Iron in PDB 3rbc: Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site

All present enzymatic activity of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site:
1.16.3.1;

The structure of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site, PDB code: 3rbc was solved by I.Bertini, D.Lalli, S.Mangani, C.Pozzi, C.Rosa, P.Turano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.13 / 2.70
Space group	P 31 2 1 1
Cell size a, b, c (Å), α, β, γ (°)	210.719, 210.719, 324.410, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 23.5

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;

Binding sites:

The binding sites of Iron atom in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site (pdb code 3rbc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 50 binding sites of Iron where determined in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site, PDB code: 3rbc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe180 b:42.1 occ:0.80 OE1 A:GLU23 2.0 32.4 1.0 OE1 A:GLU58 2.1 38.7 1.0 O A:HOH1512 2.6 29.9 1.0 ND1 A:HIS61 2.7 42.2 1.0 O A:HOH1511 2.9 57.6 1.0 CD A:GLU23 2.9 32.5 1.0 CD A:GLU58 3.0 38.0 1.0 OE2 A:GLU23 3.1 36.5 1.0 FE A:FE181 3.1 40.7 0.8 OE1 A:GLN137 3.2 43.2 1.0 OE2 A:GLU58 3.3 40.6 1.0 CE1 A:HIS61 3.4 45.8 1.0 O A:HOH1510 3.6 50.7 1.0 CG A:HIS61 3.9 38.4 1.0 CG1 A:VAL106 4.0 30.2 1.0 CB A:HIS61 4.3 33.9 1.0 CG A:GLU58 4.3 34.7 1.0 CG A:GLU23 4.4 26.4 1.0 OE1 A:GLU103 4.4 40.0 1.0 CD A:GLN137 4.5 41.0 1.0 NE2 A:HIS61 4.7 47.5 1.0 CA A:GLU58 4.8 32.3 1.0 CB A:GLU58 4.8 33.1 1.0 CD2 A:HIS61 4.9 43.4 1.0 CB A:GLU23 4.9 24.9 1.0 CB A:VAL106 4.9 30.6 1.0

Iron binding site 2 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe181 b:40.7 occ:0.80 O A:HOH1510 1.9 50.7 1.0 OE2 A:GLU58 2.0 40.6 1.0 OE2 A:GLU103 2.2 41.2 1.0 OE1 A:GLU103 2.3 40.0 1.0 CD A:GLU103 2.6 38.3 1.0 O A:HOH1512 2.6 29.9 1.0 O A:HOH176 2.8 24.5 1.0 CD A:GLU58 2.9 38.0 1.0 FE A:FE180 3.1 42.1 0.8 OE1 A:GLU58 3.3 38.7 1.0 OE1 A:GLN137 3.6 43.2 1.0 OD2 A:ASP140 3.9 47.7 1.0 CG A:GLU103 4.1 33.0 1.0 CG A:GLU58 4.2 34.7 1.0 CD A:GLN137 4.4 41.0 1.0 CE1 A:HIS61 4.4 45.8 1.0 CE2 A:TYR30 4.6 32.6 1.0 ND1 A:HIS61 4.6 42.2 1.0 NE2 A:GLN137 4.6 43.6 1.0 O A:HOH177 4.6 40.7 1.0 OH A:TYR30 4.7 39.3 1.0 ND1 A:HIS54 4.7 45.2 1.0 O A:HOH1511 4.8 57.6 1.0 CG A:ASP140 4.8 41.8 1.0 OE1 A:GLU23 4.9 32.4 1.0 CE1 A:HIS54 5.0 47.2 1.0

Iron binding site 3 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe180 b:44.3 occ:0.80 OE1 B:GLU58 2.2 35.1 1.0 OE1 B:GLU23 2.3 36.2 1.0 O B:HOH1513 2.3 42.0 1.0 ND1 B:HIS61 2.6 41.4 1.0 FE B:FE181 3.0 32.2 0.8 CD B:GLU58 3.1 30.7 1.0 CD B:GLU23 3.2 31.9 1.0 CE1 B:HIS61 3.3 42.6 1.0 OE2 B:GLU58 3.3 34.4 1.0 OE2 B:GLU23 3.4 32.2 1.0 OE1 B:GLN137 3.5 35.4 1.0 CG B:HIS61 3.8 37.8 1.0 CG1 B:VAL106 4.0 24.1 1.0 CB B:HIS61 4.2 32.6 1.0 CD B:GLN137 4.5 32.0 1.0 CG B:GLU58 4.5 27.4 1.0 NE2 B:HIS61 4.5 44.2 1.0 CG B:GLU23 4.7 26.1 1.0 O B:HOH183 4.7 39.1 1.0 OE1 B:GLU103 4.7 32.6 1.0 CD2 B:HIS61 4.8 42.3 1.0 CB B:GLU58 4.8 28.6 1.0 CA B:GLU58 4.9 29.2 1.0 CB B:VAL106 4.9 24.6 1.0

