Chlorine in PDB 8w7t: Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin

The structure of Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w7t 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)	44.95 / 2.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	179.789, 179.789, 179.789, 90, 90, 90
R / Rfree (%)	15.6 / 22

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

Magnesium	(Mg)	1 atom
Iron	(Fe)	15 atoms

The binding sites of Chlorine atom in the Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin (pdb code 8w7t). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w7t:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl217 b:52.5 occ:1.00 CE A:LYS159 3.1 31.9 1.0 NZ A:LYS159 3.2 49.1 1.0 N A:ALA95 3.5 44.6 1.0 O A:HOH406 3.5 39.8 1.0 CD1 A:PHE45 3.8 43.6 1.0 CB A:ALA95 3.8 38.8 1.0 CB A:PHE45 3.9 41.2 1.0 CB A:ASP94 3.9 32.8 1.0 CG A:PHE45 3.9 51.7 1.0 CA A:ASP94 4.0 54.8 1.0 C A:ASP94 4.2 42.5 1.0 O A:HOH338 4.2 50.4 1.0 CA A:ALA95 4.3 40.7 1.0 CA A:PHE45 4.4 54.7 1.0 O A:PHE45 4.5 45.5 1.0 CE1 A:PHE45 4.6 42.5 1.0 CD A:LYS159 4.6 41.5 1.0 CD2 A:PHE45 4.8 35.7 1.0 C A:PHE45 5.0 50.0 1.0

Chlorine binding site 2 out of 4 in the Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl218 b:54.4 occ:1.00 O A:HOH351 3.0 31.7 1.0 O A:HOH413 3.6 64.2 1.0 CA A:LEU119 3.7 41.1 1.0 N A:LEU119 3.8 38.1 1.0 C A:LYS118 4.0 36.3 1.0 CD A:LYS118 4.0 42.3 1.0 CG A:LYS118 4.0 35.9 1.0 CB A:ALA122 4.1 32.4 1.0 O A:LYS118 4.1 39.8 1.0 CB A:LEU119 4.1 44.1 1.0 CD1 A:LEU119 4.2 35.6 1.0 CB A:LYS118 4.3 35.0 1.0 CE A:LYS118 4.3 39.4 1.0 CG A:LEU119 4.8 45.1 1.0 O A:HOH388 4.8 57.4 1.0 CA A:LYS118 4.8 42.3 1.0 O A:HOH416 4.9 44.2 1.0 O A:HOH427 4.9 42.6 1.0 C A:LEU119 4.9 42.9 1.0 O A:ALA115 4.9 36.9 1.0

Chlorine binding site 3 out of 4 in the Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl219 b:66.3 occ:1.00 NZ A:LYS89 3.3 59.5 1.0 CE A:LYS89 3.5 33.5 1.0 O A:HOH398 3.8 50.2 0.5 CD A:LYS89 3.8 49.5 1.0 CB A:ALA87 4.4 43.6 1.0 CG A:LYS89 4.9 41.2 1.0

Chlorine binding site 4 out of 4 in the Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Fe-O Nanocluster of Form-VII in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl220 b:76.9 occ:1.00 CA A:ALA104 3.5 33.2 1.0 CB A:ALA104 3.7 30.8 1.0 CD1 A:TYR103 3.8 47.8 1.0 ND2 A:ASN107 3.8 51.6 1.0 O A:HOH345 3.9 66.2 1.0 CE1 A:TYR103 4.0 50.1 1.0 N A:ALA104 4.2 41.7 1.0 CB A:ASN107 4.3 53.2 1.0 CG A:ASN107 4.6 63.7 1.0 C A:ALA104 4.6 42.7 1.0 O A:TYR103 4.7 52.4 1.0 C A:TYR103 4.7 39.1 1.0 O A:ALA104 4.7 44.4 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