Magnesium 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:

Chlorine (Cl) 11 atoms
Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7o6c

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Magnesium binding site 1 out of 6 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 Magnesium with other atoms in the Mg 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:Mg209

b:15.1
occ:0.60
 O A:HOH428 2.0 17.9 0.6
O A:HOH379 2.0 15.9 0.6
O A:HOH560 2.0 19.8 0.6
O A:HOH575 2.0 21.5 0.6
O A:HOH550 2.1 20.0 0.6
O A:HOH423 2.1 24.6 1.0
O A:HOH653 3.7 25.9 0.5
OG A:SER42 4.0 11.0 0.5
OD1 A:ASN49 4.2 15.6 0.7
OG A:SER52 4.2 11.4 0.9
CB A:ASN49 4.3 13.3 1.0
O A:ASN49 4.3 11.1 1.0
CB A:SER52 4.4 11.2 0.1
O A:HOH567 4.5 29.2 0.5
CG A:ASN49 4.5 15.8 0.7
CB A:SER52 4.5 10.7 0.9
NE A:ARG53 4.5 19.3 0.5
CG A:ARG53 4.6 16.9 0.5
CA A:ASN49 4.6 11.3 1.0
O A:HOH445 4.7 25.6 1.0
O A:HOH554 4.9 29.4 0.4
CB A:SER42 4.9 12.6 0.5
OG A:SER52 5.0 11.2 0.1
C A:ASN49 5.0 10.8 1.0

Magnesium binding site 2 out of 6 in 7o6c

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Magnesium binding site 2 out of 6 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 Magnesium with other atoms in the Mg 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:Mg210

b:24.8
occ:0.50
 O A:HOH667 1.9 31.2 0.5
O A:HOH378 1.9 33.2 1.0
O A:HOH646 2.0 30.0 0.5
O A:HOH662 2.0 28.4 0.5
O A:HOH665 2.0 35.2 0.5
O A:HOH581 2.3 24.2 0.5
O A:HOH581 2.4 25.4 0.5
O A:HOH650 4.0 38.1 0.5
O A:HOH327 4.3 18.6 1.0
O A:HOH425 4.4 18.4 1.0
OE2 A:GLU17 4.5 14.2 1.0
O A:HOH538 4.6 32.8 1.0
O A:HOH593 4.6 28.7 0.6
CB A:PRO14 4.7 14.5 1.0
O A:HOH547 4.8 38.3 1.0
O A:HOH535 4.9 24.0 0.5
CG A:PRO14 4.9 16.9 1.0

Magnesium binding site 3 out of 6 in 7o6c

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Magnesium binding site 3 out of 6 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 Magnesium with other atoms in the Mg 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:Mg211

b:14.1
occ:0.70
 O A:HOH440 1.6 15.4 0.3
O A:HOH421 2.0 16.7 0.7
O A:HOH596 2.0 19.5 0.7
O A:HOH661 2.1 22.0 0.7
O A:HOH592 2.1 20.4 0.7
O A:HOH664 2.1 23.4 0.7
O A:HOH406 2.3 17.5 1.0
O A:HOH654 4.2 34.6 0.5
OD1 A:ASN25 4.3 10.5 1.0
O A:HOH578 4.3 22.7 1.0
O A:ARG22 4.4 10.0 1.0
O A:HOH644 4.4 23.6 0.5
CL A:CL221 4.4 24.3 0.7
O A:HOH627 4.4 16.7 0.5
O A:HOH405 4.5 25.2 1.0
O A:HOH336 4.6 25.6 0.4
O A:HOH627 4.8 15.5 0.5
CB A:LEU26 4.9 10.1 1.0
CB A:ARG22 4.9 12.8 0.6
O A:HOH623 4.9 28.3 1.0

Magnesium binding site 4 out of 6 in 7o6c

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Magnesium binding site 4 out of 6 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 Magnesium with other atoms in the Mg 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:Mg212

b:12.3
occ:0.50
 O A:HOH601 2.0 14.4 1.0
O A:HOH611 2.1 14.8 0.5
O A:HOH636 2.1 18.4 1.0
O A:HOH350 4.2 15.3 1.0
CD A:LYS86 4.4 13.5 0.3
O A:HOH642 4.4 24.5 1.0
CE A:LYS87 4.5 13.5 0.4
CE A:LYS86 4.6 13.9 0.3
NZ A:LYS86 4.6 12.1 0.5
O A:HOH519 4.7 21.3 1.0
CL A:CL216 4.7 15.9 0.7
CE A:LYS87 4.9 15.0 0.6
CD A:LYS86 4.9 11.8 0.5

Magnesium binding site 5 out of 6 in 7o6c

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Magnesium binding site 5 out of 6 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 Magnesium with other atoms in the Mg 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:Mg213

b:18.8
occ:0.50
 O A:HOH364 1.8 22.4 0.8
O A:HOH540 2.0 30.6 0.5
O A:HOH614 2.0 31.8 0.5
O A:GLU94 2.1 12.1 1.0
O A:HOH514 2.2 27.7 0.5
O A:HOH540 2.3 21.9 0.5
O A:HOH479 2.4 32.0 1.0
C A:GLU94 3.3 11.0 1.0
CA A:GLU94 3.9 11.7 1.0
O A:HOH459 4.2 16.3 1.0
O A:HOH453 4.2 26.6 0.5
N A:SER95 4.3 10.6 1.0
CB A:SER95 4.4 10.7 1.0
CB A:GLU94 4.4 13.3 1.0
O A:HOH326 4.4 22.2 1.0
O A:HOH380 4.4 27.2 0.6
CA A:SER95 4.6 10.8 1.0
O A:HOH420 4.7 29.2 1.0
O A:HOH496 4.7 14.6 1.0
O A:HOH480 4.7 26.6 1.0
OH A:TYR40 4.8 14.4 1.0

Magnesium binding site 6 out of 6 in 7o6c

Go back to Magnesium Binding Sites List in 7o6c
Magnesium binding site 6 out of 6 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 Magnesium with other atoms in the Mg 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:Mg214

b:18.1
occ:0.40
 O A:HOH449 1.9 24.6 0.5
O A:HOH468 2.1 22.3 0.5
O A:THR135 4.2 21.4 1.0
O A:HOH521 4.4 28.3 0.7
O A:GLU134 4.8 19.6 1.0
CA A:THR135 4.8 16.7 1.0
C A:THR135 4.9 17.7 1.0
O A:HOH429 4.9 28.1 0.5
CL A:CL218 5.0 24.1 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 Oct 3 02:34:59 2024

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