Sodium in PDB 7qdk: A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald

The structure of A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald, PDB code: 7qdk was solved by P.Kumar, N.G.Paterson, D.N.Woolfson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.25 / 1.41
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	22.22, 22.22, 128.32, 90, 90, 120
R / Rfree (%)	13.9 / 17.7

The structure of A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Sodium atom in the A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald (pdb code 7qdk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald, PDB code: 7qdk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:33.1 occ:1.00 O A:HOH216 2.9 24.0 1.0 C5 A:MPD102 3.5 32.1 1.0 CB A:GLU22 3.8 18.7 1.0 OE1 A:GLU22 3.8 31.9 1.0 O4 A:MPD102 3.9 33.8 1.0 CG A:GLU22 3.9 22.4 1.0 C4 A:MPD102 4.0 31.6 1.0 CD A:GLU22 4.1 25.1 1.0 CA A:GLU22 4.6 16.4 1.0 O A:GLU22 4.7 16.1 1.0 C A:GLU22 5.0 15.4 1.0

Sodium binding site 2 out of 3 in the A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald within 5.0Å range:

Sodium binding site 3 out of 3 in the A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Trimeric De Novo Coiled-Coil Assembly: Cc-Typen-Lald within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:44.4 occ:1.00 CD1 B:TRP15 4.2 29.4 0.5 CD1 B:TRP15 4.6 16.8 0.5 NE1 B:TRP15 5.0 18.0 0.5

P.Kumar, N.G.Paterson, J.Clayden, D.N.Woolfson. De Novo Design of Discrete, Stable 3 10 -Helix Peptide Assemblies. Nature V. 607 387 2022.
ISSN: ESSN 1476-4687
PubMed: 35732733
DOI: 10.1038/S41586-022-04868-X