Sodium in PDB 6cpr: Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group

The structure of Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group, PDB code: 6cpr was solved by B.Aruna, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.280, 66.504, 129.356, 90.00, 103.09, 90.00
R / Rfree (%)	24.9 / 28

The structure of Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group (pdb code 6cpr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group, PDB code: 6cpr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Na205 b:74.2 occ:1.00 O D:HOH308 3.3 48.6 1.0 O D:PRO50 3.8 50.5 1.0 CD D:PRO50 4.0 46.9 1.0 CB D:PRO49 4.1 34.6 1.0 CB B:ASP112 4.2 57.1 1.0 OD2 B:ASP112 4.3 60.2 1.0 CD2 B:LEU115 4.3 57.9 1.0 N D:PRO50 4.3 47.1 1.0 CB D:PRO50 4.5 49.7 1.0 CG D:PRO50 4.5 49.9 1.0 C D:PRO50 4.6 46.3 1.0 CG B:ASP112 4.7 61.1 1.0 C D:PRO49 4.7 41.8 1.0 CA D:PRO50 4.8 47.3 1.0 CG D:PRO49 4.9 34.4 1.0 CA D:PRO49 5.0 36.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 4-1BBL/4-1BB Complex in C2 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ E:Na203 b:70.5 occ:1.00 O E:CYS48 3.0 36.9 1.0 N E:CYS48 3.6 41.4 1.0 CB E:SER80 3.8 47.2 1.0 CB E:PRO47 3.8 41.9 1.0 C E:CYS48 3.9 36.9 1.0 O E:GLY34 4.0 43.5 1.0 CA E:CYS48 4.1 39.8 1.0 CB E:CYS48 4.1 40.4 1.0 C E:PRO47 4.2 44.3 1.0 CA E:PRO47 4.3 44.3 1.0 O E:HOH305 4.3 38.3 1.0 OG E:SER80 4.7 44.6 1.0 CA E:SER80 4.8 50.5 1.0

A.Bitra, T.Doukov, M.Croft, D.M.Zajonc. Crystal Structures of the Human 4-1BB Receptor Bound to Its Ligand 4-1BBL Reveal Covalent Receptor Dimerization As A Potential Signaling Amplifier. J. Biol. Chem. V. 293 9958 2018.
ISSN: ESSN 1083-351X
PubMed: 29720398
DOI: 10.1074/JBC.RA118.003176