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Iron in PDB 7o6c: Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Under Anaerobic Environment

Enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Under Anaerobic Environment

All present enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment, PDB code: 7o6c 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) 52.72 / 1.20
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.449, 182.449, 182.449, 90, 90, 90
R / Rfree (%) 12.1 / 14.3

Other elements in 7o6c:

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Under Anaerobic Environment also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 11 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Under Anaerobic Environment (pdb code 7o6c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 Minutes Under Anaerobic Environment, PDB code: 7o6c:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7o6c

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Iron binding site 1 out of 8 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:14.1
occ:0.25
 O A:HOH497 2.0 18.5 0.2
NE2 A:HIS173 2.2 11.8 0.6
NE2 A:HIS173 2.3 11.9 0.4
O A:HOH511 2.6 9.7 0.2
CE1 A:HIS173 3.1 11.8 0.6
CE1 A:HIS173 3.1 11.9 0.4
CD2 A:HIS173 3.2 11.6 0.6
CD2 A:HIS173 3.4 11.7 0.4
ND1 A:HIS173 4.2 12.0 0.6
ND1 A:HIS173 4.3 11.8 0.4
CG A:HIS173 4.3 11.8 0.6
CG A:HIS173 4.5 11.7 0.4

Iron binding site 2 out of 8 in 7o6c

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Iron binding site 2 out of 8 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:12.7
occ:1.00
 OE1 A:GLU62 2.0 17.4 1.0
OE2 A:GLU27 2.0 11.3 1.0
O A:HOH333 2.1 16.1 1.0
ND1 A:HIS65 2.2 12.8 0.6
O A:HOH302 2.3 21.0 1.0
ND1 A:HIS65 2.3 11.6 0.4
O A:HOH490 2.7 10.6 1.0
CD A:GLU62 3.0 12.8 1.0
CD A:GLU27 3.1 10.4 1.0
CE1 A:HIS65 3.1 12.9 0.6
CE1 A:HIS65 3.2 12.1 0.4
CG A:HIS65 3.2 12.2 0.6
CG A:HIS65 3.3 11.7 0.4
OE2 A:GLU62 3.4 14.7 1.0
FE A:FE2203 3.4 12.9 0.7
OE1 A:GLU27 3.4 12.0 1.0
CB A:HIS65 3.6 12.2 0.6
CB A:HIS65 3.6 11.7 0.4
OE1 A:GLN141 3.8 13.8 0.3
O A:HOH471 4.0 18.8 0.6
OE1 A:GLN141 4.0 16.4 0.7
NE2 A:HIS65 4.2 12.7 0.6
CD2 A:HIS65 4.3 12.6 0.6
CG A:GLU62 4.4 11.4 1.0
CG A:GLU27 4.4 10.1 1.0
NE2 A:HIS65 4.4 12.0 0.4
CG1 A:VAL110 4.4 18.9 1.0
CD2 A:HIS65 4.4 11.8 0.4
CA A:GLU62 4.6 10.2 1.0
CD A:GLN141 4.6 13.4 0.3
OE1 A:GLU140 4.7 22.5 0.7
CB A:GLU62 4.7 10.5 1.0
CB A:GLU27 4.8 10.0 1.0
NE2 A:GLN141 4.9 15.3 0.7
CD A:GLN141 4.9 15.2 0.7
OE1 A:GLU107 4.9 14.7 0.3
O A:HOH309 4.9 24.0 1.0

