Sodium in PDB 6zul: Crystal Structure of Dimethylated Rsl in Complex with Cucurbit[7]Uril and Zinc

The structure of Crystal Structure of Dimethylated Rsl in Complex with Cucurbit[7]Uril and Zinc, PDB code: 6zul 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)	43.44 / 1.62
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.358, 50.356, 71.513, 84.17, 82.46, 60.04
R / Rfree (%)	17.4 / 20.9

The structure of Crystal Structure of Dimethylated Rsl 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 in Complex with Cucurbit[7]Uril and Zinc (pdb code 6zul). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Dimethylated Rsl in Complex with Cucurbit[7]Uril and Zinc, PDB code: 6zul:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Dimethylated Rsl 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 in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:8.7 occ:1.00 O10 C:QQ7101 2.4 13.4 1.0 O07 C:QQ7101 2.7 13.1 1.0 H35 C:QQ7101 2.7 12.3 1.0 C23 C:QQ7101 3.4 10.4 1.0 NA C:NA105 3.6 20.6 1.0 C39 C:QQ7101 3.6 10.2 1.0 C21 C:QQ7101 3.7 16.4 1.0 N17 C:QQ7101 4.0 8.9 1.0 N15 C:QQ7101 4.1 10.4 1.0 H25 C:QQ7101 4.4 12.6 1.0 H36 C:QQ7101 4.4 12.3 1.0 O C:HOH288 4.5 18.8 1.0 N20 C:QQ7101 4.6 9.5 1.0 H9 C:QQ7101 4.8 16.3 1.0 N12 C:QQ7101 4.9 14.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Dimethylated Rsl 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 in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Na105 b:20.6 occ:1.00 H9 C:QQ7101 2.3 16.3 1.0 O07 C:QQ7101 2.6 13.1 1.0 O02 C:QQ7101 2.6 13.5 1.0 C07 C:QQ7101 3.4 13.6 1.0 C21 C:QQ7101 3.6 16.4 1.0 NA C:NA104 3.6 8.7 1.0 C08 C:QQ7101 3.6 18.8 1.0 N12 C:QQ7101 3.9 14.7 1.0 N02 C:QQ7101 4.0 14.8 1.0 H10 C:QQ7101 4.0 16.3 1.0 H35 C:QQ7101 4.8 12.3 1.0 H7 C:QQ7101 4.8 16.6 1.0 N15 C:QQ7101 4.8 10.4 1.0 N04 C:QQ7101 4.9 15.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Dimethylated Rsl 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 3 of Crystal Structure of Dimethylated Rsl in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:9.1 occ:1.00 O10 D:QQ7101 2.4 10.4 1.0 O07 D:QQ7101 2.7 14.6 1.0 H35 D:QQ7101 2.7 12.7 1.0 C23 D:QQ7101 3.4 11.3 1.0 NA D:NA105 3.5 19.1 1.0 C39 D:QQ7101 3.7 10.5 1.0 C21 D:QQ7101 3.7 16.2 1.0 N17 D:QQ7101 4.0 9.8 1.0 N15 D:QQ7101 4.1 8.8 1.0 H25 D:QQ7101 4.4 11.7 1.0 H36 D:QQ7101 4.5 12.7 1.0 N20 D:QQ7101 4.7 10.5 1.0 CH1 D:MLY34 4.7 39.5 1.0 H9 D:QQ7101 4.8 18.0 1.0 N12 D:QQ7101 5.0 16.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Dimethylated Rsl 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 4 of Crystal Structure of Dimethylated Rsl in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Na105 b:19.1 occ:1.00 H9 D:QQ7101 2.4 18.0 1.0 O07 D:QQ7101 2.6 14.6 1.0 O02 D:QQ7101 2.6 14.5 1.0 C07 D:QQ7101 3.4 15.0 1.0 NA D:NA102 3.5 9.1 1.0 C21 D:QQ7101 3.6 16.2 1.0 C08 D:QQ7101 3.6 15.5 1.0 N12 D:QQ7101 3.9 16.8 1.0 N02 D:QQ7101 3.9 11.6 1.0 H10 D:QQ7101 4.1 18.0 1.0 H35 D:QQ7101 4.7 12.7 1.0 H7 D:QQ7101 4.8 16.9 1.0 N15 D:QQ7101 4.8 8.8 1.0 N04 D:QQ7101 4.9 15.9 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