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

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

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

Protein crystallography data

The structure of Sixty Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5jac 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) 37.63 / 1.18
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.372, 184.372, 184.372, 90.00, 90.00, 90.00
R / Rfree (%) 12.1 / 13.4

Other elements in 5jac:

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

Iron (Fe) 3 atoms
Chlorine (Cl) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sixty Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A (pdb code 5jac). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Sixty Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5jac:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5jac

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Magnesium binding site 1 out of 9 in the Sixty 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 Sixty 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:12.0
occ:0.60
 O A:HOH618 2.0 15.1 0.6
O A:HOH383 2.0 11.8 0.6
O A:HOH633 2.1 15.8 0.6
O A:HOH429 2.1 12.8 0.6
O A:HOH539 2.1 12.5 0.6
O A:HOH622 2.1 14.7 0.6
O A:SER131 4.2 13.7 1.0
O A:HOH573 4.3 30.7 1.0
O A:GLU130 4.4 13.2 1.0
O A:HOH544 4.4 33.7 1.0
CA A:SER131 4.5 11.3 0.5
CA A:SER131 4.5 10.5 0.5
O A:HOH600 4.6 34.0 1.0
O A:HOH582 4.6 30.7 1.0
CB A:GLU135 4.7 12.1 1.0
C A:SER131 4.8 10.6 1.0
CG A:GLU135 4.9 12.2 0.9
CL A:CL208 4.9 13.6 0.6

Magnesium binding site 2 out of 9 in 5jac

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Magnesium binding site 2 out of 9 in the Sixty 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 Sixty 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:14.2
occ:0.50
 O A:HOH537 1.9 25.6 1.0
O A:HOH619 2.1 28.7 1.0
O A:HOH634 2.1 27.4 1.0
O A:HOH637 2.1 22.8 1.0
O A:HOH623 2.1 16.9 1.0
O A:HOH641 2.2 28.3 1.0
O A:HOH447 4.2 17.7 1.0
O A:HOH367 4.5 15.0 1.0

Magnesium binding site 3 out of 9 in 5jac

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Magnesium binding site 3 out of 9 in the Sixty 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 Sixty 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:16.3
occ:0.40
 O A:HOH527 2.1 19.5 0.4
O A:HOH604 2.1 24.0 1.0
O A:HOH506 2.2 24.4 1.0
NE2 A:HIS45 3.5 13.8 0.6
CD2 A:HIS45 3.6 12.5 0.6
CE1 A:HIS45 4.0 13.5 0.6
CG A:HIS45 4.2 11.4 0.6
O A:HOH635 4.2 39.9 1.0
ND1 A:HIS45 4.4 13.0 0.6
ND1 A:HIS45 4.7 15.7 0.4
CG A:HIS45 5.0 13.2 0.4

Magnesium binding site 4 out of 9 in 5jac

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Magnesium binding site 4 out of 9 in the Sixty 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 Sixty 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:10.5
occ:0.40
 O A:HOH556 2.0 12.3 1.0
O A:HOH501 2.0 14.1 0.5
O A:HOH592 2.1 14.1 0.5
O A:HOH564 2.1 16.1 1.0
O A:HOH338 4.2 13.5 1.0
CD A:LYS82 4.4 11.4 0.5
O A:HOH572 4.4 17.2 1.0
CE A:LYS83 4.6 10.0 0.5
NZ A:LYS82 4.6 9.5 0.4
CE A:LYS82 4.6 12.4 0.4
O A:HOH458 4.8 36.0 1.0
CE A:LYS83 4.8 10.1 0.5
CD A:LYS82 5.0 10.1 0.5

Magnesium binding site 5 out of 9 in 5jac

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Magnesium binding site 5 out of 9 in the Sixty 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 Sixty 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:10.4
occ:0.33
 O A:HOH631 2.0 12.9 1.0
O A:HOH621 2.1 11.6 1.0
OE2 A:GLU130 3.8 11.4 1.0
O A:HOH568 4.2 14.0 1.0
OE1 A:GLU130 4.3 14.3 1.0
O A:HOH406 4.3 16.5 1.0
CD A:GLU130 4.5 11.7 1.0

Magnesium binding site 6 out of 9 in 5jac

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Magnesium binding site 6 out of 9 in the Sixty 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 Sixty 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:13.4
occ:0.33
 O A:HOH614 1.9 30.8 1.0
O A:HOH628 2.0 30.3 1.0
OD1 A:ASP127 3.8 12.3 0.8
OG A:SER131 4.2 10.1 0.5
OE1 A:GLU130 4.2 14.3 1.0
O A:HOH600 4.4 34.0 1.0
O A:HOH539 4.8 12.5 0.6
CG A:ASP127 4.9 11.6 0.8
CB A:GLU130 5.0 10.4 1.0

Magnesium binding site 7 out of 9 in 5jac

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Magnesium binding site 7 out of 9 in the Sixty 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 Sixty 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:15.6
occ:0.80
 O A:HOH566 2.0 20.2 0.8
O A:HOH415 2.0 20.7 0.8
O A:HOH347 2.0 14.7 0.8
O A:HOH450 2.1 18.9 0.8
O A:HOH423 2.1 13.4 1.0
OG A:SER10 2.1 11.4 0.8
CB A:SER10 3.1 10.2 0.2
CB A:SER10 3.2 10.5 0.8
CA A:SER10 3.9 9.4 0.2
CA A:SER10 3.9 9.2 0.8
O A:SER10 4.1 8.8 1.0
OE1 A:GLU13 4.2 9.9 1.0
OG A:SER10 4.2 11.3 0.2
O A:HOH331 4.2 17.5 1.0
O A:HOH530 4.3 35.3 1.0
C A:SER10 4.4 8.6 1.0
O A:HOH521 4.4 14.6 1.0
O A:HOH511 4.4 36.6 1.0
O A:HOH627 4.5 41.6 1.0
CD A:GLU13 4.6 8.6 1.0

Magnesium binding site 8 out of 9 in 5jac

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Magnesium binding site 8 out of 9 in the Sixty 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 Sixty Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg225

b:15.3
occ:0.30
 O A:HOH424 1.8 16.4 0.3
O A:HOH555 1.9 15.1 0.3
O A:HOH553 2.0 26.5 0.3
O A:HOH561 2.1 20.5 0.3
O A:HOH632 2.2 34.8 0.6
O A:HOH380 2.3 15.3 1.0
O A:HOH620 4.0 22.6 1.0
OD1 A:ASN21 4.3 8.3 1.0
O A:HOH542 4.4 22.9 1.0
O A:HOH508 4.4 27.6 0.5
O A:HOH550 4.4 17.0 1.0
O A:ARG18 4.5 8.7 1.0
O A:HOH638 4.5 42.4 1.0
O A:HOH495 4.7 25.0 1.0
O A:HOH597 4.9 16.9 1.0
CB A:LEU22 4.9 8.9 1.0

Magnesium binding site 9 out of 9 in 5jac

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Magnesium binding site 9 out of 9 in the Sixty 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 9 of Sixty Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg226

b:32.7
occ:0.30
 O A:HOH643 1.9 16.4 0.3
O A:HOH642 2.9 19.6 1.0
O A:HOH645 3.6 33.2 1.0
O A:HOH406 4.1 16.5 1.0
CG2 A:THR118 4.2 11.6 1.0
O A:HOH372 4.5 23.9 1.0
O A:HOH603 4.9 26.5 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 17:39:40 2024

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