Sodium in PDB 8cf7: Dimethylated Rsl-R5 in Complex with Cucurbit[7]Uril, C121 Sheet Assembly

The structure of Dimethylated Rsl-R5 in Complex with Cucurbit[7]Uril, C121 Sheet Assembly, PDB code: 8cf7 was solved by K.Ramberg, P.B.Crowley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.74 / 1.14
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.695, 50.396, 140.219, 90, 90.05, 90
R / Rfree (%)	17.7 / 18.7

The binding sites of Sodium atom in the Dimethylated Rsl-R5 in Complex with Cucurbit[7]Uril, C121 Sheet Assembly (pdb code 8cf7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dimethylated Rsl-R5 in Complex with Cucurbit[7]Uril, C121 Sheet Assembly, PDB code: 8cf7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dimethylated Rsl-R5 in Complex with Cucurbit[7]Uril, C121 Sheet Assembly


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dimethylated Rsl-R5 in Complex with Cucurbit[7]Uril, C121 Sheet Assembly within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:11.2 occ:1.00 O B:QQ7101 2.4 12.1 1.0 O06 B:QQ7101 2.7 15.7 1.0 C35 B:QQ7101 3.4 11.2 1.0 C41 B:QQ7101 3.6 12.5 1.0 C17 B:QQ7101 3.7 13.9 1.0 N B:QQ7101 4.0 11.4 1.0 N14 B:QQ7101 4.1 11.4 1.0 N25 B:QQ7101 4.6 11.9 1.0 O B:HOH228 4.9 20.4 1.0 N09 B:QQ7101 4.9 13.1 1.0 CH2 B:MLY34 4.9 18.5 0.8

Sodium binding site 2 out of 2 in the Dimethylated Rsl-R5 in Complex with Cucurbit[7]Uril, C121 Sheet Assembly


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dimethylated Rsl-R5 in Complex with Cucurbit[7]Uril, C121 Sheet Assembly within 5.0Å range: probe atom residue distance (Å) B Occ E:Na104 b:19.0 occ:1.00 O E:QQ7101 2.4 12.3 1.0 O06 E:QQ7101 2.7 15.3 1.0 C35 E:QQ7101 3.4 12.1 1.0 C41 E:QQ7101 3.6 12.6 1.0 C17 E:QQ7101 3.7 13.2 1.0 N E:QQ7101 4.0 11.2 1.0 N14 E:QQ7101 4.1 11.2 1.0 N25 E:QQ7101 4.6 11.4 1.0 N09 E:QQ7101 4.9 13.1 1.0 CH2 E:MLY34 5.0 27.6 1.0 O E:HOH257 5.0 21.4 1.0

K.O.Ramberg, P.B.Crowley. Cage Versus Sheet: Probing the Determinants of Protein - Cucurbit[7]Uril Crystalline Architectures. J.Struct.Biol. V. 215 07969 2023.
ISSN: ESSN 1095-8657
PubMed: 37137399
DOI: 10.1016/J.JSB.2023.107969