Sodium in PDB 6rp6: Fragment Az-019 Binding at the TAZPS89/14-3-3 Sigma Interface

The structure of Fragment Az-019 Binding at the TAZPS89/14-3-3 Sigma Interface, PDB code: 6rp6 was solved by S.Genet, M.Wolter, X.Guillory, B.Somsen, S.Leysen, J.Patel, P.Castaldi, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.58 / 1.89
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.970, 112.020, 62.790, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 22

The structure of Fragment Az-019 Binding at the TAZPS89/14-3-3 Sigma Interface also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Fragment Az-019 Binding at the TAZPS89/14-3-3 Sigma Interface (pdb code 6rp6). 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 Fragment Az-019 Binding at the TAZPS89/14-3-3 Sigma Interface, PDB code: 6rp6:

Sodium binding site 1 out of 1 in the Fragment Az-019 Binding at the TAZPS89/14-3-3 Sigma Interface


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fragment Az-019 Binding at the TAZPS89/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:15.6 occ:1.00 O A:HOH436 2.2 18.5 1.0 O A:HOH513 2.2 38.4 1.0 OE2 A:GLU89 2.4 14.5 1.0 OE1 A:GLU86 2.4 24.9 1.0 OE2 A:GLU86 2.4 37.1 1.0 O A:HOH607 2.6 29.9 1.0 CD A:GLU86 2.7 29.4 1.0 CD A:GLU89 3.4 9.8 1.0 HG2 A:GLU89 3.7 14.9 1.0 HH12 A:ARG85 3.9 20.2 1.0 HE22 A:GLN93 4.0 11.8 1.0 CG A:GLU89 4.1 12.4 1.0 HB3 A:GLU89 4.2 9.1 1.0 CG A:GLU86 4.3 18.3 1.0 OE1 A:GLU89 4.3 10.7 1.0 HH11 A:ARG85 4.4 20.2 1.0 O A:HOH418 4.4 23.4 1.0 HA A:GLU86 4.4 8.7 1.0 OE1 A:GLN93 4.5 12.0 1.0 HG1 A:THR90 4.5 16.7 1.0 NH1 A:ARG85 4.5 16.8 1.0 O A:HOH599 4.5 23.7 1.0 NE2 A:GLN93 4.6 9.9 1.0 HG2 A:GLU86 4.7 21.9 1.0 HG3 A:GLU86 4.7 21.9 1.0 CB A:GLU89 4.7 7.6 1.0 OG1 A:THR90 4.8 13.9 1.0 O A:HOH617 4.8 24.6 1.0 O A:HOH678 4.8 34.8 1.0 O A:HOH435 4.8 35.6 1.0 HG3 A:GLU89 4.9 14.9 1.0 HB3 A:GLU86 4.9 11.2 1.0 CD A:GLN93 4.9 16.0 1.0

X.Guillory, M.Wolter, S.Leysen, J.F.Neves, A.Kuusk, S.Genet, B.Somsen, J.Morrow, E.Rivers, L.Van Beek, J.Patel, R.Goodnow, H.Schoenherr, N.Fuller, Q.Cao, R.G.Doveston, L.Brunsveld, M.R.Arkin, M.P.Castaldi, H.Boyd, I.Landrieu, H.Chen, C.Ottmann. Fragment-Based Differential Targeting of Ppi Stabilizer Interfaces. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32501690
DOI: 10.1021/ACS.JMEDCHEM.9B01942