Iron in PDB 4y08: One Minute Iron Loaded Human H Ferritin

All present enzymatic activity of One Minute Iron Loaded Human H Ferritin:
1.16.3.1;

The structure of One Minute Iron Loaded Human H Ferritin, PDB code: 4y08 was solved by C.Pozzi, F.Di Pisa, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.76 / 1.34
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	184.140, 184.140, 184.140, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 17.3

The structure of One Minute Iron Loaded Human H Ferritin also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	9 atoms

The binding sites of Iron atom in the One Minute Iron Loaded Human H Ferritin (pdb code 4y08). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the One Minute Iron Loaded Human H Ferritin, PDB code: 4y08:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of One Minute Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:8.2 occ:0.70 O A:HOH627 1.9 11.0 0.5 OE2 A:GLU27 2.0 8.0 1.0 O2 A:OXY219 2.0 7.9 0.2 OE2 A:GLU62 2.1 11.1 1.0 O A:HOH611 2.1 9.9 1.0 ND1 A:HIS65 2.2 9.6 1.0 O1 A:OXY219 2.4 7.9 0.2 O A:HOH625 2.5 12.7 0.3 CE1 A:HIS65 3.1 10.1 1.0 CD A:GLU27 3.1 7.8 1.0 CD A:GLU62 3.1 10.8 1.0 CG A:HIS65 3.2 9.3 1.0 OE1 A:GLU62 3.4 12.3 1.0 OE1 A:GLU27 3.4 8.2 1.0 FE A:FE2202 3.5 12.2 0.2 CB A:HIS65 3.6 8.5 1.0 OE1 A:GLN141 3.8 10.9 0.5 O A:HOH494 4.1 17.4 1.0 OE1 A:GLN141 4.1 7.4 0.5 NE2 A:HIS65 4.2 10.2 1.0 CG1 A:VAL110 4.2 10.6 1.0 CD2 A:HIS65 4.3 9.8 1.0 CG A:GLU27 4.4 7.6 1.0 CG A:GLU62 4.4 10.1 1.0 CA A:GLU62 4.6 8.7 1.0 CB A:GLU62 4.7 9.2 1.0 O1 A:OXY220 4.7 10.4 0.3 CB A:GLU27 4.7 7.3 1.0 O2 A:OXY220 4.8 10.4 0.3 CD A:GLN141 4.9 7.6 0.5 OE1 A:GLU107 5.0 9.5 0.4 CA A:GLU27 5.0 7.0 1.0 CD A:GLN141 5.0 10.1 0.5

Iron binding site 2 out of 5 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of One Minute Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:12.2 occ:0.20 O A:HOH627 1.8 11.0 0.5 O1 A:OXY219 1.9 7.9 0.2 O2 A:OXY219 1.9 7.9 0.2 OE1 A:GLU107 2.0 11.7 0.6 OE1 A:GLU62 2.1 12.3 1.0 OE1 A:GLU107 2.2 9.5 0.4 OE2 A:GLU107 2.2 9.9 0.4 CD A:GLU107 2.4 11.1 0.6 CD A:GLU107 2.4 9.6 0.4 OE2 A:GLU107 2.5 11.4 0.6 O A:HOH625 2.5 12.7 0.3 O2 A:OXY220 2.7 10.4 0.3 FE A:FE2203 2.7 15.8 0.3 CD A:GLU62 3.0 10.8 1.0 O1 A:OXY220 3.1 10.4 0.3 OE2 A:GLU62 3.3 11.1 1.0 FE A:FE2201 3.5 8.2 0.7 OE1 A:GLN141 3.6 7.4 0.5 OE1 A:GLN141 3.7 10.9 0.5 O A:HOH620 3.8 10.5 0.4 CG A:GLU107 3.8 10.6 0.6 NE2 A:GLN141 3.9 7.7 0.5 CG A:GLU107 3.9 9.6 0.4 CD A:GLN141 4.2 7.6 0.5 O A:HOH622 4.3 14.8 0.3 CE1 A:HIS65 4.3 10.1 1.0 CG A:GLU62 4.3 10.1 1.0 NE2 A:GLN141 4.4 10.6 0.5 CD A:GLN141 4.4 10.1 0.5 CE2 A:TYR34 4.5 9.2 1.0 ND1 A:HIS65 4.5 9.6 1.0 CB A:GLU107 4.6 10.0 0.6 O A:HOH619 4.6 4.4 0.3 O A:HOH611 4.6 9.9 1.0 OE1 A:GLN58 4.7 9.0 0.3 OH A:TYR34 4.8 10.9 1.0 CB A:GLU107 4.8 9.4 0.4 CA A:GLU107 4.9 9.7 0.6 O A:HOH621 4.9 12.8 0.4 CA A:GLU107 5.0 9.4 0.4

