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Magnesium in PDB 7o6d: Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment

Enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment

All present enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 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 3 Minutes Under Anaerobic Environment, PDB code: 7o6d 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) 28.09 / 1.47
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.09, 184.09, 184.09, 90, 90, 90
R / Rfree (%) 14.6 / 15.7

Other elements in 7o6d:

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment (pdb code 7o6d). 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 3 Minutes Under Anaerobic Environment, PDB code: 7o6d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7o6d

Go back to Magnesium Binding Sites List in 7o6d
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


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 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:24.3
occ:0.40
 O A:HOH650 1.9 26.0 0.4
O A:HOH546 2.2 21.8 0.4
O A:HOH543 2.3 31.4 0.5
O A:HOH546 3.3 17.1 0.6
NH2 A:ARG7 4.2 26.1 1.0
NE A:ARG7 4.4 23.8 1.0
O A:HOH569 4.4 37.8 1.0
O A:HOH616 4.4 36.3 0.5
O A:HOH543 4.4 36.1 0.5
CZ A:ARG7 4.8 24.9 1.0

Magnesium binding site 2 out of 3 in 7o6d

Go back to Magnesium Binding Sites List in 7o6d
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


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 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:22.1
occ:0.50
 O A:HOH384 1.9 32.7 1.0
O A:HOH606 1.9 26.6 0.5
O A:HOH581 2.1 37.8 1.0
O A:HOH651 2.1 28.4 0.5
O A:HOH422 2.3 22.4 1.0
O A:HOH608 4.3 34.3 0.5
OD1 A:ASN25 4.3 14.6 1.0
O A:HOH653 4.3 34.0 0.5
O A:HOH610 4.4 22.2 1.0
O A:HOH637 4.4 17.2 0.3
O A:ARG22 4.4 13.8 1.0
O A:HOH580 4.4 28.8 1.0
O A:HOH376 4.7 28.9 1.0
CB A:LEU26 4.9 13.5 1.0
O A:HOH612 5.0 34.8 1.0

Magnesium binding site 3 out of 3 in 7o6d

Go back to Magnesium Binding Sites List in 7o6d
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


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 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:22.4
occ:0.50
 O A:HOH371 2.0 21.9 0.5
O A:HOH416 2.0 30.1 1.0
O A:HOH505 2.1 30.1 0.5
O A:HOH309 2.1 20.1 0.5
O A:HOH561 2.1 24.3 0.5
O A:HOH649 3.6 38.4 1.0
NH1 A:ARG53 3.8 29.5 0.5
OG A:SER42 4.0 16.2 0.5
O A:HOH588 4.0 32.3 1.0
OG A:SER52 4.2 16.6 1.0
OD1 A:ASN49 4.2 24.3 1.0
CB A:ASN49 4.3 17.6 1.0
O A:ASN49 4.4 14.5 1.0
CG A:ASN49 4.4 24.4 1.0
CB A:SER52 4.5 15.0 1.0
CG A:ARG53 4.6 20.1 0.5
CA A:ASN49 4.7 14.6 1.0
O A:HOH411 4.7 34.4 1.0
CZ A:ARG53 4.8 26.4 0.5
CB A:SER42 4.8 14.4 0.5

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 14 11:36:26 2025

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