Iron binding site 4 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe181 b:32.2 occ:0.80 OE2 B:GLU58 2.0 34.4 1.0 O B:HOH183 2.1 39.1 1.0 OE1 B:GLU103 2.4 32.6 1.0 OE2 B:GLU103 2.5 27.5 1.0 O B:HOH1513 2.6 42.0 1.0 CD B:GLU103 2.8 29.4 1.0 CD B:GLU58 3.0 30.7 1.0 FE B:FE180 3.0 44.3 0.8 OE1 B:GLN137 3.2 35.4 1.0 OE1 B:GLU58 3.3 35.1 1.0 O B:HOH1425 3.5 38.0 1.0 OD2 B:ASP140 4.1 37.9 1.0 CD B:GLN137 4.1 32.0 1.0 CG B:GLU103 4.3 27.1 1.0 NE2 B:GLN137 4.3 32.7 1.0 CE1 B:HIS61 4.3 42.6 1.0 CG B:GLU58 4.3 27.4 1.0 ND1 B:HIS61 4.5 41.4 1.0 CE2 B:TYR30 4.8 23.8 1.0 OH B:TYR30 4.9 32.3 1.0 ND1 B:HIS54 4.9 42.1 1.0

Iron binding site 5 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe180 b:39.2 occ:0.80 OE1 C:GLU58 1.9 33.1 1.0 OE1 C:GLU23 2.3 30.5 1.0 O C:HOH1515 2.5 53.0 1.0 ND1 C:HIS61 2.7 49.3 1.0 O C:HOH1514 2.8 30.1 1.0 CD C:GLU58 2.9 34.0 1.0 FE C:FE181 3.0 43.3 0.7 OE2 C:GLU58 3.1 35.0 1.0 CD C:GLU23 3.2 30.5 1.0 CE1 C:HIS61 3.3 48.9 1.0 OE2 C:GLU23 3.3 34.7 1.0 OE1 C:GLN137 3.3 43.1 1.0 CG C:HIS61 3.8 44.4 1.0 CG1 C:VAL106 4.0 29.1 1.0 CG C:GLU58 4.3 33.4 1.0 CB C:HIS61 4.4 38.8 1.0 O C:HOH177 4.4 46.9 1.0 NE2 C:HIS61 4.4 49.4 1.0 CD C:GLN137 4.5 40.6 1.0 OE1 C:GLU103 4.5 37.1 1.0 CG C:GLU23 4.6 28.0 1.0 CB C:GLU58 4.7 35.2 1.0 CD2 C:HIS61 4.8 45.1 1.0 CB C:VAL106 4.9 29.4 1.0 CA C:GLU58 4.9 36.0 1.0 CB C:GLU23 4.9 27.2 1.0

Iron binding site 6 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe181 b:43.3 occ:0.70 OE2 C:GLU58 1.9 35.0 1.0 OE2 C:GLU103 2.4 33.0 1.0 OE1 C:GLU103 2.4 37.1 1.0 O C:HOH1514 2.6 30.1 1.0 CD C:GLU103 2.7 34.7 1.0 CD C:GLU58 2.9 34.0 1.0 OE1 C:GLN137 3.0 43.1 1.0 FE C:FE180 3.0 39.2 0.8 O C:HOH177 3.1 46.9 1.0 O C:HOH1087 3.2 42.1 1.0 OE1 C:GLU58 3.3 33.1 1.0 OD2 C:ASP140 3.9 51.0 1.0 CE1 C:HIS61 4.0 48.9 1.0 CD C:GLN137 4.0 40.6 1.0 CG C:GLU103 4.2 31.7 1.0 CG C:GLU58 4.3 33.4 1.0 NE2 C:GLN137 4.4 38.5 1.0 ND1 C:HIS61 4.4 49.3 1.0 O C:HOH1515 4.7 53.0 1.0 CG C:ASP140 4.7 46.6 1.0 CE2 C:TYR30 4.8 26.5 1.0 CB C:ASP140 5.0 37.7 1.0

Iron binding site 7 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe180 b:43.0 occ:0.80 OE1 D:GLU58 2.0 32.7 1.0 O D:HOH1517 2.1 47.5 1.0 OE1 D:GLU23 2.6 29.2 1.0 ND1 D:HIS61 2.6 41.3 1.0 O D:HOH1516 2.7 23.7 1.0 CD D:GLU58 3.0 33.5 1.0 FE D:FE181 3.1 41.5 0.7 OE1 D:GLN137 3.3 38.8 1.0 OE2 D:GLU58 3.3 35.1 1.0 CE1 D:HIS61 3.3 43.5 1.0 OE2 D:GLU23 3.4 28.7 1.0 CD D:GLU23 3.4 28.1 1.0 CG D:HIS61 3.8 39.1 1.0 CG1 D:VAL106 3.9 26.8 1.0 CB D:HIS61 4.2 34.0 1.0 CG D:GLU58 4.4 31.3 1.0 OE1 D:GLU103 4.5 39.2 1.0 CD D:GLN137 4.5 34.6 1.0 NE2 D:HIS61 4.5 46.1 1.0 CA D:GLU58 4.6 30.3 1.0 CB D:GLU58 4.7 30.4 1.0 CD2 D:HIS61 4.8 43.4 1.0 CG D:GLU23 4.8 24.6 1.0 O D:HOH391 4.8 55.2 1.0 O D:HOH707 4.9 62.9 1.0 CB D:VAL106 5.0 26.3 1.0 OE2 D:GLU103 5.0 35.7 1.0