Iron binding site 3 out of 5 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of One Minute Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:15.8 occ:0.30 O2 A:OXY220 1.8 10.4 0.3 O A:HOH620 1.9 10.5 0.4 O A:HOH619 1.9 4.4 0.3 OE1 A:GLN58 2.4 9.0 0.3 OE2 A:GLU107 2.4 11.4 0.6 O A:HOH622 2.5 14.8 0.3 O A:HOH621 2.6 12.8 0.4 OE1 A:GLU62 2.7 12.3 1.0 FE A:FE2202 2.7 12.2 0.2 O1 A:OXY220 3.0 10.4 0.3 OE2 A:GLU107 3.2 9.9 0.4 CD A:GLU107 3.3 11.1 0.6 OE1 A:GLN58 3.4 10.0 0.5 OE1 A:GLU107 3.4 11.7 0.6 CD A:GLN58 3.5 8.9 0.3 O1 A:OXY219 3.6 7.9 0.2 CD A:GLU107 3.8 9.6 0.4 CD A:GLU62 3.9 10.8 1.0 OE1 A:GLU61 4.0 14.9 0.7 NE2 A:GLN58 4.0 9.0 0.3 O A:HOH627 4.0 11.0 0.5 OE1 A:GLU107 4.1 9.5 0.4 OE2 A:GLU140 4.2 11.4 0.5 OH A:TYR34 4.2 10.9 1.0 CE2 A:TYR34 4.2 9.2 1.0 O A:HOH514 4.3 18.7 0.6 O2 A:OXY219 4.3 7.9 0.2 CB A:ALA144 4.3 7.9 1.0 CD A:GLN58 4.4 9.7 0.5 CE1 A:HIS65 4.5 10.1 1.0 CZ A:TYR34 4.6 9.6 1.0 CG A:GLU107 4.7 10.6 0.6 CG A:GLU62 4.7 10.1 1.0 CG A:GLU107 4.7 9.6 0.4 CG A:GLN58 4.7 8.8 0.3 CB A:GLN58 4.8 8.9 0.5 OE2 A:GLU62 4.8 11.1 1.0 O A:HOH491 4.9 20.7 1.0 CB A:GLN58 4.9 8.6 0.3 CG A:GLN58 5.0 9.4 0.5 O A:GLN58 5.0 8.7 1.0

Iron binding site 4 out of 5 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of One Minute Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:13.8 occ:0.05 CL A:CL208 2.5 8.7 0.2 CE1 A:HIS173 2.7 13.2 1.0 NE2 A:HIS173 2.7 14.0 1.0 CL A:CL210 3.1 15.7 0.1 ND1 A:HIS173 3.9 13.1 1.0 CD2 A:HIS173 4.0 13.0 1.0 CG A:HIS173 4.6 12.0 1.0

Iron binding site 5 out of 5 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of One Minute Iron Loaded Human H Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe221 b:18.8 occ:0.20 NE2 A:HIS57 2.0 13.3 0.7 OE2 A:GLU61 2.0 14.5 0.7 CE1 A:HIS57 2.7 13.1 0.7 CD A:GLU61 3.2 13.7 0.7 CD2 A:HIS57 3.3 12.7 0.7 CG A:GLU61 3.7 12.6 1.0 ND1 A:HIS57 3.9 12.7 0.7 CG A:HIS57 4.2 11.9 0.7 OE1 A:GLU61 4.2 14.9 0.7 O A:HOH542 4.3 30.0 1.0 O A:HOH527 4.5 26.2 1.0

C.Pozzi, F.Di Pisa, C.Bernacchioni, S.Ciambellotti, P.Turano, S.Mangani. Iron Binding to Human Heavy-Chain Ferritin. Acta Crystallogr.,Sect.D V. 71 1909 2015.
ISSN: ESSN 1399-0047
PubMed: 26327381
DOI: 10.1107/S1399004715013073