Iron in PDB 3rgd: Iron Loaded Frog M Ferritin. Short Soaking Time

All present enzymatic activity of Iron Loaded Frog M Ferritin. Short Soaking Time:
1.16.3.1;

The structure of Iron Loaded Frog M Ferritin. Short Soaking Time, PDB code: 3rgd was solved by I.Bertini, D.Lalli, S.Mangani, C.Pozzi, C.Rosa, E.C.Theil, P.Turano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.54 / 2.89
Space group	P 31 2 1 1
Cell size a, b, c (Å), α, β, γ (°)	210.744, 210.744, 322.036, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 62;

Binding sites:

The binding sites of Iron atom in the Iron Loaded Frog M Ferritin. Short Soaking Time (pdb code 3rgd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 62 binding sites of Iron where determined in the Iron Loaded Frog M Ferritin. Short Soaking Time, PDB code: 3rgd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe180 b:43.1 occ:1.00 OE1 A:GLU59 2.5 31.9 1.0 OE1 A:GLU24 2.7 33.4 1.0 ND1 A:HIS62 2.9 44.8 1.0 OE2 A:GLU24 2.9 37.8 1.0 CD A:GLU24 3.2 34.3 1.0 O A:HOH903 3.3 41.2 1.0 CD A:GLU59 3.5 37.2 1.0 CE1 A:HIS62 3.7 44.8 1.0 OE2 A:GLU59 3.7 43.6 1.0 CG A:HIS62 3.8 38.5 1.0 FE A:FE181 3.8 56.6 1.0 CG1 A:VAL107 3.9 25.5 1.0 OE1 A:GLN138 4.0 40.0 1.0 CB A:HIS62 4.1 27.0 1.0 CD A:GLN138 4.2 34.5 1.0 NE2 A:GLN138 4.5 32.5 1.0 CG A:GLU24 4.7 24.0 1.0 NE2 A:HIS62 4.7 48.3 1.0 CD2 A:HIS62 4.8 43.6 1.0 CD2 A:TYR134 4.8 33.9 1.0 CG A:GLU59 4.8 29.3 1.0 OE1 A:GLU104 4.9 40.2 1.0 CG A:GLN138 4.9 31.5 1.0

Iron binding site 2 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe181 b:56.6 occ:1.00 OE2 A:GLU59 2.2 43.6 1.0 OE1 A:GLU104 2.5 40.2 1.0 O A:HOH900 2.5 37.7 1.0 OE2 A:GLU104 2.7 44.8 1.0 OD2 A:ASP141 2.9 49.3 1.0 CD A:GLU104 2.9 40.4 1.0 OE1 A:GLN138 3.1 40.0 1.0 CD A:GLU59 3.2 37.2 1.0 OE1 A:GLU59 3.7 31.9 1.0 FE A:FE180 3.8 43.1 1.0 CG A:ASP141 4.0 52.1 1.0 CD A:GLN138 4.0 34.5 1.0 O A:HOH901 4.2 47.2 1.0 NE2 A:GLN138 4.2 32.5 1.0 CG A:GLU59 4.3 29.3 1.0 CE1 A:HIS62 4.4 44.8 1.0 CB A:ASP141 4.4 37.8 1.0 CG A:GLU104 4.5 32.0 1.0 CD2 A:HIS55 4.5 43.8 1.0 NE2 A:HIS55 4.6 49.6 1.0 ND1 A:HIS62 4.6 44.8 1.0 CE2 A:TYR31 4.9 32.4 1.0

Iron binding site 3 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe180 b:56.0 occ:1.00 OE1 B:GLU59 2.5 36.4 1.0 OE1 B:GLU24 2.6 35.2 1.0 OE2 B:GLU59 2.7 31.6 1.0 CD B:GLU59 2.9 36.3 1.0 ND1 B:HIS62 2.9 45.4 1.0 O B:HOH904 3.2 36.8 1.0 OE1 B:GLN138 3.4 28.9 1.0 CD B:GLU24 3.4 30.4 1.0 OE2 B:GLU24 3.4 32.8 1.0 CE1 B:HIS62 3.7 41.1 1.0 CG B:HIS62 3.8 41.6 1.0 CG1 B:VAL107 4.0 26.3 1.0 CB B:HIS62 4.1 27.2 1.0 CG B:GLU59 4.3 33.9 1.0 CD B:GLN138 4.6 27.9 1.0 FE B:FE181 4.6 62.4 1.0 CD2 B:TYR134 4.8 26.8 1.0 NE2 B:HIS62 4.8 43.5 1.0 OE1 B:GLU104 4.8 42.0 1.0 CG B:GLU24 4.9 25.6 1.0 CD2 B:HIS62 4.9 39.8 1.0