Iron binding site 3 out of 8 in 7o6c

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Iron binding site 3 out of 8 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:12.9
occ:0.65
 O A:HOH302 1.9 21.0 1.0
OE2 A:GLU62 2.0 14.7 1.0
OE1 A:GLU107 2.1 14.2 0.7
OE1 A:GLU107 2.1 14.7 0.3
OE2 A:GLU107 2.1 15.4 0.3
O A:HOH309 2.2 24.0 1.0
OE2 A:GLU107 2.2 13.7 0.7
CD A:GLU107 2.4 14.9 0.3
CD A:GLU107 2.4 13.9 0.7
O A:HOH490 2.4 10.6 1.0
CD A:GLU62 3.0 12.8 1.0
OE1 A:GLU62 3.4 17.4 1.0
FE A:FE2202 3.4 12.7 1.0
OE1 A:GLN141 3.5 13.8 0.3
NE2 A:GLN141 3.8 14.0 0.3
O A:HOH394 3.8 21.1 1.0
CG A:GLU107 3.9 14.3 0.3
CG A:GLU107 3.9 12.9 0.7
OE1 A:GLN141 4.0 16.4 0.7
NE2 A:GLN141 4.0 15.3 0.7
CD A:GLN141 4.1 13.4 0.3
O A:HOH308 4.2 25.2 1.0
CE1 A:HIS65 4.3 12.9 0.6
CD A:GLN141 4.3 15.2 0.7
CG A:GLU62 4.3 11.4 1.0
FE A:FE2205 4.3 11.1 0.1
OE1 A:GLU140 4.3 22.5 0.7
OG A:SER144 4.4 14.3 0.3
ND1 A:HIS65 4.4 12.8 0.6
O A:HOH333 4.5 16.1 1.0
CE2 A:TYR34 4.5 12.7 0.5
CE2 A:TYR34 4.6 10.2 0.5
OH A:TYR34 4.6 14.4 0.5
OH A:TYR34 4.7 11.2 0.5
CB A:GLU107 4.7 13.8 0.3
CB A:GLU107 4.7 12.0 0.7
OG A:SER144 4.8 16.1 0.7
CB A:SER144 4.9 13.8 0.3
CB A:SER144 4.9 14.7 0.7
CA A:GLU107 4.9 13.3 0.3
CA A:GLU107 4.9 11.5 0.7
O A:HOH305 5.0 27.2 1.0
ND1 A:HIS65 5.0 11.6 0.4

Iron binding site 4 out of 8 in 7o6c

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Iron binding site 4 out of 8 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:14.3
occ:0.40
 O A:HOH305 1.9 27.2 1.0
OE1 A:GLU61 2.0 18.9 0.5
O A:HOH493 2.1 22.7 0.6
O A:HOH332 2.1 26.1 1.0
OE1 A:GLN58 2.1 21.0 1.0
OE1 A:GLU61 2.2 16.9 0.3
O A:HOH491 2.2 28.3 1.0
O A:HOH430 3.0 24.0 0.4
CD A:GLU61 3.0 15.5 0.3
CD A:GLU61 3.0 16.6 0.5
CD A:GLN58 3.1 16.8 1.0
O A:HOH493 3.1 21.4 0.4
OE2 A:GLU61 3.3 17.2 0.3
FE A:FE2205 3.3 11.1 0.1
OE2 A:GLU61 3.4 19.1 0.5
NE2 A:GLN58 3.4 21.8 1.0
O A:HOH394 4.0 21.1 1.0
O A:HOH430 4.1 27.3 0.6
OE2 A:GLU140 4.2 26.7 0.7
O A:HOH410 4.2 28.2 1.0
O A:HOH565 4.2 30.8 1.0
CG A:GLU61 4.4 14.8 0.4
OG A:SER144 4.4 16.1 0.7
CG A:GLU61 4.4 15.4 0.6
CG A:GLN58 4.4 14.8 1.0
O A:HOH308 4.5 25.2 1.0
O A:HOH337 4.5 28.3 1.0
OE1 A:GLU147 4.7 19.0 1.0
O A:HOH478 4.7 28.7 0.4
O A:HOH309 4.7 24.0 1.0
CD2 A:HIS57 4.8 24.5 1.0
CB A:GLU61 4.8 13.9 0.4
CB A:GLU61 4.8 13.8 0.6
CA A:GLN58 4.8 10.9 1.0
CB A:GLN58 5.0 12.1 1.0

