Magnesium 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:

Chlorine (Cl) 6 atoms
Iron (Fe) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7o69

Go back to Magnesium Binding Sites List in 7o69
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg212

b:18.0
occ:0.50
 OD1 A:ASN49 1.9 4.2 0.1
O A:HOH561 2.0 20.6 0.5
O A:HOH425 2.0 19.0 0.5
O A:HOH364 2.0 16.4 0.5
O A:HOH422 2.1 15.8 0.5
O A:HOH564 2.1 22.6 0.5
O A:HOH659 2.1 25.7 0.5
CG A:ASN49 3.0 4.2 0.1
ND2 A:ASN49 3.5 4.2 0.1
O A:HOH649 3.6 37.5 1.0
OG A:SER42 3.9 12.2 0.5
O A:HOH585 4.0 25.9 1.0
OD1 A:ASN49 4.2 18.5 0.9
OG A:SER52 4.2 10.8 1.0
CB A:ASN49 4.3 4.1 0.1
NH2 A:ARG53 4.3 23.5 0.5
CB A:ASN49 4.3 14.8 0.9
O A:ASN49 4.4 9.2 1.0
NE A:ARG53 4.4 21.4 0.5
CG A:ASN49 4.4 17.3 0.9
CZ A:ARG53 4.5 21.8 0.5
CB A:SER52 4.5 10.1 1.0
O A:HOH551 4.5 23.4 0.3
CG A:ARG53 4.6 16.6 0.5
CA A:ASN49 4.7 12.7 0.9
CA A:ASN49 4.7 4.0 0.1
O A:HOH453 4.8 28.7 1.0
CB A:SER42 4.9 8.4 0.5
C A:ASN49 5.0 9.2 1.0

Magnesium binding site 2 out of 3 in 7o69

Go back to Magnesium Binding Sites List in 7o69
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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:Mg213

b:21.7
occ:0.40
 O A:HOH399 2.0 31.3 1.0
O A:HOH638 2.0 20.9 0.4
O A:HOH653 2.1 24.6 0.4
O A:HOH664 2.2 28.7 0.4
O A:HOH590 2.2 32.4 0.8
O A:HOH365 4.1 17.8 1.0
O A:HOH430 4.4 15.4 1.0
O A:HOH586 4.4 40.9 1.0
OE1 A:GLU17 4.5 12.7 1.0
CB A:PRO14 4.7 11.9 1.0
O A:HOH610 4.8 41.1 1.0
O A:HOH654 4.9 27.4 0.4
CG A:PRO14 4.9 13.7 1.0
O A:HOH524 4.9 34.8 1.0

Magnesium binding site 3 out of 3 in 7o69

Go back to Magnesium Binding Sites List in 7o69
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg 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:Mg214

b:25.9
occ:0.50
 O A:HOH652 1.8 32.8 0.5
O A:HOH534 2.2 25.2 0.5
O A:HOH547 2.2 13.1 0.3
O A:HOH505 2.3 32.4 1.0
O A:HOH547 3.3 11.6 0.7
NH2 A:ARG7 4.2 20.3 0.7
NE A:ARG7 4.3 17.5 0.7
NH2 A:ARG7 4.3 19.4 0.3
NE A:ARG7 4.3 18.0 0.3
O A:HOH608 4.3 28.7 0.5
O A:HOH576 4.5 35.2 1.0
CZ A:ARG7 4.7 17.7 0.7
CZ A:ARG7 4.8 18.3 0.3

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 Oct 3 02:34:39 2024

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