Sodium in PDB 8w45: X-Ray Crystal Structure of V30M-Ttr in Complex with Pinostilbene

The structure of X-Ray Crystal Structure of V30M-Ttr in Complex with Pinostilbene, PDB code: 8w45 was solved by T.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.61 / 1.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.401, 84.371, 63.229, 90, 90, 90
R / Rfree (%)	14.3 / 16.5

The binding sites of Sodium atom in the X-Ray Crystal Structure of V30M-Ttr in Complex with Pinostilbene (pdb code 8w45). 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 Pinostilbene, PDB code: 8w45:
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 Pinostilbene


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 Pinostilbene within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:29.4 occ:1.00 O A:ASP99 2.2 27.4 1.0 O A:HOH406 2.3 32.5 1.0 O A:HOH373 2.3 43.5 1.0 O A:HOH365 2.4 28.4 1.0 O A:HOH320 2.5 36.0 1.0 O A:HOH385 2.5 43.2 1.0 C A:ASP99 3.4 26.6 1.0 HA A:SER100 3.7 37.1 1.0 HB2 A:ASP99 3.8 36.1 1.0 HA A:ASP99 4.2 30.4 1.0 OE1 A:GLU66 4.3 24.0 1.0 CA A:ASP99 4.3 25.3 1.0 N A:SER100 4.4 28.1 1.0 CA A:SER100 4.4 30.9 1.0 CB A:ASP99 4.5 30.1 1.0 CD A:GLU66 4.7 24.3 1.0 OE2 A:GLU66 4.8 24.7 1.0

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


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 Pinostilbene within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:34.3 occ:1.00 O B:HOH411 2.4 38.4 1.0 O B:HOH327 2.4 42.5 1.0 O B:HOH390 2.5 21.2 1.0 O B:HOH389 2.5 43.4 1.0 O B:ASP99 2.5 18.8 1.0 HG B:SER100 3.4 27.8 1.0 C B:ASP99 3.5 16.9 1.0 HA B:SER100 3.5 20.9 1.0 HB2 B:ASP99 3.7 27.5 1.0 OG B:SER100 4.0 23.2 1.0 O B:HOH340 4.1 20.5 1.0 N B:SER100 4.2 16.5 1.0 CA B:SER100 4.2 17.4 1.0 O B:HOH415 4.3 36.8 1.0 CB B:ASP99 4.4 22.9 1.0 CA B:ASP99 4.5 17.0 1.0 HA B:ASP99 4.7 20.4 1.0 OD2 B:ASP99 4.7 32.3 1.0 CG B:ASP99 4.7 30.4 1.0 CB B:SER100 4.7 20.1 1.0 H B:SER100 4.9 19.8 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