Sodium in PDB 6s7x: DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom

The structure of DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom, PDB code: 6s7x was solved by M.A.Cottee, I.A.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.41 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.334, 70.386, 142.821, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.3

The structure of DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom (pdb code 6s7x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom, PDB code: 6s7x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:39.5 occ:1.00 O A:GLU104 2.3 23.8 1.0 O A:HOH545 2.3 32.4 1.0 O A:HOH553 2.3 33.0 1.0 O B:HOH536 2.5 28.2 1.0 O A:HOH572 2.6 27.2 1.0 OE1 A:GLU110 2.8 26.0 1.0 CD A:GLU110 3.4 26.7 1.0 HG23 A:THR106 3.4 28.1 1.0 C A:GLU104 3.5 25.1 1.0 HE2 B:HIS189 3.6 29.0 0.0 HB3 A:GLU104 3.8 23.8 1.0 H A:THR106 3.8 25.8 1.0 HB3 A:GLU110 3.9 22.6 1.0 OE2 A:GLU110 3.9 31.7 1.0 HA A:ALA105 4.0 26.6 1.0 HA A:GLU104 4.1 23.8 1.0 HG2 A:GLU110 4.1 24.7 1.0 HD2 B:HIS189 4.2 28.2 1.0 O A:HOH409 4.2 25.6 1.0 NE2 B:HIS189 4.2 29.0 1.0 CG A:GLU110 4.2 24.9 1.0 CA A:GLU104 4.3 23.7 1.0 O A:HOH588 4.4 37.9 1.0 CG2 A:THR106 4.4 28.8 1.0 O A:HOH501 4.4 32.6 1.0 N A:ALA105 4.5 23.9 1.0 CB A:GLU104 4.5 23.2 1.0 CD2 B:HIS189 4.5 29.1 1.0 CB A:GLU110 4.5 22.5 1.0 N A:THR106 4.6 24.9 1.0 CA A:ALA105 4.7 26.9 1.0 O B:HOH562 4.7 34.7 1.0 HG22 A:THR106 4.8 28.0 1.0 HG21 A:THR106 4.8 28.0 1.0 HD12 A:LEU114 4.8 22.3 1.0 O A:HOH494 4.8 19.6 1.0 HB2 A:GLU110 4.8 22.6 1.0 OG1 A:THR106 4.9 27.0 1.0 HB2 A:GLU104 4.9 23.8 1.0 HG1 A:THR106 5.0 27.3 0.0

Sodium binding site 2 out of 2 in the DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:33.5 occ:1.00 O B:HOH532 2.3 35.1 1.0 O B:HOH454 2.5 26.4 1.0 O B:HIS182 2.5 21.6 1.0 O B:HOH503 2.5 22.2 1.0 C B:HIS182 3.2 19.6 1.0 H B:SER184 3.3 19.5 1.0 O B:HOH406 3.7 30.6 1.0 HB2 B:SER184 3.7 22.2 1.0 N B:SER184 3.8 19.3 1.0 HA B:HIS182 3.8 20.8 1.0 HA B:ILE183 3.9 18.5 1.0 N B:ILE183 4.0 18.1 1.0 CA B:HIS182 4.1 20.4 1.0 O B:HOH423 4.2 30.1 1.0 CA B:ILE183 4.3 18.2 1.0 C B:ILE183 4.3 19.2 1.0 HB3 B:SER184 4.3 22.2 1.0 CB B:SER184 4.4 21.2 1.0 O B:LYS181 4.5 23.0 1.0 O A:HOH504 4.5 30.3 1.0 O B:HOH563 4.5 37.8 1.0 CA B:SER184 4.6 20.0 1.0 H B:ILE183 4.7 18.5 1.0 HA B:SER184 4.8 19.8 1.0 N B:HIS182 4.9 20.2 1.0

M.A.Cottee, S.C.Letham, G.R.Young, J.P.Stoye, I.A.Taylor. Structure of Drosophila Melanogaster ARC1 Reveals A Repurposed Molecule with Characteristics of Retroviral Gag Sci Adv 2020.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.AAY6354