Sodium in PDB 7byf: The Crystal Structure of Mouse ORF10-RAE1-NUP98 Complex

The structure of The Crystal Structure of Mouse ORF10-RAE1-NUP98 Complex, PDB code: 7byf was solved by P.Gao, H.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.90 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.397, 150.63, 101.618, 90, 111.03, 90
R / Rfree (%)	18.4 / 23.3

The structure of The Crystal Structure of Mouse ORF10-RAE1-NUP98 Complex also contains other interesting chemical elements:

Mercury

(Hg)

24 atoms

The binding sites of Sodium atom in the The Crystal Structure of Mouse ORF10-RAE1-NUP98 Complex (pdb code 7byf). 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 Mouse ORF10-RAE1-NUP98 Complex, PDB code: 7byf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Crystal Structure of Mouse ORF10-RAE1-NUP98 Complex


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 Mouse ORF10-RAE1-NUP98 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Na501 b:70.0 occ:1.00 O F:PRO342 2.9 44.8 1.0 OE1 F:GLU316 3.2 69.3 1.0 O F:HOH672 3.6 47.2 1.0 CD F:GLU316 3.7 71.8 1.0 OE2 F:GLU316 3.7 68.4 1.0 C F:PRO342 4.1 42.9 1.0 CD1 F:LEU343 4.3 42.9 1.0 CA F:LEU343 4.3 45.8 1.0 CB F:LYS341 4.6 43.4 1.0 N F:LEU343 4.7 43.5 1.0 N F:LEU344 4.7 48.3 1.0 CG F:GLU316 4.9 67.4 1.0

Sodium binding site 2 out of 4 in the The Crystal Structure of Mouse ORF10-RAE1-NUP98 Complex


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 Mouse ORF10-RAE1-NUP98 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Na502 b:54.1 occ:1.00 N F:ASP275 3.4 67.3 1.0 CB F:ASP275 3.6 68.9 1.0 CD2 F:LEU288 3.6 48.1 1.0 CA F:ASP275 4.2 67.7 1.0 O F:THR273 4.2 50.7 1.0 CA F:CYS274 4.3 54.8 1.0 CD1 F:LEU288 4.3 51.7 1.0 C F:CYS274 4.3 63.9 1.0 CG F:ASP275 4.5 75.0 1.0 CG F:LEU288 4.6 52.8 1.0 HG F:HG504 4.7 39.2 0.5 N F:THR276 4.7 67.5 1.0 OD2 F:ASP275 4.9 81.0 1.0

Sodium binding site 3 out of 4 in the The Crystal Structure of Mouse ORF10-RAE1-NUP98 Complex


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 Mouse ORF10-RAE1-NUP98 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:76.2 occ:1.00 O C:ALA173 2.8 80.4 1.0 C C:ALA173 3.8 77.2 1.0 CA C:SER174 4.3 69.3 1.0 N C:SER174 4.5 74.4 1.0 CA C:ALA173 4.8 72.5 1.0

Sodium binding site 4 out of 4 in the The Crystal Structure of Mouse ORF10-RAE1-NUP98 Complex


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 Mouse ORF10-RAE1-NUP98 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:67.2 occ:1.00 OD2 D:ASP24 4.1 53.0 1.0 CB D:ASP24 4.5 40.4 1.0 CG D:ASP24 4.8 46.0 1.0

H.Feng, H.Tian, Y.Wang, Q.Zhang, N.Lin, S.Liu, Y.Yu, H.Deng, P.Gao. Molecular Mechanism Underlying Selective Inhibition of Mrna Nuclear Export By Herpesvirus Protein ORF10. Proc.Natl.Acad.Sci.Usa V. 117 26719 2020.
ISSN: ESSN 1091-6490
PubMed: 33033226
DOI: 10.1073/PNAS.2007774117