Sodium in PDB 7slv: Vanin-1 Complexed with Compound 3

All present enzymatic activity of Vanin-1 Complexed with Compound 3:
3.5.1.92;

The structure of Vanin-1 Complexed with Compound 3, PDB code: 7slv was solved by F.F.Vajdos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.93 / 2.13
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.656, 111.511, 147.44, 90, 90, 90
R / Rfree (%)	18.1 / 22.3

The binding sites of Sodium atom in the Vanin-1 Complexed with Compound 3 (pdb code 7slv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Vanin-1 Complexed with Compound 3, PDB code: 7slv:

Sodium binding site 1 out of 1 in the Vanin-1 Complexed with Compound 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Vanin-1 Complexed with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:89.8 occ:1.00 O A:HOH717 2.2 71.8 1.0 O A:PHE66 2.2 54.7 1.0 OD1 A:ASN165 2.5 84.8 1.0 OE1 A:GLN166 2.7 50.7 1.0 O A:GLY163 2.8 69.0 1.0 C A:PHE66 3.4 55.7 1.0 CD A:GLN166 3.6 58.0 1.0 CG A:ASN165 3.7 88.6 1.0 C A:GLY163 3.9 67.0 1.0 N A:ASN165 3.9 54.7 1.0 N A:GLN166 4.1 47.1 1.0 NE2 A:GLN166 4.2 49.6 1.0 N A:PHE66 4.2 53.2 1.0 CA A:PHE66 4.3 52.1 1.0 N A:ASN67 4.4 52.9 1.0 CA A:GLU164 4.4 57.6 1.0 CB A:GLN166 4.4 49.1 1.0 C A:GLU164 4.6 58.1 1.0 ND2 A:ASN165 4.6 83.3 1.0 CA A:ASN67 4.6 52.4 1.0 CG A:GLN166 4.6 54.7 1.0 N A:GLU164 4.6 59.8 1.0 CA A:ASN165 4.6 53.2 1.0 CB A:ASN165 4.6 56.0 1.0 O A:HOH735 4.7 64.5 1.0 C A:ASN165 4.7 53.4 1.0 O A:TRP64 4.8 55.8 1.0 CB A:PHE66 4.9 53.8 1.0 CA A:GLN166 4.9 47.1 1.0 CA A:GLY163 4.9 63.0 1.0

A.Casimiro-Garcia, C.Allais, A.Brennan, C.Choi, G.Dower, K.A.Farley, M.Fleming, A.Flick, R.K.Frisbie, J.Hall, D.Hepworth, H.Jones, J.D.Knafels, S.Kortum, F.E.Lovering, J.P.Mathias, S.Mohan, P.M.Morgan, C.Parng, K.Parris, N.Pullen, F.Schlerman, J.Stansfield, J.W.Strohbach, F.F.Vajdos, F.Vincent, H.Wang, X.Wang, R.Webster, S.W.Wright. Discovery of A Series of Pyrimidine Carboxamides As Inhibitors of Vanin-1. J.Med.Chem. V. 65 757 2022.
ISSN: ISSN 0022-2623
PubMed: 34967602
DOI: 10.1021/ACS.JMEDCHEM.1C01849