Iron in PDB 8w6m: Native Strucutre of Ferritin From Ureaplasma Diversum

The structure of Native Strucutre of Ferritin From Ureaplasma Diversum, PDB code: 8w6m 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)	34.63 / 2.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	179.938, 179.938, 179.938, 90, 90, 90
R / Rfree (%)	18.6 / 24.6

The structure of Native Strucutre of Ferritin From Ureaplasma Diversum also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	5 atoms

The binding sites of Iron atom in the Native Strucutre of Ferritin From Ureaplasma Diversum (pdb code 8w6m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Native Strucutre of Ferritin From Ureaplasma Diversum, PDB code: 8w6m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in the Native Strucutre 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 Native Strucutre of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:56.4 occ:0.77 OD2 A:ASP138 1.9 41.5 1.0 O A:HOH306 2.1 51.1 1.0 O A:HOH343 2.2 42.4 1.0 OD2 A:ASP142 2.5 41.8 1.0 NE2 A:HIS65 2.6 23.6 1.0 OD1 A:ASP142 2.8 41.4 1.0 CG A:ASP138 2.9 38.4 1.0 CG A:ASP142 3.0 40.4 1.0 OD1 A:ASP138 3.2 31.6 1.0 OD2 A:ASP60 3.4 53.9 0.4 CE1 A:HIS65 3.5 25.6 1.0 CG A:ASP60 3.5 41.6 0.4 OD1 A:ASP60 3.6 56.0 0.4 CD2 A:HIS65 3.6 19.8 1.0 CB A:ASP138 4.2 36.0 1.0 CB A:ASP60 4.3 34.1 0.6 CB A:ASP60 4.4 34.1 0.4 OD2 A:ASP60 4.4 50.4 0.6 CB A:ASP142 4.5 35.2 1.0 O A:HOH342 4.5 36.9 1.0 ND1 A:HIS65 4.7 26.8 1.0 CH2 A:TRP134 4.7 25.0 1.0 CG A:ASP60 4.7 42.2 0.6 CG A:HIS65 4.7 26.9 1.0 O A:ASP138 4.8 26.5 1.0 NZ A:LYS61 4.8 26.7 1.0

Iron binding site 2 out of 7 in the Native Strucutre 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 Native Strucutre of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:107.8 occ:1.00 O A:HOH304 2.3 52.9 1.0 O A:HOH417 3.1 45.8 1.0 OD2 A:ASP60 3.1 50.4 0.6 OD2 A:ASP60 3.6 53.9 0.4 CG A:ASP60 4.1 42.2 0.6 OE1 A:GLU145 4.3 59.1 1.0 OE2 A:GLU145 4.3 69.8 1.0 OD1 A:ASP60 4.3 56.0 0.6 CD A:GLU145 4.7 70.9 1.0 CG A:ASP60 4.7 41.6 0.4 O A:HOH306 4.8 51.1 1.0 OE2 A:GLU174 4.9 85.4 1.0 O A:HOH312 4.9 36.8 1.0

Iron binding site 3 out of 7 in the Native Strucutre 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 Native Strucutre of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:110.3 occ:0.25 OE1 A:GLU164 2.4 89.3 1.0 O A:HOH335 2.5 63.1 0.2 CD A:GLU164 3.0 73.0 1.0 OE2 A:GLU164 3.1 80.5 1.0 CG A:GLU164 4.4 57.7 1.0

Iron binding site 4 out of 7 in the Native Strucutre 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 Native Strucutre of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:91.8 occ:1.00 O A:HOH351 2.3 39.4 1.0 OD2 A:ASP94 2.4 43.1 1.0 O A:HOH372 2.6 42.0 1.0 O A:HOH370 2.6 54.9 1.0 CG A:ASP94 3.4 30.2 1.0 OD1 A:ASP94 3.7 34.2 1.0 NZ A:LYS96 4.6 57.8 1.0 CB A:ASP94 4.7 21.4 1.0 O A:HOH302 4.8 41.7 1.0 OG A:SER93 4.9 35.4 1.0

Iron binding site 5 out of 7 in the Native Strucutre 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 5 of Native Strucutre of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:69.6 occ:1.00 O A:HOH318 2.4 24.6 1.0 OE1 A:GLN55 2.7 31.4 1.0 O A:HOH399 2.8 41.7 1.0 CD A:GLN55 3.7 29.2 1.0 O A:HOH409 4.0 29.1 1.0 CG A:GLN55 4.4 18.5 1.0 NE2 A:GLN55 4.5 25.1 1.0 CB A:ALA38 4.6 15.1 1.0 N A:HIS39 4.7 20.8 1.0 O A:ALA35 4.7 25.5 1.0 CB A:GLN55 4.9 19.6 1.0 CA A:HIS39 4.9 22.4 1.0 O A:HOH426 5.0 42.9 1.0

Iron binding site 6 out of 7 in the Native Strucutre 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 6 of Native Strucutre of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe206 b:101.9 occ:1.00 O A:HOH324 2.5 42.1 1.0 O A:HOH348 2.7 55.9 1.0 OD2 A:ASP43 2.7 43.2 1.0 CG A:ASP43 3.7 40.0 1.0 OD1 A:ASP43 3.9 33.9 1.0 NE2 A:HIS39 4.8 32.5 1.0 CB A:ASP43 5.0 26.9 1.0

Iron binding site 7 out of 7 in the Native Strucutre 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 7 of Native Strucutre of Ferritin From Ureaplasma Diversum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe207 b:87.6 occ:1.00 O A:HOH363 2.5 50.0 1.0 O A:HOH414 2.7 58.6 1.0 OD1 A:ASN17 2.8 22.7 1.0 O A:HOH395 2.9 59.6 1.0 OD1 A:ASN14 3.5 60.5 1.0 CG A:ASN17 3.7 29.9 1.0 CB A:ASN17 3.8 21.4 1.0 O A:HOH379 3.8 41.9 1.0 CA A:ASN14 4.3 42.8 1.0 CG A:ASN14 4.4 69.0 1.0 O A:SER13 4.6 33.2 1.0 N A:LYS79 4.6 32.0 1.0 CA A:MET78 4.6 29.7 1.0 CB A:ASN14 4.6 45.1 1.0 N A:ASN14 4.7 53.6 1.0 O A:HOH301 4.7 58.5 1.0 CG A:MET78 4.9 26.2 1.0 C A:SER13 4.9 56.0 1.0 ND2 A:ASN17 4.9 27.3 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