Iron in PDB 8w73: Fe-O Nanocluster of Form-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin

The structure of Fe-O Nanocluster of Form-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w73 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)	45.08 / 2.60
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.328, 180.328, 180.328, 90, 90, 90
R / Rfree (%)	18 / 23.6

The structure of Fe-O Nanocluster of Form-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Iron atom in the Fe-O Nanocluster of Form-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin (pdb code 8w73). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Fe-O Nanocluster of Form-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w73:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Fe-O Nanocluster of Form-I 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-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:61.8 occ:1.00 OD2 A:ASP138 1.8 62.4 1.0 OD2 A:ASP60 2.0 60.0 1.0 OD2 A:ASP142 2.1 61.2 1.0 NE2 A:HIS65 2.2 52.0 1.0 O A:HOH335 2.5 56.1 1.0 CG A:ASP142 2.9 54.9 1.0 OD1 A:ASP142 2.9 57.7 1.0 CG A:ASP138 3.0 55.6 1.0 CE1 A:HIS65 3.1 54.8 1.0 CG A:ASP60 3.1 52.4 1.0 CD2 A:HIS65 3.3 48.1 1.0 OD1 A:ASP60 3.6 47.7 1.0 OD1 A:ASP138 3.7 60.9 1.0 NZ A:LYS141 4.1 72.6 1.0 O A:HOH339 4.2 49.4 1.0 CB A:ASP138 4.2 48.2 1.0 ND1 A:HIS65 4.3 48.8 1.0 CH2 A:TRP134 4.3 53.3 1.0 CB A:ASP142 4.3 48.1 1.0 CB A:ASP60 4.4 46.6 1.0 CG A:HIS65 4.4 55.4 1.0 CE A:LYS141 4.5 64.6 1.0 NZ A:LYS61 4.7 50.1 1.0 O A:ASP138 4.8 48.5 1.0 CZ2 A:TRP134 5.0 48.2 1.0

Iron binding site 2 out of 8 in the Fe-O Nanocluster of Form-I 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-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:145.3 occ:1.00 CE1 A:HIS56 2.3 59.2 0.5 NE2 A:HIS56 2.5 56.5 0.5 O A:HOH379 2.9 72.1 1.0 ND1 A:HIS56 3.5 50.5 0.5 NZ A:LYS141 3.8 72.6 1.0 OE1 A:GLU145 3.8 92.7 1.0 CD2 A:HIS56 3.8 44.0 0.5 OE2 A:GLU145 3.8 65.9 1.0 CD A:GLU145 4.2 76.7 1.0 CG A:HIS56 4.3 48.0 0.5

Iron binding site 3 out of 8 in the Fe-O Nanocluster of Form-I 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-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:150.9 occ:1.00 O A:HOH307 2.2 62.1 1.0 OD2 A:ASP94 2.5 72.4 1.0 CG A:ASP94 3.5 52.6 1.0 OD1 A:ASP94 3.8 53.1 1.0 CB A:ASP94 4.8 41.6 1.0 OG A:SER93 4.9 64.5 1.0

Iron binding site 4 out of 8 in the Fe-O Nanocluster of Form-I 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-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:145.8 occ:1.00 O A:HOH353 2.3 77.5 1.0 OD2 A:ASP42 4.0 58.4 1.0 OD1 A:ASP42 4.5 59.3 1.0 CG A:ASP42 4.7 46.6 1.0 CB A:PRO48 4.8 36.7 1.0

Iron binding site 5 out of 8 in the Fe-O Nanocluster of Form-I 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-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:99.0 occ:0.25 FE A:FE206 2.3 122.0 0.2 OE2 A:GLU164 2.4 109.1 1.0 OE1 A:GLU164 2.7 75.7 1.0 CD A:GLU164 2.9 98.0 1.0 O A:HOH303 3.9 104.0 1.0 CG A:GLU164 4.4 68.5 1.0 O A:HOH378 4.5 126.1 0.2

Iron binding site 6 out of 8 in the Fe-O Nanocluster of Form-I 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-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe206 b:122.0 occ:0.25 O A:HOH378 2.2 126.1 0.2 OE2 A:GLU164 2.2 109.1 1.0 FE A:FE205 2.3 99.0 0.2 O A:HOH303 2.5 104.0 1.0 CD A:GLU164 3.3 98.0 1.0 FE A:FE207 3.9 169.3 1.0 OE1 A:GLU164 3.9 75.7 1.0 O A:HOH396 4.4 111.7 0.2 CG A:GLU164 4.4 68.5 1.0

Iron binding site 7 out of 8 in the Fe-O Nanocluster of Form-I 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-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe207 b:169.3 occ:1.00 O A:HOH378 2.4 126.1 0.2 O A:HOH396 2.4 111.7 0.2 O A:HOH303 2.5 104.0 1.0 OE1 A:GLU168 3.2 105.3 1.0 FE A:FE206 3.9 122.0 0.2 O A:HOH397 3.9 62.9 0.2 CD A:GLU168 4.1 86.2 1.0 OE2 A:GLU168 4.4 93.2 1.0 OE2 A:GLU164 4.7 109.1 1.0

Iron binding site 8 out of 8 in the Fe-O Nanocluster of Form-I 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-I in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe208 b:103.3 occ:1.00 OD2 A:ASP43 2.1 82.4 1.0 CE1 A:HIS39 2.7 54.6 1.0 CG A:ASP43 3.0 63.5 1.0 CB A:ASP43 3.2 55.1 1.0 ND1 A:HIS39 3.5 42.8 1.0 NE2 A:HIS39 3.8 52.0 1.0 OD1 A:ASP43 4.2 59.9 1.0 CG A:GLU44 4.5 94.5 1.0 CA A:ASP43 4.6 48.5 1.0 OE2 A:GLU44 4.7 81.9 1.0 CG A:HIS39 4.7 54.1 1.0 N A:GLU44 4.8 56.0 1.0 C A:ASP43 4.8 59.4 1.0 CD2 A:HIS39 4.9 52.8 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