Iron binding site 8 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe181 b:41.5 occ:0.70 OE2 D:GLU58 2.2 35.1 1.0 OE1 D:GLU103 2.4 39.2 1.0 O D:HOH391 2.4 55.2 1.0 O D:HOH1516 2.4 23.7 1.0 OE2 D:GLU103 2.5 35.7 1.0 CD D:GLU103 2.8 34.5 1.0 FE D:FE180 3.1 43.0 0.8 OD2 D:ASP140 3.1 49.2 1.0 CD D:GLU58 3.1 33.5 1.0 OE1 D:GLN137 3.3 38.8 1.0 OE1 D:GLU58 3.4 32.7 1.0 O D:HOH707 3.7 62.9 1.0 CE1 D:HIS61 4.0 43.5 1.0 CD D:GLN137 4.1 34.6 1.0 NE2 D:GLN137 4.2 33.0 1.0 CG D:GLU103 4.3 27.5 1.0 CG D:ASP140 4.3 41.8 1.0 ND1 D:HIS61 4.4 41.3 1.0 CG D:GLU58 4.5 31.3 1.0 O D:HOH1082 4.6 47.7 1.0 O D:HOH1517 4.6 47.5 1.0 ND1 D:HIS54 4.7 42.4 1.0 CE1 D:HIS54 4.8 46.2 1.0 CB D:ASP140 4.9 33.6 1.0 CE2 D:TYR30 4.9 31.8 1.0

Iron binding site 9 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe180 b:39.3 occ:0.80 OE2 E:GLU58 1.9 34.4 1.0 OE2 E:GLU103 2.1 31.0 1.0 O E:HOH1518 2.5 30.8 1.0 OE1 E:GLU103 2.5 36.6 1.0 CD E:GLU103 2.6 31.3 1.0 CD E:GLU58 2.9 33.5 1.0 OD2 E:ASP140 3.1 45.8 1.0 FE E:FE181 3.2 40.2 0.8 O E:HOH767 3.2 53.6 1.0 OE1 E:GLU58 3.3 37.2 1.0 OE1 E:GLN137 3.3 35.0 1.0 CG E:GLU103 4.1 23.7 1.0 CG E:ASP140 4.2 39.1 1.0 CG E:GLU58 4.2 31.6 1.0 CD E:GLN137 4.3 30.4 1.0 CE1 E:HIS61 4.3 39.0 1.0 ND1 E:HIS61 4.5 38.0 1.0 NE2 E:GLN137 4.6 30.7 1.0 CB E:ASP140 4.7 30.0 1.0 ND1 E:HIS54 4.8 36.0 1.0 CE2 E:TYR30 4.8 23.9 1.0 CE1 E:HIS54 4.8 37.7 1.0 OH E:TYR30 4.9 30.8 1.0 O E:HOH354 5.0 42.0 1.0

Iron binding site 10 out of 50 in the Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Bullfrog M Ferritin with Iron(III) Bound to the Ferroxidase Site within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe181 b:40.2 occ:0.80 OE1 E:GLU58 2.0 37.2 1.0 OE1 E:GLU23 2.4 29.7 1.0 ND1 E:HIS61 2.5 38.0 1.0 O E:HOH1518 2.8 30.8 1.0 CD E:GLU58 3.0 33.5 1.0 O E:HOH354 3.1 42.0 1.0 CE1 E:HIS61 3.1 39.0 1.0 FE E:FE180 3.2 39.3 0.8 CD E:GLU23 3.2 26.9 1.0 OE2 E:GLU58 3.2 34.4 1.0 OE1 E:GLN137 3.4 35.0 1.0 OE2 E:GLU23 3.4 28.1 1.0 CG E:HIS61 3.7 33.9 1.0 CG1 E:VAL106 4.1 23.8 1.0 CB E:HIS61 4.2 30.6 1.0 NE2 E:HIS61 4.4 41.1 1.0 CG E:GLU58 4.4 31.6 1.0 O E:HOH767 4.5 53.6 1.0 CD E:GLN137 4.5 30.4 1.0 CD2 E:HIS61 4.6 37.8 1.0 CG E:GLU23 4.7 21.3 1.0 OE1 E:GLU103 4.8 36.6 1.0 CA E:GLU58 4.8 29.7 1.0 CB E:GLU58 4.8 29.3 1.0 OE2 E:GLU103 4.9 31.0 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