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Magnesium in PDB 8aav: Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand

Protein crystallography data

The structure of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand, PDB code: 8aav was solved by H.Boehler, T.Beck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.54 / 2.00
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 181.44, 181.44, 181.44, 90, 90, 90
R / Rfree (%) 14.4 / 17.7

Other elements in 8aav:

The structure of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand (pdb code 8aav). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand, PDB code: 8aav:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 8aav

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Magnesium binding site 1 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:26.2
occ:1.00
 O C:HOH419 1.9 30.2 1.0
O D:HOH411 2.0 41.3 1.0
O D:HOH350 2.0 23.1 1.0
O A:HOH408 2.1 37.4 1.0
O A:HOH314 2.1 26.1 1.0
O C:HOH311 2.1 24.1 1.0
OE2 A:GLU134 3.7 25.4 1.0
OE2 D:GLU134 3.8 23.5 1.0
O A:HOH346 3.8 31.7 1.0
OE2 C:GLU134 3.9 22.0 1.0
O C:HOH344 3.9 36.6 1.0
O D:HOH337 4.0 31.9 1.0
O A:HOH431 4.1 31.6 1.0
O D:HOH366 4.1 25.9 1.0
O A:HOH333 4.2 26.6 1.0
OE1 A:GLU134 4.4 31.8 1.0
OE1 D:GLU134 4.4 33.2 1.0
CD A:GLU134 4.5 24.2 1.0
OE1 C:GLU134 4.5 33.5 1.0
CD D:GLU134 4.5 23.5 1.0
CD C:GLU134 4.6 24.5 1.0

Magnesium binding site 2 out of 15 in 8aav

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Magnesium binding site 2 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:45.7
occ:1.00
 OE1 A:GLN58 2.1 33.5 1.0
O A:HOH332 2.2 33.0 1.0
O A:HOH403 2.2 35.8 1.0
O A:HOH301 2.3 41.2 1.0
OE1 A:GLU61 3.1 54.0 1.0
CD A:GLN58 3.3 29.8 1.0
O A:HOH358 3.4 49.3 1.0
CD A:GLU61 3.6 49.2 1.0
OE2 A:GLU107 3.8 33.0 1.0
OE2 A:GLU62 3.9 25.4 1.0
OE2 A:GLU61 4.0 50.7 1.0
NE2 A:GLN58 4.0 34.9 1.0
OE2 A:GLU140 4.0 56.9 1.0
CB A:ALA144 4.2 16.4 1.0
CG A:GLN58 4.4 21.9 1.0
CG A:GLU61 4.5 36.4 1.0
CD A:GLU107 4.7 29.3 1.0
CB A:GLN58 4.7 17.7 1.0
CA A:GLN58 4.8 15.5 1.0
O A:HOH306 4.9 28.4 1.0
CB A:GLU61 4.9 23.7 1.0
OH A:TYR34 4.9 24.9 1.0
CD A:GLU62 5.0 19.3 1.0

Magnesium binding site 3 out of 15 in 8aav

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Magnesium binding site 3 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:27.2
occ:0.33
 O B:HOH417 1.9 31.0 1.0
O B:HOH313 2.1 22.6 1.0
OE2 B:GLU134 3.8 26.7 1.0
O B:HOH360 4.0 32.9 1.0
O B:HOH342 4.2 22.4 1.0
OE1 B:GLU134 4.4 32.8 1.0
CD B:GLU134 4.5 27.6 1.0

Magnesium binding site 4 out of 15 in 8aav

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Magnesium binding site 4 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:14.2
occ:0.50
 O B:HOH347 2.0 14.9 1.0
OD2 B:ASP84 2.0 12.8 1.0
CG B:ASP84 3.1 12.9 1.0
CB B:ASP84 3.5 11.5 1.0
O B:HOH349 4.2 15.8 1.0
OD1 B:ASP84 4.2 12.3 1.0
O B:HOH441 4.4 23.7 1.0
O B:HOH371 4.5 14.0 1.0
O B:HOH327 4.9 16.7 1.0
O B:HOH316 4.9 27.4 1.0
CA B:ASP84 4.9 12.0 1.0

Magnesium binding site 5 out of 15 in 8aav

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Magnesium binding site 5 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:46.4
occ:1.00
 O B:HOH305 2.0 42.5 1.0
O B:HOH424 2.1 43.3 1.0
OE1 B:GLN58 2.1 36.0 1.0
O B:HOH312 2.2 30.5 1.0
O B:HOH302 2.2 40.0 1.0
O B:HOH409 2.3 33.5 1.0
CD B:GLN58 3.3 28.8 1.0
NE2 B:GLN58 3.9 33.9 1.0
OE2 B:GLU62 4.1 27.2 1.0
O B:HOH356 4.1 49.6 1.0
OE2 B:GLU140 4.1 60.5 1.0
OE2 B:GLU107 4.3 36.6 1.0
CB B:ALA144 4.4 16.5 1.0
CG B:GLN58 4.5 23.2 1.0
CB B:GLU61 4.5 23.0 1.0
CB B:GLN58 4.7 19.6 1.0
CA B:GLN58 4.7 16.9 1.0
O B:GLN58 4.9 15.0 1.0
CE1 B:HIS65 4.9 23.8 1.0
O B:HOH310 5.0 30.4 1.0

