Sodium in PDB 7slx: Vanin-1 Complexed with Compound 11

All present enzymatic activity of Vanin-1 Complexed with Compound 11:
3.5.1.92;

The structure of Vanin-1 Complexed with Compound 11, PDB code: 7slx 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)	25.63 / 2.35
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.55, 111.83, 147.53, 90, 90, 90
R / Rfree (%)	17.4 / 21.7

The binding sites of Sodium atom in the Vanin-1 Complexed with Compound 11 (pdb code 7slx). 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 11, PDB code: 7slx:

Sodium binding site 1 out of 1 in the Vanin-1 Complexed with Compound 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:85.1 occ:1.00 O A:HOH681 2.2 60.1 1.0 O A:PHE66 2.2 59.6 1.0 OD1 A:ASN165 2.3 85.4 1.0 O A:GLY163 2.7 66.5 1.0 OE1 A:GLN166 2.8 53.6 1.0 C A:PHE66 3.5 59.3 1.0 CG A:ASN165 3.5 87.9 1.0 CD A:GLN166 3.6 60.7 1.0 C A:GLY163 3.8 66.7 1.0 N A:ASN165 4.0 59.4 1.0 N A:PHE66 4.1 55.3 1.0 NE2 A:GLN166 4.2 52.5 1.0 N A:GLN166 4.2 52.7 1.0 ND2 A:ASN165 4.3 78.9 1.0 CA A:PHE66 4.4 54.9 1.0 N A:ASN67 4.4 55.5 1.0 CA A:GLU164 4.5 59.5 1.0 CB A:ASN165 4.6 60.1 1.0 N A:GLU164 4.6 60.7 1.0 CB A:GLN166 4.6 53.0 1.0 CA A:ASN67 4.6 55.4 1.0 CA A:ASN165 4.7 58.7 1.0 O A:HOH699 4.7 52.7 1.0 C A:GLU164 4.7 62.6 1.0 CG A:GLN166 4.7 54.0 1.0 CA A:GLY163 4.8 64.7 1.0 O A:TRP64 4.8 59.2 1.0 C A:ASN165 4.9 60.1 1.0 CB A:PHE66 5.0 56.2 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