Sodium in PDB 8w44: X-Ray Crystal Structure of V30M-Ttr in Complex with Oxyresveratrol

The structure of X-Ray Crystal Structure of V30M-Ttr in Complex with Oxyresveratrol, PDB code: 8w44 was solved by T.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.63 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.226, 84.334, 62.916, 90, 90, 90
R / Rfree (%)	15.2 / 18.1

The binding sites of Sodium atom in the X-Ray Crystal Structure of V30M-Ttr in Complex with Oxyresveratrol (pdb code 8w44). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of V30M-Ttr in Complex with Oxyresveratrol, PDB code: 8w44:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of V30M-Ttr in Complex with Oxyresveratrol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of V30M-Ttr in Complex with Oxyresveratrol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:36.1 occ:1.00 O A:ASP99 2.2 28.3 1.0 O A:HOH357 2.4 47.9 1.0 O A:HOH347 2.4 37.2 1.0 O A:HOH329 2.5 41.0 1.0 C A:ASP99 3.5 26.5 1.0 O A:HOH373 4.3 56.3 1.0 CA A:ASP99 4.3 24.1 1.0 OE1 A:GLU66 4.4 32.4 1.0 N A:SER100 4.4 27.1 1.0 CA A:SER100 4.4 29.7 1.0 CB A:ASP99 4.6 27.8 1.0 OE2 A:GLU66 4.8 38.4 1.0 CD A:GLU66 4.8 33.5 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of V30M-Ttr in Complex with Oxyresveratrol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of V30M-Ttr in Complex with Oxyresveratrol within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:32.3 occ:1.00 O B:HOH319 2.4 44.4 1.0 O B:ASP99 2.5 22.9 1.0 C B:ASP99 3.5 20.1 1.0 OG B:SER100 3.9 25.3 1.0 O B:HOH340 4.1 22.0 1.0 N B:SER100 4.2 19.2 1.0 CA B:SER100 4.2 19.7 1.0 CB B:ASP99 4.3 28.1 1.0 CA B:ASP99 4.4 20.9 1.0 CB B:SER100 4.7 21.9 1.0 OD2 B:ASP99 4.7 43.2 1.0 CG B:ASP99 4.8 39.2 1.0

T.Yokoyama, K.Kusaka, M.Mizuguchi, Y.Nabeshima, S.Fujiwara. Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights Into the Interactions Between Resveratrol Derivatives and Transthyretin. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37910439
DOI: 10.1021/ACS.JMEDCHEM.3C01698