Sodium in PDB 6qyl: Structure of Mbp-Mcl-1 in Complex with Compound 8A

The structure of Structure of Mbp-Mcl-1 in Complex with Compound 8A, PDB code: 6qyl was solved by P.Dokurno, Z.Szlavik, L.Ondi, M.Csekei, A.Paczal, Z.B.Szabo, G.Radics, J.Murray, J.Davidson, I.Chen, B.Davis, R.E.Hubbard, C.Pedder, A.E.Surgenor, J.Smith, A.Robertson, G.Letoumelin-Braizat, N.Cauquil, M.Zarka, D.Demarles, F.Perron-Sierra, O.Geneste, A.Kotschy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.120, 136.260, 37.850, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.5

The binding sites of Sodium atom in the Structure of Mbp-Mcl-1 in Complex with Compound 8A (pdb code 6qyl). 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 Structure of Mbp-Mcl-1 in Complex with Compound 8A, PDB code: 6qyl:

Sodium binding site 1 out of 1 in the Structure of Mbp-Mcl-1 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Mbp-Mcl-1 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:56.1 occ:1.00 O A:HOH731 2.2 53.7 1.0 O A:HOH557 2.4 33.4 1.0 O A:HOH714 2.4 53.0 1.0 O A:HOH585 2.9 36.7 1.0 O A:HOH667 3.1 43.9 1.0 OD1 A:ASN-184 4.2 35.4 1.0 OE1 A:GLU-152 4.5 33.0 1.0 OE2 A:GLU-152 4.5 38.1 1.0 O A:HOH690 4.5 41.3 1.0 CH2 A:TRP-134 4.5 32.1 1.0 O A:HOH548 4.5 37.8 1.0 OE1 A:GLU-43 4.6 33.5 1.0 ND2 A:ASN-184 4.7 31.4 1.0 O A:HOH527 4.8 27.5 1.0 CG A:ASN-184 4.8 32.7 1.0 CD A:GLU-152 4.9 35.7 1.0 O6' A:MAL402 5.0 33.2 1.0

Z.Szlavik, L.Ondi, M.Csekei, A.Paczal, Z.B.Szabo, G.Radics, J.Murray, J.Davidson, I.Chen, B.Davis, R.E.Hubbard, C.Pedder, P.Dokurno, A.Surgenor, J.Smith, A.Robertson, G.Letoumelin-Braizat, N.Cauquil, M.Zarka, D.Demarles, F.Perron-Sierra, A.Claperon, F.Colland, O.Geneste, A.Kotschy. Structure-Guided Discovery of A Selective Mcl-1 Inhibitor with Cellular Activity. J.Med.Chem. V. 62 6913 2019.
ISSN: ISSN 0022-2623
PubMed: 31339316
DOI: 10.1021/ACS.JMEDCHEM.9B00134