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Magnesium in PDB 5j93: Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

Enzymatic activity of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

All present enzymatic activity of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A:
1.16.3.1;

Protein crystallography data

The structure of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j93 was solved by C.Pozzi, F.Di Pisa, S.Mangani, C.Bernacchioni, P.Turano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.95 / 1.10
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.782, 183.782, 183.782, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 14.3

Other elements in 5j93:

The structure of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Chlorine (Cl) 13 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A (pdb code 5j93). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j93:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5j93

Go back to Magnesium Binding Sites List in 5j93
Magnesium binding site 1 out of 8 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg217

b:13.0
occ:0.50
 O A:HOH624 1.9 16.4 0.5
O A:HOH325 2.0 12.6 1.0
O A:HOH320 2.1 19.5 0.5
O A:HOH619 2.1 14.8 1.0
OD2 A:ASP80 4.1 7.9 1.0
OD1 A:ASP80 4.1 6.7 1.0
CG A:ASP80 4.5 6.4 1.0
O A:HOH473 4.8 10.0 1.0

Magnesium binding site 2 out of 8 in 5j93

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Magnesium binding site 2 out of 8 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg218

b:12.4
occ:0.90
 O A:HOH607 2.0 15.5 0.9
O A:HOH614 2.0 16.1 0.9
O A:HOH386 2.1 12.3 0.9
O A:HOH629 2.1 16.9 0.9
O A:HOH539 2.1 13.9 0.9
O A:HOH419 2.1 13.9 0.9
O A:SER131 4.2 10.4 1.0
O A:HOH578 4.2 27.0 1.0
O A:HOH519 4.3 25.0 1.0
O A:GLU130 4.4 11.7 1.0
CA A:SER131 4.5 11.5 0.4
CA A:SER131 4.5 9.7 0.6
O A:HOH420 4.6 23.9 1.0
O A:HOH586 4.6 30.0 1.0
C A:SER131 4.7 8.7 1.0
CB A:GLU135 4.7 10.5 1.0
CL A:CL207 4.9 13.6 0.8
CG A:GLU135 4.9 10.4 0.9

Magnesium binding site 3 out of 8 in 5j93

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Magnesium binding site 3 out of 8 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg219

b:15.3
occ:0.60
 O A:HOH518 2.0 22.2 0.6
O A:HOH527 2.0 16.1 0.4
O A:HOH625 2.0 22.9 0.6
O A:HOH506 2.1 13.4 0.6
O A:HOH599 2.1 20.1 0.6
O A:HOH533 2.1 20.9 0.6
O A:HOH564 2.4 12.9 0.4
NE2 A:HIS45 3.5 11.3 0.5
CD2 A:HIS45 3.7 10.9 0.5
CE1 A:HIS45 3.9 11.2 0.5
CG A:HIS45 4.2 10.5 0.5
O A:HOH437 4.2 17.4 0.5
O A:HOH582 4.3 36.0 1.0
ND1 A:HIS45 4.3 10.9 0.5
O A:HOH536 4.4 42.7 1.0
ND1 A:HIS45 4.6 13.8 0.5
CG A:HIS45 5.0 12.9 0.5

Magnesium binding site 4 out of 8 in 5j93

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Magnesium binding site 4 out of 8 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg220

b:9.6
occ:0.25
 O A:HOH490 1.6 16.8 0.8
O A:HOH482 2.1 23.1 0.8
OD1 A:ASP127 3.8 13.4 1.0
OG A:SER131 4.2 10.3 0.6
O A:HOH420 4.2 23.9 1.0
OE1 A:GLU130 4.3 13.0 1.0
O A:HOH539 4.9 13.9 0.9
CG A:ASP127 4.9 10.9 1.0
CB A:GLU130 4.9 9.0 1.0

Magnesium binding site 5 out of 8 in 5j93

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Magnesium binding site 5 out of 8 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg221

b:13.7
occ:0.60
 O A:HOH372 2.0 19.0 0.6
O A:HOH556 2.0 19.7 0.6
O A:HOH562 2.1 18.9 0.6
O A:HOH622 2.1 25.6 0.6
O A:HOH626 2.2 26.5 0.6
O A:HOH410 2.3 13.3 1.0
O A:HOH597 2.4 18.4 0.4
O A:HOH612 4.1 22.4 1.0
OD1 A:ASN21 4.3 7.7 1.0
O A:HOH628 4.3 36.2 1.0
O A:HOH550 4.4 21.5 1.0
O A:ARG18 4.4 7.2 1.0
CL A:CL212 4.5 20.5 0.7
O A:HOH529 4.6 24.9 1.0
O A:HOH486 4.7 52.4 1.0
O A:HOH593 4.8 17.0 1.0
CB A:LEU22 4.8 7.6 1.0

Magnesium binding site 6 out of 8 in 5j93

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Magnesium binding site 6 out of 8 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg222

b:13.3
occ:0.80
 O A:HOH362 2.0 13.9 0.8
O A:HOH457 2.0 16.8 0.8
O A:HOH567 2.1 18.7 0.8
O A:HOH435 2.1 17.2 0.8
O A:HOH414 2.1 12.6 1.0
OG A:SER10 2.1 9.4 0.8
CB A:SER10 3.2 9.6 0.2
CB A:SER10 3.2 8.9 0.8
CA A:SER10 3.9 9.3 0.2
CA A:SER10 3.9 8.3 0.8
O A:SER10 4.1 8.3 1.0
OE1 A:GLU13 4.2 9.6 1.0
O A:HOH335 4.3 16.2 1.0
OG A:SER10 4.3 9.8 0.2
C A:SER10 4.4 7.5 1.0
O A:HOH512 4.4 32.0 1.0
O A:HOH525 4.4 14.0 1.0
O A:HOH623 4.5 41.6 1.0
CD A:GLU13 4.6 8.1 1.0

Magnesium binding site 7 out of 8 in 5j93

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Magnesium binding site 7 out of 8 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg223

b:16.0
occ:0.60
 O A:HOH534 2.0 19.0 0.6
O A:HOH633 2.0 17.6 0.6
O A:HOH630 2.1 20.4 0.6
O A:HOH616 2.1 17.2 1.0
O A:HOH606 2.1 22.0 0.6
O A:HOH634 2.1 34.5 0.6
O A:HOH427 4.2 17.2 1.0
O A:HOH369 4.5 15.1 1.0

Magnesium binding site 8 out of 8 in 5j93

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Magnesium binding site 8 out of 8 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg224

b:8.0
occ:0.33
 O A:HOH520 2.0 8.4 0.8
O A:HOH333 2.1 7.7 0.8
OE2 A:GLU130 3.9 10.4 1.0
O A:HOH566 4.2 12.4 1.0
OE1 A:GLU130 4.3 13.0 1.0
O A:HOH404 4.3 15.8 1.0
CD A:GLU130 4.5 10.8 1.0

Reference:

C.Bernacchioni, C.Pozzi, F.Di Pisa, S.Mangani, P.Turano. Ferroxidase Activity in Eukaryotic Ferritin Is Controlled By Accessory-Iron-Binding Sites in the Catalytic Cavity. Chemistry V. 22 16213 2016.
ISSN: ISSN 0947-6539
PubMed: 27650996
DOI: 10.1002/CHEM.201602842
Page generated: Sun Sep 29 17:39:01 2024

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