Zinc 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:

Sodium

(Na)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn104 b:62.2 occ:1.00 O A:ACT103 1.8 62.7 1.0 OXT A:ACT103 1.8 64.2 1.0 O A:HOH203 2.1 58.0 1.0 C A:ACT103 2.1 64.4 1.0 NE2 A:HIS23 2.3 73.4 1.0 CE1 A:HIS23 2.6 63.0 1.0 CH3 A:ACT103 3.6 80.6 1.0 CD2 A:HIS23 3.6 64.4 1.0 ND1 A:HIS23 3.9 63.9 1.0 H3 A:ACT103 4.0 96.7 1.0 H2 A:ACT103 4.1 96.7 1.0 H1 A:ACT103 4.1 96.7 1.0 CG A:HIS23 4.4 53.4 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn105 b:78.1 occ:0.53 N A:SNM1 0.6 53.4 0.7 C2 A:SNM1 1.7 57.9 0.7 C1 A:SNM1 1.7 73.8 0.7 CA A:SNM1 1.9 63.2 0.7 O A:SNM1 2.5 57.2 0.7 C A:SNM1 2.6 56.3 0.7 CB A:SNM1 3.1 62.0 0.7 N A:SER2 3.9 61.7 1.0 OG A:SNM1 4.3 63.6 0.7 CA A:SER2 4.9 45.3 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