Chlorine in PDB 8w7q: Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin

The structure of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w7q 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)	45.02 / 2.10
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.096, 180.096, 180.096, 90, 90, 90
R / Rfree (%)	16.6 / 21.5

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

Iron	(Fe)	10 atoms
Magnesium	(Mg)	1 atom

The binding sites of Chlorine atom in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin (pdb code 8w7q). 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-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w7q:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Fe-O Nanocluster of Form-VI 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-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl212 b:47.8 occ:1.00 N A:ALA95 3.2 41.9 1.0 CE A:LYS159 3.3 45.0 1.0 NZ A:LYS159 3.3 41.3 1.0 CB A:ASP94 3.7 40.5 1.0 CB A:ALA95 3.7 37.2 1.0 O A:HOH419 3.8 41.5 1.0 CD1 A:PHE45 3.8 37.4 1.0 CG A:PHE45 3.9 41.7 1.0 CA A:ASP94 3.9 45.5 1.0 CB A:PHE45 3.9 35.1 1.0 C A:ASP94 4.0 40.4 1.0 CA A:ALA95 4.1 42.1 1.0 CE1 A:PHE45 4.5 41.4 1.0 CA A:PHE45 4.5 34.2 1.0 CD2 A:PHE45 4.6 33.5 1.0 O A:PHE45 4.6 42.0 1.0 CD A:LYS159 4.7 54.9 1.0 O A:HOH322 4.9 48.3 1.0 CG A:ASP94 4.9 45.3 1.0

Chlorine binding site 2 out of 4 in the Fe-O Nanocluster of Form-VI 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-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl213 b:47.0 occ:1.00 O A:HOH362 2.9 39.6 1.0 O A:HOH443 3.4 59.6 1.0 CA A:LEU119 3.6 37.7 1.0 N A:LEU119 3.9 39.6 1.0 CG A:LYS118 3.9 43.6 1.0 CB A:LEU119 4.1 34.2 1.0 C A:LYS118 4.1 35.5 1.0 CD1 A:LEU119 4.1 45.8 1.0 O A:LYS118 4.1 38.9 1.0 CD A:LYS118 4.2 43.0 1.0 CB A:ALA122 4.2 35.9 1.0 CB A:LYS118 4.5 37.5 1.0 CE A:LYS118 4.5 46.2 1.0 CG A:LEU119 4.8 43.1 1.0 O A:HOH413 4.8 62.0 1.0 O A:HOH442 4.8 46.6 1.0 O A:HOH453 4.8 40.9 1.0 C A:LEU119 4.9 45.8 1.0 O A:ALA115 5.0 35.0 1.0 CA A:LYS118 5.0 33.2 1.0

Chlorine binding site 3 out of 4 in the Fe-O Nanocluster of Form-VI 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-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl214 b:59.3 occ:1.00 NZ A:LYS89 3.1 48.6 1.0 CE A:LYS89 3.6 47.6 1.0 CD A:LYS89 3.8 45.9 1.0 O A:HOH422 3.8 54.2 0.5 CB A:ALA87 4.2 45.1 1.0 CG A:LYS89 4.8 43.8 1.0 O A:HOH386 4.9 49.1 1.0

Chlorine binding site 4 out of 4 in the Fe-O Nanocluster of Form-VI 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-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl215 b:63.5 occ:1.00 O A:HOH350 3.4 50.4 1.0 ND2 A:ASN107 3.5 52.9 1.0 CA A:ALA104 3.7 38.4 1.0 CB A:ALA104 3.9 41.2 1.0 CB A:ASN107 4.0 47.7 1.0 CD1 A:TYR103 4.0 42.9 1.0 CE1 A:TYR103 4.1 43.8 1.0 CG A:ASN107 4.2 53.1 1.0 N A:ALA104 4.4 38.9 1.0 O A:ALA104 4.6 37.6 1.0 C A:ALA104 4.6 43.4 1.0 O A:TYR103 4.7 42.6 1.0 C A:TYR103 4.9 37.2 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