Iron binding site 5 out of 8 in 7o6c

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Iron binding site 5 out of 8 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:11.1
occ:0.10
 OE2 A:GLU140 1.6 26.7 0.7
O A:HOH305 1.8 27.2 1.0
OG A:SER144 1.9 16.1 0.7
O A:HOH309 2.3 24.0 1.0
CD A:GLU140 2.6 24.3 0.7
O A:HOH332 2.9 26.1 1.0
OE1 A:GLU140 3.0 22.5 0.7
CB A:SER144 3.2 13.8 0.3
CB A:SER144 3.2 14.7 0.7
O A:HOH337 3.2 28.3 1.0
FE A:FE2204 3.3 14.3 0.4
OG A:SER144 3.5 14.3 0.3
O A:HOH491 3.5 28.3 1.0
O A:HOH394 3.6 21.1 1.0
OE1 A:GLU61 3.9 18.9 0.5
CG A:GLU140 3.9 22.8 0.7
O A:HOH308 4.0 25.2 1.0
O A:GLU140 4.1 13.6 1.0
O A:HOH302 4.2 21.0 1.0
OE1 A:GLN58 4.2 21.0 1.0
CA A:SER144 4.3 13.4 0.3
CA A:SER144 4.3 13.7 0.7
FE A:FE2203 4.3 12.9 0.7
CE1 A:HIS65 4.3 12.9 0.6
O A:HOH565 4.5 30.8 1.0
O A:HOH396 4.5 38.4 1.0
OE1 A:GLU61 4.5 16.9 0.3
OE2 A:GLU61 4.6 17.2 0.3
O A:HOH410 4.6 28.2 1.0
OE2 A:GLU107 4.7 15.4 0.3
CD A:GLU61 4.7 15.5 0.3
OE1 A:GLU107 4.7 14.2 0.7
N A:SER144 4.7 11.9 1.0
OE2 A:GLU62 4.8 14.7 1.0
NE2 A:HIS65 4.8 12.7 0.6
C A:GLU140 4.8 13.5 1.0
OE1 A:GLN141 4.8 13.8 0.3
CD A:GLU61 4.9 16.6 0.5

Iron binding site 6 out of 8 in 7o6c

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Iron binding site 6 out of 8 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:48.6
occ:0.20
 O A:HOH320 1.9 17.0 0.6
O A:HOH347 2.2 19.3 0.6
OD1 A:ASP131 3.4 23.9 1.0
O A:HOH602 3.4 30.8 0.2
O A:HOH329 4.0 22.3 0.2
OG1 A:THR135 4.3 21.0 1.0
OE1 A:GLU134 4.4 21.4 1.0
CG A:ASP131 4.5 19.7 1.0
CB A:GLU134 5.0 14.5 1.0

Iron binding site 7 out of 8 in 7o6c

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Iron binding site 7 out of 8 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:15.0
occ:0.20
 O A:HOH663 2.1 18.8 1.0
O A:HOH657 2.1 16.2 1.0
O A:HOH329 3.0 22.3 0.2
OE2 A:GLU134 3.9 15.0 1.0
OE1 A:GLU134 4.3 21.4 1.0
O A:HOH616 4.3 16.6 1.0
O A:HOH334 4.4 31.2 1.0
CD A:GLU134 4.5 17.0 1.0

Iron binding site 8 out of 8 in 7o6c

Go back to Iron Binding Sites List in 7o6c
Iron binding site 8 out of 8 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 15 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 15 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:19.0
occ:0.30
 O A:HOH338 1.8 29.4 0.4
OE2 A:GLU61 2.0 19.1 0.5
NE2 A:HIS57 2.0 27.1 1.0
O A:HOH502 2.1 24.9 0.4
O A:HOH478 2.2 28.7 0.4
O A:HOH509 2.3 29.1 0.4
CE1 A:HIS57 2.8 30.2 1.0
OE2 A:GLU61 3.1 17.2 0.3
CD A:GLU61 3.1 16.6 0.5
CD2 A:HIS57 3.2 24.5 1.0
CD A:GLU61 3.2 15.5 0.3
O A:HOH583 3.7 35.3 0.5
CG A:GLU61 3.7 15.4 0.6
OE1 A:GLU61 3.7 16.9 0.3
CG A:GLU61 3.7 14.8 0.4
O A:HOH493 3.9 21.4 0.4
ND1 A:HIS57 4.0 26.6 1.0
O A:HOH493 4.0 22.7 0.6
OE1 A:GLU61 4.2 18.9 0.5
CG A:HIS57 4.2 19.4 1.0
O A:HOH640 4.4 29.9 0.5
O A:HOH332 4.9 26.1 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: Thu Aug 8 14:06:32 2024

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