Iron in PDB 8wpt: Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum

The structure of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum, PDB code: 8wpt 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)	32.10 / 2.36
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.6, 181.6, 181.6, 90, 90, 90
R / Rfree (%)	18.2 / 24.1

The structure of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum (pdb code 8wpt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum, PDB code: 8wpt:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:119.1 occ:1.00 O A:HOH327 2.5 69.8 1.0 OD2 A:ASP60 2.5 75.6 1.0 O A:HOH301 2.7 59.9 1.0 O A:HOH310 3.3 70.4 1.0 CG A:ASP60 3.7 59.9 1.0 OD1 A:ASP138 3.7 67.1 1.0 NZ A:LYS141 4.0 75.5 1.0 OD2 A:ASP138 4.1 74.1 1.0 CE1 A:HIS65 4.1 44.6 1.0 OD1 A:ASP60 4.2 75.1 1.0 CG A:ASP138 4.3 69.0 1.0 OD2 A:ASP142 4.4 72.2 1.0 O A:HOH365 4.4 61.1 1.0 OD1 A:ASP142 4.4 83.1 1.0 CZ2 A:TRP134 4.7 58.9 1.0 CB A:ASP60 4.8 45.7 1.0 CG A:ASP142 4.8 75.7 1.0 CH2 A:TRP134 4.8 57.7 1.0 ND1 A:HIS65 5.0 53.8 1.0

Iron binding site 2 out of 4 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:117.2 occ:1.00 OD1 A:ASP124 3.6 61.5 1.0 OD2 A:ASP124 4.0 66.6 1.0 CG A:ASP124 4.2 58.4 1.0 O A:LEU121 4.2 63.6 1.0 O A:HOH377 4.3 48.7 1.0 O A:ALA122 4.5 52.4 1.0

Iron binding site 3 out of 4 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:127.2 occ:1.00 O A:HOH366 2.8 66.7 1.0 O A:HOH363 2.9 62.7 1.0 OD1 A:ASP148 3.2 67.4 1.0 OD2 A:ASP147 4.4 59.1 1.0 CG A:ASP148 4.5 60.3 1.0 O A:HOH322 4.7 50.1 1.0

Iron binding site 4 out of 4 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:123.6 occ:0.25 OE2 A:GLU164 2.8 114.7 1.0 OE1 A:GLU164 3.4 92.8 1.0 CD A:GLU164 3.5 104.2 1.0 CG A:GLU164 4.9 74.0 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