.4 1.0
OE1 A:GLU107 2.0 16.8 0.5
OE2 A:GLU107 2.1 16.0 0.5
OE2 A:GLU107 2.2 25.3 0.5
O A:HOH316 2.3 24.4 0.4
CD A:GLU107 2.3 16.7 0.5
CD A:GLU107 2.3 23.7 0.5
O A:HOH484 2.4 24.0 1.0
O A:HOH316 2.6 11.1 0.2
CD A:GLU62 3.0 19.1 1.0
OE1 A:GLU62 3.4 20.9 1.0
FE A:FE2202 3.5 15.7 0.8
OE1 A:GLN141 3.5 31.0 1.0
O A:HOH352 3.7 14.9 0.2
O A:HOH385 3.8 28.2 1.0
CG A:GLU107 3.8 21.3 0.5
CG A:GLU107 3.8 15.7 0.5
NE2 A:GLN141 4.0 28.0 1.0
O A:HOH514 4.2 23.2 0.5
CD A:GLN141 4.2 20.6 1.0
CE1 A:HIS65 4.3 19.9 0.8
FE A:FE2209 4.3 19.6 0.2
CG A:GLU62 4.3 17.2 1.0
OE1 A:GLU140 4.3 26.1 0.7
CE2 A:TYR34 4.5 16.8 0.5
OH A:TYR34 4.5 20.2 0.5
ND1 A:HIS65 4.5 18.4 0.8
O A:HOH314 4.5 22.5 1.0
CE2 A:TYR34 4.6 13.2 0.5
CB A:GLU107 4.6 14.3 0.5
CB A:GLU107 4.7 19.2 0.5
O A:HOH320 4.7 19.9 0.4
OH A:TYR34 4.8 13.9 0.5
OG A:SER144 4.9 23.9 1.0
CA A:GLU107 4.9 14.3 0.5
CA A:GLU107 4.9 18.8 0.5
CB A:SER144 5.0 18.6 1.0
CZ A:TYR34 5.0 17.5 0.5

Iron binding site 4 out of 9 in 7o6a

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Iron binding site 4 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:42.0
occ:0.20
 O A:HOH440 2.0 38.2 1.0
O A:HOH306 2.1 46.5 1.0
OD1 A:ASP131 3.4 23.9 1.0
O A:HOH614 3.6 37.8 0.3
OG1 A:THR135 4.2 24.6 1.0
OE1 A:GLU134 4.4 27.7 1.0
CG A:ASP131 4.5 20.8 1.0

Iron binding site 5 out of 9 in 7o6a

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Iron binding site 5 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:18.2
occ:0.40
 O A:HOH320 2.0 19.9 0.4
O A:HOH429 2.0 33.6 1.0
O A:HOH476 2.0 20.5 0.5
OE1 A:GLU61 2.1 31.6 1.0
O A:HOH504 2.1 30.9 1.0
OE1 A:GLN58 2.1 23.9 1.0
CD A:GLN58 3.1 22.4 1.0
CD A:GLU61 3.1 28.9 1.0
O A:HOH476 3.1 19.5 0.4
FE A:FE2209 3.1 19.6 0.2
O A:HOH418 3.3 21.6 0.3
O A:HOH352 3.3 14.9 0.2
NE2 A:GLN58 3.3 27.9 1.0
OE2 A:GLU61 3.5 36.8 1.0
O A:HOH385 4.0 28.2 1.0
OE2 A:GLU140 4.1 31.3 0.7
O A:HOH506 4.1 30.5 1.0
O A:HOH418 4.2 18.9 0.3
O A:HOH563 4.2 37.1 1.0
OG A:SER144 4.3 23.9 1.0
CG A:GLU61 4.4 17.8 1.0
O A:HOH329 4.5 33.5 1.0
O A:HOH514 4.5 23.2 0.5
CG A:GLN58 4.5 18.4 1.0
O A:HOH442 4.5 24.4 0.4
O A:HOH316 4.6 24.4 0.4
CD2 A:HIS57 4.8 28.3 1.0
OE1 A:GLU147 4.8 24.8 1.0
CB A:GLU61 4.8 16.1 1.0
CA A:GLN58 4.9 13.6 1.0
CB A:GLN58 5.0 14.8 1.0

