Iron in PDB 8w6y: Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min

The structure of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min, PDB code: 8w6y was solved by W.M.Wang, H.F.Xi, W.J.Gong, D.Y.Ma, H.F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.91 / 2.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.513, 180.513, 180.513, 90, 90, 90
R / Rfree (%)	19.7 / 24.7

The binding sites of Iron atom in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min (pdb code 8w6y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min, PDB code: 8w6y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:122.5 occ:0.25 FE A:FE202 2.6 136.6 0.2 OE1 A:GLU164 2.7 85.6 1.0 OE2 A:GLU164 3.1 110.1 1.0 CD A:GLU164 3.3 98.4 1.0 CD1 A:ILE161 4.6 53.7 1.0 CG A:GLU164 4.8 69.2 1.0

Iron binding site 2 out of 8 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:136.6 occ:0.25 OE2 A:GLU164 2.0 110.1 1.0 FE A:FE201 2.6 122.5 0.2 O A:HOH308 2.8 83.2 1.0 CD A:GLU164 3.0 98.4 1.0 OE1 A:GLU164 3.5 85.6 1.0 CG A:GLU164 4.3 69.2 1.0

Iron binding site 3 out of 8 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:61.0 occ:1.00 OD2 A:ASP138 1.9 69.3 1.0 OD2 A:ASP142 2.1 54.3 1.0 OD2 A:ASP60 2.1 58.5 1.0 NE2 A:HIS65 2.3 58.6 1.0 CG A:ASP142 2.9 65.0 1.0 OD1 A:ASP142 2.9 63.1 1.0 CG A:ASP138 3.0 59.1 1.0 CG A:ASP60 3.1 51.5 1.0 CE1 A:HIS65 3.1 54.0 1.0 CD2 A:HIS65 3.3 55.0 1.0 NZ A:LYS141 3.4 63.6 1.0 OD1 A:ASP60 3.5 59.0 1.0 OD1 A:ASP138 3.5 67.0 1.0 O A:HOH309 4.0 49.0 1.0 CB A:ASP138 4.3 55.7 1.0 ND1 A:HIS65 4.3 59.7 1.0 CB A:ASP142 4.3 61.0 1.0 CB A:ASP60 4.4 48.6 1.0 CG A:HIS65 4.4 60.7 1.0 CH2 A:TRP134 4.5 54.9 1.0 NZ A:LYS61 4.5 54.5 1.0 CE A:LYS141 4.6 67.2 1.0 O A:ASP138 4.7 58.4 1.0

Iron binding site 4 out of 8 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:99.5 occ:1.00 OD2 A:ASP43 1.8 78.2 1.0 NE2 A:HIS39 2.3 65.0 1.0 O A:HOH301 2.5 57.8 1.0 CG A:ASP43 2.8 72.2 1.0 CD2 A:HIS39 3.3 45.8 1.0 CE1 A:HIS39 3.3 44.8 1.0 CB A:ASP43 3.4 66.9 1.0 OD1 A:ASP43 3.8 63.2 1.0 ND1 A:HIS39 4.4 58.3 1.0 CG A:HIS39 4.4 49.2 1.0 O A:HOH310 4.4 53.4 1.0 OE2 A:GLU44 4.8 96.0 1.0 CA A:ASP43 4.9 51.7 1.0

Iron binding site 5 out of 8 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:136.5 occ:1.00 CE1 A:HIS56 2.6 77.7 0.5 ND1 A:HIS56 3.5 73.2 0.5 NE2 A:HIS56 3.6 76.1 0.5 NZ A:LYS141 4.1 63.6 1.0 CG A:HIS56 4.7 62.9 0.5 OE1 A:GLU145 4.7 63.2 1.0 CE A:LYS141 4.7 67.2 1.0 CD2 A:HIS56 4.8 75.5 0.5 OE2 A:GLU145 4.8 80.2 1.0

Iron binding site 6 out of 8 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe206 b:103.6 occ:1.00 OD1 A:ASP124 3.7 53.6 1.0 OD2 A:ASP124 4.0 61.7 1.0 CG A:ASP124 4.3 55.1 1.0 O A:LEU121 4.5 53.9 1.0

Iron binding site 7 out of 8 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe207 b:146.0 occ:1.00 OD2 A:ASP18 4.1 60.7 1.0 CB A:ASN14 4.1 55.1 1.0 OD1 A:ASP18 4.4 61.3 1.0 CG A:ASN14 4.5 67.8 1.0 ND2 A:ASN14 4.5 67.9 1.0 CG A:ASP18 4.7 48.4 1.0

Iron binding site 8 out of 8 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe208 b:90.3 occ:1.00 NZ A:LYS159 3.2 57.4 1.0 N A:ALA95 3.2 50.9 1.0 CE A:LYS159 3.4 42.8 1.0 CD1 A:PHE45 3.7 51.9 1.0 CB A:ALA95 3.7 42.9 1.0 CG A:PHE45 3.7 55.2 1.0 CB A:PHE45 3.8 54.8 1.0 CB A:ASP94 3.9 37.0 1.0 CA A:ASP94 3.9 57.9 1.0 CA A:ALA95 4.1 46.3 1.0 C A:ASP94 4.1 48.7 1.0 CA A:PHE45 4.3 57.1 1.0 O A:PHE45 4.4 43.0 1.0 CE1 A:PHE45 4.4 48.7 1.0 CD2 A:PHE45 4.5 48.7 1.0 CD A:LYS159 4.8 45.6 1.0 C A:PHE45 4.9 60.0 1.0

W.Wang, H.Xi, D.Fu, D.Ma, W.Gong, Y.Zhao, X.Li, L.Wu, Y.Guo, G.Zhao, H.Wang. Growth Process of Fe-O Nanoclusters with Different Sizes Biosynthesized By Protein Nanocages. J.Am.Chem.Soc. V. 146 11657 2024.
ISSN: ESSN 1520-5126
PubMed: 38641862
DOI: 10.1021/JACS.3C13830