Iron binding site 4 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe181 b:62.4 occ:1.00 OE2 B:GLU104 2.5 38.8 1.0 OE2 B:GLU59 2.5 31.6 1.0 NE2 B:HIS55 3.0 54.4 1.0 CD2 B:HIS55 3.1 39.3 1.0 CD B:GLU104 3.1 37.8 1.0 OD2 B:ASP141 3.3 51.8 1.0 OE1 B:GLU104 3.3 42.0 1.0 CD B:GLU59 3.5 36.3 1.0 CG B:GLU59 3.7 33.9 1.0 CG B:ASP141 4.0 52.9 1.0 CE1 B:HIS55 4.1 49.2 1.0 CG B:HIS55 4.3 43.1 1.0 CB B:ASP141 4.3 36.0 1.0 CE2 B:TYR31 4.3 35.4 1.0 OH B:TYR31 4.4 35.3 1.0 CG B:GLU104 4.4 35.0 1.0 FE B:FE180 4.6 56.0 1.0 OE1 B:GLU59 4.6 36.4 1.0 OE1 B:GLN138 4.7 28.9 1.0 ND1 B:HIS55 4.8 44.8 1.0 CZ B:TYR31 4.8 34.2 1.0 OD1 B:ASP141 4.8 56.0 1.0 CE1 B:HIS62 4.9 41.1 1.0 OE1 B:GLU58 4.9 72.0 1.0

Iron binding site 5 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe183 b:59.3 occ:1.00 O V:HOH270 2.9 21.2 1.0 OE2 E:GLU131 3.3 35.5 1.0 OE2 B:GLU131 3.4 32.2 1.0 OE2 V:GLU131 3.7 31.2 1.0 OE1 B:GLU131 3.9 34.7 1.0 OE1 E:GLU131 4.0 39.2 1.0 CD E:GLU131 4.0 35.7 1.0 CD B:GLU131 4.1 37.4 1.0 OE1 V:GLU131 4.1 38.0 1.0 CD V:GLU131 4.3 34.4 1.0

Iron binding site 6 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe180 b:54.1 occ:1.00 OE1 C:GLU59 2.1 37.5 1.0 OE2 C:GLU59 2.8 33.5 1.0 CD C:GLU59 2.8 37.7 1.0 OE1 C:GLU24 2.9 39.2 1.0 ND1 C:HIS62 2.9 37.7 1.0 OE2 C:GLU24 3.1 42.5 1.0 NE2 C:GLN138 3.4 27.8 1.0 CD C:GLU24 3.4 41.8 1.0 O C:HOH905 3.5 51.7 1.0 CE1 C:HIS62 3.7 45.5 1.0 CG C:HIS62 3.8 39.9 1.0 FE C:FE181 4.0 56.8 1.0 CB C:HIS62 4.1 35.5 1.0 CG1 C:VAL107 4.1 28.4 1.0 OE1 C:GLN138 4.2 31.9 1.0 CG C:GLU59 4.2 29.4 1.0 CD C:GLN138 4.2 31.9 1.0 OE1 C:GLU104 4.6 41.4 1.0 NE2 C:HIS62 4.7 51.3 1.0 CD2 C:HIS62 4.7 43.8 1.0 CA C:GLU59 4.8 32.4 1.0 CB C:GLU59 4.9 32.5 1.0 CG C:GLU24 4.9 28.3 1.0

Iron binding site 7 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe181 b:56.8 occ:1.00 OE2 C:GLU59 2.4 33.5 1.0 OE2 C:GLU104 2.6 37.7 1.0 O C:HOH905 2.7 51.7 1.0 OE1 C:GLU104 2.8 41.4 1.0 CD C:GLU104 2.9 38.4 1.0 NE2 C:HIS55 3.2 50.3 1.0 CD C:GLU59 3.3 37.7 1.0 CD2 C:HIS55 3.7 37.6 1.0 OE1 C:GLN138 3.8 31.9 1.0 O C:HOH279 3.9 42.0 1.0 CG C:ASP141 4.0 51.6 1.0 OD2 C:ASP141 4.0 54.3 1.0 CG C:GLU59 4.0 29.4 1.0 FE C:FE180 4.0 54.1 1.0 OE1 C:GLU59 4.2 37.5 1.0 CG C:GLU104 4.2 32.0 1.0 OD1 C:ASP141 4.2 49.5 1.0 CE1 C:HIS55 4.4 52.3 1.0 CB C:ASP141 4.5 39.0 1.0 CD C:GLN138 4.8 31.9 1.0 CE1 C:HIS62 4.8 45.5 1.0 CE2 C:TYR31 4.9 32.3 1.0 OH C:TYR31 4.9 34.5 1.0 ND1 C:HIS62 5.0 37.7 1.0

