Sodium in PDB 8y6f: The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin

The structure of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin, PDB code: 8y6f was solved by C.Yuan, M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.52 / 2.01
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	219.66, 219.66, 148.31, 90, 90, 90
R / Rfree (%)	24.5 / 28.7

The structure of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Iron	(Fe)	17 atoms

The binding sites of Sodium atom in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin (pdb code 8y6f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin, PDB code: 8y6f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:12.1 occ:1.00 OE1 C:GLU135 2.2 17.2 1.0 OE1 I:GLU135 2.5 18.3 1.0 OD1 I:ASP132 2.5 18.4 1.0 OD1 C:ASP132 2.6 23.6 1.0 FE I:FE201 3.0 65.5 1.0 CD C:GLU135 3.4 18.9 1.0 CG I:ASP132 3.6 21.4 1.0 CD I:GLU135 3.7 19.5 1.0 CG C:ASP132 3.7 21.4 1.0 O C:HOH444 4.0 27.4 1.0 OE2 C:GLU135 4.0 20.0 1.0 CB I:ASP132 4.3 15.2 1.0 OE2 I:GLU135 4.4 19.7 1.0 CB C:ASP132 4.4 18.0 1.0 CB C:GLU135 4.5 19.0 1.0 CG C:GLU135 4.5 16.8 1.0 OD2 I:ASP132 4.6 18.9 1.0 OD2 C:ASP132 4.7 17.7 1.0 CA I:ASP132 4.7 17.5 1.0 CB I:GLU135 4.7 20.1 1.0 CA C:ASP132 4.8 17.2 1.0 CG I:GLU135 4.8 14.2 1.0

Sodium binding site 2 out of 4 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:21.9 occ:1.00 O D:HOH307 2.1 28.9 1.0 O D:HOH423 2.2 27.4 1.0 OE2 D:GLU63 2.7 27.5 1.0 OE1 D:GLU108 3.1 20.6 1.0 OE1 D:GLN59 3.3 31.8 1.0 CD D:GLU108 3.5 18.4 1.0 OE2 D:GLU108 3.7 21.2 1.0 O D:HOH304 3.9 22.5 1.0 CD D:GLU63 3.9 19.9 1.0 O D:HOH401 4.1 25.6 1.0 CB D:ALA145 4.2 15.6 1.0 OH D:TYR35 4.2 17.5 1.0 CD D:GLN59 4.3 23.2 1.0 CE2 D:TYR35 4.3 15.4 1.0 CG D:GLU63 4.6 16.7 1.0 CG D:GLU108 4.6 20.5 1.0 CZ D:TYR35 4.6 16.7 1.0 CE1 D:HIS66 4.7 26.0 1.0 OE1 D:GLU63 4.9 25.3 1.0 CB D:GLN59 4.9 19.1 1.0

Sodium binding site 3 out of 4 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ J:Na201 b:22.0 occ:1.00 NE2 F:HIS181 2.8 21.0 1.0 NE2 J:HIS181 2.9 22.2 1.0 NE2 G:HIS181 3.0 20.9 1.0 NE2 K:HIS181 3.1 21.4 1.0 CD2 J:LEU177 3.4 17.0 1.0 CD2 F:HIS181 3.7 17.6 1.0 CE1 F:HIS181 3.7 20.8 1.0 CD2 K:LEU177 3.8 15.4 1.0 CD2 F:LEU177 3.8 17.0 1.0 CE1 J:HIS181 3.8 24.0 1.0 CD2 J:HIS181 3.9 21.3 1.0 CE1 G:HIS181 3.9 22.8 1.0 CE1 K:HIS181 3.9 22.1 1.0 CD2 K:HIS181 3.9 23.7 1.0 CD2 G:HIS181 4.0 23.0 1.0 CD2 G:LEU177 4.0 18.9 1.0 ND1 F:HIS181 4.8 19.2 1.0 CG F:HIS181 4.8 20.4 1.0 CG J:LEU177 4.9 15.9 1.0 ND1 J:HIS181 4.9 23.1 1.0 CG J:HIS181 5.0 19.6 1.0

Sodium binding site 4 out of 4 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ L:Na202 b:23.7 occ:1.00 O L:HOH320 2.2 32.6 1.0 O L:HOH394 2.4 29.5 1.0 OE2 L:GLU63 2.5 23.6 1.0 OE2 L:GLU108 2.5 22.6 1.0 O L:HOH310 3.0 24.2 1.0 CD L:GLU108 3.2 22.4 1.0 OE1 L:GLU108 3.2 24.3 1.0 CD L:GLU63 3.7 23.3 1.0 OE1 L:GLN59 4.0 29.4 1.0 CB L:ALA145 4.1 14.7 1.0 CE1 L:HIS66 4.3 26.5 1.0 OH L:TYR35 4.4 18.2 1.0 O L:HOH448 4.5 31.0 1.0 CE2 L:TYR35 4.5 14.9 1.0 CG L:GLU108 4.6 16.1 1.0 CG L:GLU63 4.6 18.0 1.0 OE1 L:GLU63 4.6 19.2 1.0 OE1 L:GLN142 4.7 22.6 1.0 CZ L:TYR35 4.9 18.1 1.0 FE L:FE203 4.9 31.7 1.0 ND1 L:HIS66 5.0 23.9 1.0

W.Yan, H.Li, J.Ning, S.Huang, L.Jiang, P.Xu, M.Huang, C.Yuan. Engineered Protein Cages with Enhanced Extracellular Drug Release For Elevated Antitumor Efficacy. Int.J.Biol.Macromol. V. 267 31492 2024.
ISSN: ISSN 0141-8130
PubMed: 38604418
DOI: 10.1016/J.IJBIOMAC.2024.131492