Iron in PDB 8wqy: Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin (pdb code 8wqy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8wqy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:130.3 occ:1.00 OD2 A:ASP142 2.0 108.8 1.0 OD2 A:ASP138 2.0 104.4 1.0 NE2 A:HIS65 2.1 104.1 1.0 CE1 A:HIS65 2.6 104.1 1.0 CG A:ASP142 3.0 108.8 1.0 CG A:ASP138 3.2 104.4 1.0 CD2 A:HIS65 3.3 104.1 1.0 OD1 A:ASP142 3.4 108.8 1.0 OD2 A:ASP60 3.5 107.9 1.0 ND1 A:HIS65 3.9 104.1 1.0 OD1 A:ASP138 3.9 104.4 1.0 O A:HOH301 4.1 91.8 1.0 CG A:ASP60 4.2 107.9 1.0 CG A:HIS65 4.2 104.1 1.0 CB A:ASP138 4.3 104.4 1.0 CB A:ASP142 4.3 108.8 1.0 NZ A:LYS61 4.4 102.3 1.0 O A:ASP138 4.4 104.4 1.0 OD1 A:ASP60 4.6 107.9 1.0 C A:ASP138 4.9 104.4 1.0 CB A:ASP60 4.9 107.9 1.0

Iron binding site 2 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:127.8 occ:1.00 NE2 B:HIS65 2.0 105.2 1.0 OD2 B:ASP138 2.1 107.7 1.0 OD2 B:ASP60 2.4 109.3 1.0 CD2 B:HIS65 2.8 105.2 1.0 OD2 B:ASP142 2.9 108.6 1.0 CE1 B:HIS65 3.1 105.2 1.0 CG B:ASP138 3.1 107.7 1.0 CG B:ASP60 3.2 109.3 1.0 OD1 B:ASP60 3.2 109.3 1.0 OD1 B:ASP138 3.6 107.7 1.0 OD1 B:ASP142 3.6 108.6 1.0 CG B:ASP142 3.6 108.6 1.0 CG B:HIS65 4.0 105.2 1.0 ND1 B:HIS65 4.1 105.2 1.0 CB B:ASP138 4.4 107.7 1.0 CB B:ASP60 4.6 109.3 1.0 CH2 B:TRP134 4.9 99.6 1.0 O B:ASP138 4.9 107.7 1.0 O B:ASP60 5.0 109.3 1.0

Iron binding site 3 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:133.8 occ:1.00 OD2 C:ASP138 2.1 104.6 1.0 NE2 C:HIS65 2.1 104.5 1.0 OD2 C:ASP142 2.2 109.7 1.0 OD1 C:ASP60 2.7 108.2 1.0 CE1 C:HIS65 2.8 104.5 1.0 CG C:ASP138 3.2 104.6 1.0 CG C:ASP142 3.2 109.7 1.0 CD2 C:HIS65 3.3 104.5 1.0 CG C:ASP60 3.6 108.2 1.0 OD1 C:ASP142 3.7 109.7 1.0 OD1 C:ASP138 3.7 104.6 1.0 OD2 C:ASP60 3.9 108.2 1.0 ND1 C:HIS65 4.0 104.5 1.0 CG C:HIS65 4.2 104.5 1.0 NZ C:LYS61 4.4 99.0 1.0 CB C:ASP138 4.4 104.6 1.0 CB C:ASP142 4.5 109.7 1.0 CE C:LYS61 4.8 99.0 1.0 O C:ASP138 4.8 104.6 1.0 CB C:ASP60 4.8 108.2 1.0

Iron binding site 4 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:122.7 occ:1.00 OD2 D:ASP142 2.2 110.8 1.0 NE2 D:HIS65 2.4 102.7 1.0 OD2 D:ASP60 2.7 107.5 1.0 CE1 D:HIS65 2.9 102.7 1.0 O D:HOH301 3.1 89.2 1.0 CG D:ASP142 3.1 110.8 1.0 OD1 D:ASP142 3.5 110.8 1.0 CG D:ASP60 3.6 107.5 1.0 CD2 D:HIS65 3.7 102.7 1.0 OD1 D:ASP60 3.8 107.5 1.0 ND1 D:HIS65 4.2 102.7 1.0 CB D:ASP138 4.2 104.3 1.0 NZ D:LYS61 4.5 99.4 1.0 CB D:ASP142 4.5 110.8 1.0 CG D:ASP138 4.5 104.3 1.0 CG D:HIS65 4.6 102.7 1.0 CE D:LYS61 4.6 99.4 1.0 OD2 D:ASP138 4.8 104.3 1.0 O D:ASP138 4.8 104.3 1.0 CB D:ASP60 5.0 107.5 1.0

Iron binding site 5 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:131.6 occ:1.00 OD2 E:ASP138 2.1 106.2 1.0 OD2 E:ASP142 2.2 108.4 1.0 OD2 E:ASP60 2.6 105.5 1.0 OD1 E:ASP142 2.8 108.4 1.0 CG E:ASP142 2.8 108.4 1.0 NE2 E:HIS65 2.8 97.2 1.0 CG E:ASP138 3.0 106.2 1.0 OD1 E:ASP138 3.3 106.2 1.0 CE1 E:HIS65 3.4 97.2 1.0 CG E:ASP60 3.6 105.5 1.0 OD1 E:ASP60 3.9 105.5 1.0 CD2 E:HIS65 4.0 97.2 1.0 CB E:ASP142 4.3 108.4 1.0 CB E:ASP138 4.4 106.2 1.0 O E:ASP138 4.4 106.2 1.0 ND1 E:HIS65 4.6 97.2 1.0 NZ E:LYS141 4.8 104.8 1.0 CE E:LYS141 4.8 104.8 1.0 NZ E:LYS61 4.8 98.5 1.0 CG E:HIS65 4.9 97.2 1.0 CB E:ASP60 5.0 105.5 1.0

