Iron in PDB 5j93: 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;

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

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

Magnesium	(Mg)	8 atoms
Chlorine	(Cl)	13 atoms

The binding sites of Iron 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 Iron atom.
In total 3 binding sites of Iron where determined in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j93:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe201 b:8.4 occ:0.80 OE1 A:GLU23 2.0 9.5 1.0 O A:HOH336 2.0 13.7 0.8 OE1 A:GLU58 2.1 12.2 1.0 ND1 A:HIS61 2.2 10.9 1.0 O A:HOH317 2.2 11.1 1.0 O A:HOH417 2.6 3.9 0.2 CD A:GLU23 3.0 8.5 1.0 CE1 A:HIS61 3.0 12.3 1.0 CD A:GLU58 3.1 10.8 1.0 CG A:HIS61 3.3 9.8 1.0 OE2 A:GLU23 3.3 11.4 1.0 OE2 A:GLU58 3.5 14.4 1.0 FE A:FE2202 3.6 11.6 0.6 CB A:HIS61 3.6 8.0 1.0 CG1 A:VAL106 4.1 10.7 1.0 OE1 A:GLN137 4.1 8.8 0.5 NE2 A:HIS61 4.2 12.5 1.0 OE1 A:GLN137 4.2 13.4 0.4 O A:HOH455 4.3 14.8 1.0 CG A:GLU23 4.3 8.1 1.0 CD2 A:HIS61 4.3 11.1 1.0 CG A:GLU58 4.4 9.5 1.0 CA A:GLU58 4.5 8.4 1.0 CB A:GLU58 4.6 8.7 1.0 CB A:GLU23 4.7 7.5 1.0 CD A:GLN137 4.9 9.0 0.5 O A:HOH319 4.9 19.3 0.6 O A:HOH319 4.9 11.9 0.4 NE2 A:GLN137 4.9 13.4 0.4 CA A:GLU23 5.0 6.8 1.0 OE1 A:GLU103 5.0 10.4 0.4 CD A:GLN137 5.0 12.7 0.4

Iron binding site 2 out of 3 in the Five Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe202 b:11.6 occ:0.60 OE2 A:GLU58 1.9 14.4 1.0 O A:HOH336 1.9 13.7 0.8 O A:HOH319 2.1 11.9 0.4 OE1 A:GLU103 2.1 10.4 0.4 OE2 A:GLU103 2.2 10.7 0.6 OE1 A:GLU103 2.3 11.0 0.6 OE2 A:GLU103 2.3 11.1 0.4 O A:HOH417 2.4 3.9 0.2 CD A:GLU103 2.5 10.4 0.4 CD A:GLU103 2.6 10.5 0.6 CD A:GLU58 2.9 10.8 1.0 OE1 A:GLU58 3.3 12.2 1.0 FE A:FE2201 3.6 8.4 0.8 OE1 A:GLN137 3.6 8.8 0.5 NE2 A:GLN137 3.7 13.4 0.4 O A:HOH314 3.8 19.5 0.6 CG A:GLU103 4.0 9.9 0.4 O A:HOH307 4.1 17.3 0.5 CG A:GLU103 4.1 9.9 0.6 O A:HOH319 4.2 19.3 0.6 CG A:GLU58 4.2 9.5 1.0 NE2 A:GLN137 4.2 9.2 0.5 OE1 A:GLN137 4.2 13.4 0.4 CE1 A:HIS61 4.3 12.3 1.0 CD A:GLN137 4.3 9.0 0.5 CE2 A:TYR30 4.4 12.0 0.9 CD A:GLN137 4.4 12.7 0.4 ND1 A:HIS61 4.6 10.9 1.0 OH A:TYR30 4.6 15.1 0.9 ND1 A:HIS54 4.6 18.7 0.5 O A:HOH572 4.7 30.1 1.0 O A:HOH317 4.8 11.1 1.0 CB A:GLU103 4.9 9.5 0.4 CE1 A:HIS54 4.9 19.2 0.5 CZ A:TYR30 5.0 12.5 0.9 CB A:GLU103 5.0 9.3 0.6

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe203 b:5.7 occ:0.20 O A:HOH491 2.2 10.6 0.2 NE2 A:HIS169 2.3 7.4 1.0 CL A:CL204 2.4 6.3 0.2 CE1 A:HIS169 3.1 7.7 1.0 CD2 A:HIS169 3.3 7.7 1.0 ND1 A:HIS169 4.3 7.8 1.0 CG A:HIS169 4.4 8.2 1.0

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