Sodium in PDB 2xyn: Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680

All present enzymatic activity of Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680:
2.7.10.2;

The structure of Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680, PDB code: 2xyn was solved by E.Salah, E.Ugochukwu, J.M.Elkins, A.J.Barr, B.Shrestha, P.Savitsky, P.Mahajan, J.R.C.Muniz, W.W.Yue, A.Chaikuad, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, S.Knapp, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	147.66 / 2.81
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	170.500, 170.500, 100.651, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 28.4

The structure of Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680 (pdb code 2xyn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680, PDB code: 2xyn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:65.8 occ:1.00 O A:THR452 2.6 53.9 1.0 O A:ILE449 2.6 54.5 1.0 O A:HOH2004 2.7 30.8 1.0 CD1 A:LEU498 3.5 53.5 1.0 C A:THR452 3.7 54.4 1.0 O A:LYS450 3.7 52.6 1.0 C A:ILE449 3.8 55.0 1.0 N A:THR452 3.9 53.8 1.0 C A:LYS450 4.0 52.6 1.0 CG1 A:VAL494 4.0 55.3 1.0 NE1 A:TRP469 4.0 52.3 1.0 CD1 A:LEU457 4.1 56.5 1.0 CA A:LYS450 4.2 53.5 1.0 CA A:THR452 4.3 54.6 1.0 N A:LYS450 4.5 54.9 1.0 N A:TRP451 4.6 53.0 1.0 CE2 A:TRP469 4.6 51.9 1.0 OH A:TYR486 4.6 51.5 1.0 C A:TRP451 4.6 53.1 1.0 CZ2 A:TRP469 4.6 52.7 1.0 CG2 A:ILE449 4.6 57.3 1.0 N A:ALA453 4.8 55.3 1.0 CG A:LEU498 4.9 54.7 1.0 CE2 A:TYR486 4.9 53.1 1.0 CA A:ILE449 4.9 56.6 1.0 CB A:THR452 4.9 56.2 1.0 CD1 A:TRP469 4.9 52.8 1.0

Sodium binding site 2 out of 2 in the Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human ABL2 in Complex with Aurora Kinase Inhibitor Vx-680 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na549 b:73.1 occ:1.00 O A:HOH2006 2.5 26.7 1.0 O A:ARG519 2.9 59.6 1.0 NE A:ARG519 3.3 62.1 1.0 O A:TRP522 3.4 58.0 1.0 NE A:ARG503 3.5 55.0 1.0 C A:TRP522 3.6 57.4 1.0 CB A:TRP522 3.7 54.8 1.0 C A:ARG519 3.7 59.6 1.0 CG A:ARG503 3.7 55.1 1.0 CD A:ARG503 3.8 53.3 1.0 CA A:ARG519 3.9 58.9 1.0 CD A:ARG519 4.0 60.6 1.0 CB A:ARG519 4.0 60.7 1.0 N A:LYS523 4.0 58.7 1.0 CA A:TRP522 4.1 55.8 1.0 CZ A:ARG519 4.3 62.0 1.0 NH2 A:ARG519 4.3 63.1 1.0 CZ A:ARG503 4.4 57.0 1.0 CA A:LYS523 4.5 60.2 1.0 N A:TRP522 4.6 56.8 1.0 CG A:ARG519 4.6 60.6 1.0 CB A:ARG503 4.6 56.1 1.0 NH2 A:ARG503 4.7 58.6 1.0 CE3 A:TRP522 4.8 54.1 1.0 CG A:TRP522 4.8 53.8 1.0 N A:ALA520 4.9 61.2 1.0

E.Salah, E.Ugochukwu, A.J.Barr, F.Von Delft, S.Knapp, J.M.Elkins. Crystal Structures of Abl-Related Gene (ABL2) in Complex with Imatinib, Tozasertib (Vx-680), and A Type I Inhibitor of the Triazole Carbothioamide Class. J.Med.Chem. V. 54 2359 2011.
ISSN: ISSN 0022-2623
PubMed: 21417343
DOI: 10.1021/JM101506N