Iron binding site 6 out of 9 in 7o6a

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Iron binding site 6 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:17.8
occ:0.20
 O A:HOH661 2.1 22.6 1.0
O A:HOH472 2.1 20.6 1.0
OE2 A:GLU134 3.9 18.2 1.0
O A:HOH435 4.2 33.1 1.0
O A:HOH628 4.2 20.6 1.0
OE1 A:GLU134 4.3 27.7 1.0
CD A:GLU134 4.5 18.3 1.0

Iron binding site 7 out of 9 in 7o6a

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Iron binding site 7 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:22.8
occ:0.40
 OE2 A:GLU61 2.0 36.8 1.0
NE2 A:HIS57 2.1 32.2 1.0
O A:HOH497 2.1 27.4 0.4
O A:HOH442 2.1 24.4 0.4
O A:HOH502 2.2 31.4 0.5
O A:HOH382 2.2 22.3 0.4
CE1 A:HIS57 2.9 35.2 1.0
CD A:GLU61 3.1 28.9 1.0
CD2 A:HIS57 3.2 28.3 1.0
CG A:GLU61 3.7 17.8 1.0
O A:HOH476 4.0 19.5 0.4
O A:HOH476 4.0 20.5 0.5
OE1 A:GLU61 4.1 31.6 1.0
ND1 A:HIS57 4.1 29.9 1.0
O A:HOH360 4.1 38.5 0.5
CG A:HIS57 4.3 24.1 1.0
O A:HOH547 4.3 37.4 0.6
O A:HOH312 4.7 35.0 0.6
O A:HOH429 4.9 33.6 1.0

Iron binding site 8 out of 9 in 7o6a

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Iron binding site 8 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:23.4
occ:0.35
 O A:HOH395 2.0 20.9 0.5
O A:HOH663 2.1 16.9 1.0
O A:HOH658 2.2 19.6 1.0
OD1 A:ASP84 4.2 12.6 1.0
OD2 A:ASP84 4.2 14.8 1.0
CG A:ASP84 4.6 12.4 1.0
CL A:CL215 4.8 17.9 0.6

Iron binding site 9 out of 9 in 7o6a

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Iron binding site 9 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


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 Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe209

b:19.6
occ:0.20
 O A:HOH320 1.5 19.9 0.4
OE2 A:GLU140 1.7 31.3 0.7
O A:HOH352 2.0 14.9 0.2
OG A:SER144 2.0 23.9 1.0
O A:HOH316 2.2 11.1 0.2
O A:HOH316 2.3 24.4 0.4
CD A:GLU140 2.7 27.7 0.7
O A:HOH429 2.8 33.6 1.0
OE1 A:GLU140 3.1 26.1 0.7
FE A:FE2205 3.1 18.2 0.4
CB A:SER144 3.3 18.6 1.0
O A:HOH329 3.4 33.5 1.0
O A:HOH504 3.4 30.9 1.0
O A:HOH385 3.5 28.2 1.0
OE1 A:GLU61 3.7 31.6 1.0
O A:HOH514 4.0 23.2 0.5
OE1 A:GLN58 4.0 23.9 1.0
CG A:GLU140 4.1 25.7 0.7
O A:GLU140 4.1 17.8 0.3
OE2 A:GLU107 4.2 25.3 0.5
O A:GLU140 4.3 17.7 0.7
FE A:FE2203 4.3 19.6 0.4
CE1 A:HIS65 4.3 19.9 0.8
CA A:SER144 4.3 15.5 1.0
O A:HOH307 4.4 30.7 1.0
OE1 A:GLU107 4.4 16.8 0.5
O A:HOH563 4.5 37.1 1.0
O A:HOH506 4.5 30.5 1.0
O A:HOH468 4.6 33.4 0.6
CD A:GLU61 4.8 28.9 1.0
NE2 A:HIS65 4.8 19.8 0.8
OE2 A:GLU62 4.8 21.4 1.0
N A:SER144 4.9 15.4 1.0
C A:GLU140 4.9 17.5 0.3
CD A:GLU107 4.9 23.7 0.5
OE1 A:GLU140 4.9 21.8 0.3
C A:GLU140 5.0 18.0 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 14:03:08 2024

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