Iron binding site 6 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:123.8 occ:1.00 O F:HOH302 2.0 107.9 1.0 OD2 F:ASP138 2.0 106.1 1.0 NE2 F:HIS65 2.3 104.2 1.0 OD2 F:ASP142 2.6 104.2 1.0 OD1 F:ASP60 2.9 107.7 1.0 CG F:ASP138 2.9 106.1 1.0 OD1 F:ASP138 3.1 106.1 1.0 CD2 F:HIS65 3.3 104.2 1.0 CE1 F:HIS65 3.3 104.2 1.0 CG F:ASP142 3.5 104.2 1.0 CG F:ASP60 3.7 107.7 1.0 OD1 F:ASP142 3.8 104.2 1.0 OD2 F:ASP60 4.1 107.7 1.0 CB F:ASP138 4.3 106.1 1.0 O F:HOH301 4.3 96.3 1.0 ND1 F:HIS65 4.4 104.2 1.0 CG F:HIS65 4.4 104.2 1.0 CB F:ASP142 4.7 104.2 1.0 O F:ASP138 4.8 106.1 1.0 CB F:ASP60 4.9 107.7 1.0 CH2 F:TRP134 4.9 100.2 1.0

Iron binding site 7 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe201 b:144.2 occ:1.00 OD2 G:ASP142 1.9 113.3 1.0 OD2 G:ASP138 2.0 110.1 1.0 NE2 G:HIS65 2.5 106.7 1.0 CG G:ASP138 2.9 110.1 1.0 CG G:ASP142 2.9 113.3 1.0 CE1 G:HIS65 3.1 106.7 1.0 OD1 G:ASP138 3.1 110.1 1.0 OD1 G:ASP142 3.3 113.3 1.0 CD2 G:HIS65 3.8 106.7 1.0 CB G:ASP138 4.3 110.1 1.0 CB G:ASP142 4.3 113.3 1.0 ND1 G:HIS65 4.3 106.7 1.0 O G:ASP138 4.6 110.1 1.0 NZ G:LYS61 4.6 100.1 1.0 CG G:HIS65 4.7 106.7 1.0 CB G:ASP60 4.7 106.6 1.0 OD2 G:ASP60 4.8 106.6 1.0 CG G:ASP60 4.9 106.6 1.0

Iron binding site 8 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe201 b:128.2 occ:1.00 NE2 H:HIS65 2.1 101.0 1.0 OD2 H:ASP60 2.2 105.9 1.0 OD2 H:ASP142 2.4 110.2 1.0 OD2 H:ASP138 2.4 108.7 1.0 CE1 H:HIS65 3.0 101.0 1.0 CD2 H:HIS65 3.2 101.0 1.0 CG H:ASP60 3.2 105.9 1.0 CG H:ASP142 3.3 110.2 1.0 CG H:ASP138 3.6 108.7 1.0 OD1 H:ASP142 3.6 110.2 1.0 OD1 H:ASP60 3.7 105.9 1.0 OD1 H:ASP138 4.1 108.7 1.0 ND1 H:HIS65 4.2 101.0 1.0 CG H:HIS65 4.3 101.0 1.0 CB H:ASP60 4.5 105.9 1.0 CB H:ASP142 4.7 110.2 1.0 CB H:ASP138 4.8 108.7 1.0

Iron binding site 9 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe201 b:126.0 occ:1.00 OD2 I:ASP60 2.0 106.2 1.0 NE2 I:HIS65 2.3 99.7 1.0 OD2 I:ASP138 2.4 105.0 1.0 CG I:ASP60 2.9 106.2 1.0 OD2 I:ASP142 2.9 105.9 1.0 OD1 I:ASP60 3.2 106.2 1.0 CG I:ASP138 3.2 105.0 1.0 CD2 I:HIS65 3.2 99.7 1.0 CE1 I:HIS65 3.3 99.7 1.0 OD1 I:ASP138 3.3 105.0 1.0 CG I:ASP142 3.8 105.9 1.0 OD1 I:ASP142 3.8 105.9 1.0 CB I:ASP60 4.3 106.2 1.0 ND1 I:HIS65 4.4 99.7 1.0 CG I:HIS65 4.4 99.7 1.0 CB I:ASP138 4.6 105.0 1.0 CH2 I:TRP134 4.8 97.5 1.0

Iron binding site 10 out of 24 in the Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Fe-O Nanocluster of Form-XI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe201 b:128.6 occ:1.00 OD2 J:ASP138 2.0 110.7 1.0 OD2 J:ASP142 2.0 111.7 1.0 NE2 J:HIS65 2.5 102.9 1.0 CG J:ASP142 2.9 111.7 1.0 CG J:ASP138 3.1 110.7 1.0 OD1 J:ASP142 3.2 111.7 1.0 CE1 J:HIS65 3.3 102.9 1.0 OD1 J:ASP60 3.4 104.1 1.0 OD1 J:ASP138 3.5 110.7 1.0 CD2 J:HIS65 3.6 102.9 1.0 OD2 J:ASP60 3.7 104.1 1.0 CG J:ASP60 3.7 104.1 1.0 NZ J:LYS61 4.0 99.5 1.0 CB J:ASP142 4.3 111.7 1.0 CB J:ASP138 4.4 110.7 1.0 ND1 J:HIS65 4.4 102.9 1.0 O J:ASP138 4.5 110.7 1.0 CG J:HIS65 4.6 102.9 1.0 CB J:ASP60 4.7 104.1 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