Iron binding site 8 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe183 b:61.0 occ:1.00 O C:HOH741 2.9 36.8 1.0 OE2 S:GLU131 3.3 47.4 1.0 OE2 C:GLU131 3.5 44.8 1.0 OE2 R:GLU131 3.8 42.3 1.0 OE1 R:GLU131 4.0 49.0 1.0 OE1 S:GLU131 4.0 45.8 1.0 CD S:GLU131 4.0 48.1 1.0 OE1 C:GLU131 4.2 40.9 1.0 CD C:GLU131 4.2 46.5 1.0 CD R:GLU131 4.3 47.5 1.0

Iron binding site 9 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe184 b:51.0 occ:1.00 NE2 C:HIS170 2.9 37.3 1.0 NE2 V:HIS170 3.0 33.9 1.0 NE2 F:HIS170 3.0 44.0 1.0 NE2 M:HIS170 3.2 39.3 1.0 O V:HOH188 3.3 28.8 1.0 CE1 C:HIS170 3.3 36.7 1.0 CE1 M:HIS170 3.4 35.3 1.0 CE1 V:HIS170 3.5 40.5 1.0 CE1 F:HIS170 3.7 41.7 1.0 CD2 C:HIS170 4.2 35.1 1.0 CD2 F:HIS170 4.2 31.7 1.0 CD2 V:HIS170 4.2 33.6 1.0 CD2 C:LEU166 4.3 26.8 1.0 CD2 M:HIS170 4.5 34.5 1.0 CD2 F:LEU166 4.5 25.1 1.0 CD2 M:LEU166 4.6 31.0 1.0 CD2 V:LEU166 4.6 22.8 1.0 ND1 C:HIS170 4.6 33.1 1.0 ND1 M:HIS170 4.6 35.7 1.0 ND1 V:HIS170 4.8 37.1 1.0 ND1 F:HIS170 5.0 32.8 1.0

Iron binding site 10 out of 62 in the Iron Loaded Frog M Ferritin. Short Soaking Time


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Iron Loaded Frog M Ferritin. Short Soaking Time within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe180 b:37.2 occ:1.00 OE1 D:GLU59 2.3 28.5 1.0 OE1 D:GLU24 2.5 31.8 1.0 ND1 D:HIS62 3.1 36.9 1.0 OE2 D:GLU24 3.1 29.6 1.0 CD D:GLU24 3.2 31.4 1.0 CD D:GLU59 3.2 34.0 1.0 OE1 D:GLN138 3.4 30.0 1.0 OE2 D:GLU59 3.4 34.2 1.0 O D:HOH906 3.4 35.0 1.0 FE D:FE181 3.4 63.8 1.0 CG D:HIS62 3.6 35.7 1.0 CE1 D:HIS62 3.6 37.4 1.0 CB D:HIS62 3.9 27.9 1.0 CG1 D:VAL107 4.1 20.6 1.0 CD2 D:HIS62 4.3 37.9 1.0 NE2 D:HIS62 4.3 44.9 1.0 CD D:GLN138 4.4 26.5 1.0 CG D:GLU59 4.6 32.2 1.0 CA D:GLU59 4.7 29.1 1.0 CG D:GLU24 4.7 25.0 1.0 OE1 D:GLU104 4.7 28.1 1.0 CB D:GLU59 4.9 30.3 1.0

I.Bertini, D.Lalli, S.Mangani, C.Pozzi, C.Rosa, E.C.Theil, P.Turano. Structural Insights Into the Ferroxidase Site of Ferritins From Higher Eukaryotes. J.Am.Chem.Soc. V. 134 6169 2012.
ISSN: ISSN 0002-7863
PubMed: 22424302
DOI: 10.1021/JA210084N