Iron in PDB 8w7u: Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking

The structure of Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking, PDB code: 8w7u 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)	34.65 / 2.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.07, 180.07, 180.07, 90, 90, 90
R / Rfree (%)	20.8 / 26.4

The structure of Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking (pdb code 8w7u). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking, PDB code: 8w7u:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:78.9 occ:1.00 OD2 A:ASP138 1.9 54.7 1.0 OD2 A:ASP142 1.9 48.8 1.0 OD1 A:ASP60 2.3 64.4 1.0 NE2 A:HIS65 2.4 34.8 1.0 O A:HOH310 2.7 30.0 1.0 CG A:ASP142 2.7 44.0 1.0 OD1 A:ASP142 2.9 40.9 1.0 CG A:ASP138 3.1 43.3 1.0 CE1 A:HIS65 3.2 33.6 1.0 CG A:ASP60 3.4 56.2 1.0 CD2 A:HIS65 3.5 30.3 1.0 OD1 A:ASP138 3.8 42.8 1.0 OD2 A:ASP60 4.1 64.6 1.0 CB A:ASP138 4.1 39.2 1.0 CB A:ASP142 4.2 39.7 1.0 NZ A:LYS61 4.3 39.9 1.0 O A:HOH340 4.4 40.1 1.0 ND1 A:HIS65 4.4 43.3 1.0 CB A:ASP60 4.5 41.2 1.0 CG A:HIS65 4.6 35.5 1.0 O A:ASP138 4.7 33.9 1.0 CH2 A:TRP134 4.8 33.7 1.0 CE A:LYS61 5.0 33.6 1.0

Iron binding site 2 out of 4 in the Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:96.5 occ:1.00 OD1 A:ASP124 3.6 37.1 1.0 OD2 A:ASP124 3.7 38.0 1.0 O A:LEU121 3.9 36.0 1.0 CG A:ASP124 4.0 39.5 1.0 O A:ALA122 5.0 35.2 1.0

Iron binding site 3 out of 4 in the Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:105.4 occ:1.00 NE2 A:HIS56 2.1 61.2 1.0 O A:HOH328 2.3 30.0 1.0 CE1 A:HIS56 3.0 68.5 1.0 CD2 A:HIS56 3.1 55.2 1.0 OE2 A:GLU174 3.9 30.0 1.0 ND1 A:HIS56 4.2 66.6 1.0 CG A:HIS56 4.2 52.9 1.0 OE1 A:GLU145 4.3 66.3 1.0 OE2 A:GLU145 4.4 59.6 1.0 O A:HOH335 4.5 63.1 1.0 CD A:GLU174 4.6 30.0 1.0 OE1 A:GLU174 4.7 30.0 1.0 CD A:GLU145 4.8 62.4 1.0 O A:HOH310 4.9 30.0 1.0 OD2 A:ASP60 4.9 64.6 1.0

Iron binding site 4 out of 4 in the Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mutant of Ferritin From Ureaplasma Diversum (Udif-E164A-E168A) Without Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:30.0 occ:1.00 OD2 A:ASP42 3.5 46.3 1.0 CB A:PRO48 4.2 31.1 1.0 CG A:ASP42 4.4 39.0 1.0 O A:HOH341 4.4 51.5 1.0 OD1 A:ASP42 4.5 42.0 1.0 CG A:PRO48 5.0 27.6 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