Magnesium binding site 6 out of 15 in 8aav

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Magnesium binding site 6 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg204

b:49.7
occ:1.00
 O C:HOH364 2.0 42.0 1.0
O C:HOH306 2.0 47.2 1.0
OE1 C:GLN58 2.2 31.6 1.0
O C:HOH307 2.2 31.8 1.0
O C:HOH432 2.3 44.3 1.0
O C:HOH414 2.4 40.9 1.0
CD C:GLN58 3.4 29.3 1.0
NE2 C:GLN58 4.0 37.0 1.0
OE2 C:GLU62 4.1 26.8 1.0
O C:HOH418 4.2 39.6 1.0
CB C:GLU61 4.4 21.9 1.0
OE2 C:GLU107 4.4 25.4 1.0
CB C:ALA144 4.5 17.1 1.0
CG C:GLN58 4.5 22.3 1.0
O C:HOH411 4.6 27.0 1.0
CB C:GLN58 4.6 18.1 1.0
CA C:GLN58 4.7 16.4 1.0
CG C:GLU61 4.7 31.1 1.0
O C:GLN58 4.9 14.2 1.0
CE1 C:HIS65 4.9 23.2 1.0

Magnesium binding site 7 out of 15 in 8aav

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Magnesium binding site 7 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg205

b:20.5
occ:0.50
 OD2 C:ASP84 2.0 16.2 1.0
O E:HOH327 2.1 14.8 1.0
O C:HOH380 2.2 16.4 1.0
CG C:ASP84 3.1 15.1 1.0
CB C:ASP84 3.5 12.9 1.0
OD1 C:ASP84 4.2 15.1 1.0
NE2 E:GLN86 4.2 20.8 1.0
OE1 E:GLN86 4.3 28.2 1.0
OD2 E:ASP84 4.3 18.6 1.0
O C:HOH338 4.5 12.5 1.0
O C:HOH318 4.7 15.5 1.0
CD E:GLN86 4.7 21.6 1.0
CA C:ASP84 4.9 13.5 1.0

Magnesium binding site 8 out of 15 in 8aav

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Magnesium binding site 8 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:27.9
occ:0.33
 O E:HOH415 2.1 31.5 1.0
O E:HOH305 2.2 26.9 1.0
OE2 E:GLU134 3.9 21.1 1.0
O E:HOH307 4.0 30.2 0.3
O E:HOH313 4.2 23.0 1.0
OE1 E:GLU134 4.6 31.7 1.0
CD E:GLU134 4.6 23.1 1.0

Magnesium binding site 9 out of 15 in 8aav

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Magnesium binding site 9 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg205

b:46.6
occ:1.00
 OE1 E:GLN58 2.1 33.4 1.0
O E:HOH396 2.1 32.4 1.0
O E:HOH324 2.1 47.9 1.0
O E:HOH330 2.1 35.0 1.0
CD E:GLN58 3.3 27.4 1.0
NE2 E:GLN58 3.9 30.1 1.0
OE2 E:GLU62 4.2 27.2 1.0
CB E:GLU61 4.4 21.1 1.0
CG E:GLN58 4.5 21.1 1.0
O E:HOH413 4.5 26.9 1.0
CB E:GLN58 4.6 19.3 1.0
CA E:GLN58 4.6 16.2 1.0
OE2 E:GLU107 4.6 32.1 1.0
CB E:ALA144 4.6 17.2 1.0
CG E:GLU61 4.7 29.4 1.0
CE1 E:HIS65 5.0 24.0 1.0
O E:GLN58 5.0 14.6 1.0

Magnesium binding site 10 out of 15 in 8aav

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Magnesium binding site 10 out of 15 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg204

b:25.1
occ:1.00
 O H:HOH411 2.0 30.7 1.0
O F:HOH427 2.0 33.1 1.0
O H:HOH316 2.0 26.2 1.0
O F:HOH311 2.2 22.4 1.0
OE2 F:GLU134 3.8 22.2 1.0
OE2 H:GLU134 3.9 26.4 1.0
O F:HOH354 3.9 35.8 1.0
O F:HOH374 4.0 37.1 1.0
O H:HOH357 4.0 24.0 1.0
O F:HOH319 4.3 23.9 1.0
OE1 F:GLU134 4.5 30.2 1.0
OE1 H:GLU134 4.5 33.2 1.0
CD F:GLU134 4.6 24.2 1.0
CD H:GLU134 4.6 25.6 1.0

Reference:

H.Bohler, S.Orth-Alampour, C.Baaten, M.Riedner, J.Jankowski, T.Beck. Assembly of Chemically Modified Protein Nanocages Into 3D Materials For the Adsorption of Uremic Toxins. J Mater Chem B V. 11 55 2022.
ISSN: ESSN 2050-7518
PubMed: 36504125
DOI: 10.1039/D2TB02386E
Page generated: Thu Oct 3 18:02:33 2024

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