Sodium in PDB 6zum: Crystal Structure of Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc

The structure of Crystal Structure of Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc, PDB code: 6zum was solved by F.Guagnini, S.Engilberge, R.J.Flood, K.O.Ramberg, P.B.Crowley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.16 / 1.59
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	51.057, 51.057, 102.477, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 20.3

The structure of Crystal Structure of Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc (pdb code 6zum). 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 Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc, PDB code: 6zum:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc


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 Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:56.1 occ:0.33 O07 A:QQ7106 2.5 50.3 1.0 O02 A:QQ7106 2.5 52.0 1.0 H9 A:QQ7106 2.8 55.1 1.0 C21 A:QQ7106 3.5 47.0 1.0 C08 A:QQ7106 3.6 49.1 1.0 C07 A:QQ7106 3.7 46.1 1.0 N12 A:QQ7106 4.1 44.7 1.0 O A:HOH207 4.1 57.5 1.0 N02 A:QQ7106 4.1 46.0 1.0 NA A:NA108 4.1 60.5 0.2 H10 A:QQ7106 4.5 55.1 1.0 H35 A:QQ7106 4.5 63.8 1.0 H7 A:QQ7106 4.5 62.6 1.0 N15 A:QQ7106 4.8 46.6 1.0 N04 A:QQ7106 4.8 48.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc


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 Dimethylated Rsl-N23H (Rsl-B3) in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:60.5 occ:0.25 H35 A:QQ7106 2.4 63.8 1.0 O07 A:QQ7106 3.2 50.3 1.0 C39 A:QQ7106 3.3 53.1 1.0 H36 A:QQ7106 3.4 63.8 1.0 C21 A:QQ7106 3.6 47.0 1.0 N15 A:QQ7106 3.8 46.6 1.0 NA A:NA107 4.1 56.1 0.3 O10 A:QQ7106 4.3 54.0 1.0 H9 A:QQ7106 4.5 55.1 1.0 N17 A:QQ7106 4.5 47.8 1.0 N12 A:QQ7106 4.5 44.7 1.0 C23 A:QQ7106 4.8 51.1 1.0 C22 A:QQ7106 4.9 44.4 1.0 H20 A:QQ7106 5.0 53.3 1.0

F.Guagnini, S.Engilberge, R.J.Flood, K.O.Ramberg, P.B.Crowley. Metal-Mediated Protein-Cucurbituril Crystalline Architectures Cryst.Growth Des. 2020.
ISSN: ESSN 1528-7505
DOI: 10.1021/ACS.CGD.0C01023