Sodium in PDB 5n84: Ttk Kinase Domain in Complex with Mps-BAY2B

All present enzymatic activity of Ttk Kinase Domain in Complex with Mps-BAY2B:
2.7.12.1;

The structure of Ttk Kinase Domain in Complex with Mps-BAY2B, PDB code: 5n84 was solved by J.Uitdehaag, N.Willemsen-Seegers, J.De Man, R.C.Buijsman, G.J.R.Zaman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.73 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.178, 112.199, 115.983, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 26.1

The binding sites of Sodium atom in the Ttk Kinase Domain in Complex with Mps-BAY2B (pdb code 5n84). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Ttk Kinase Domain in Complex with Mps-BAY2B, PDB code: 5n84:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Ttk Kinase Domain in Complex with Mps-BAY2B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ttk Kinase Domain in Complex with Mps-BAY2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:64.8 occ:1.00 O A:PRO621 2.5 60.4 1.0 OE1 A:GLU761 2.8 58.2 1.0 OH A:TYR790 2.9 47.5 1.0 NE A:ARG624 3.0 64.0 1.0 C A:PRO621 3.3 69.2 1.0 CA A:PRO621 3.4 62.0 1.0 NH2 A:ARG624 3.5 66.7 1.0 OE2 A:GLU761 3.5 62.7 1.0 CD A:GLU761 3.5 68.5 1.0 CB A:PRO621 3.7 63.7 1.0 CB A:ARG624 3.7 55.9 1.0 CZ A:ARG624 3.7 62.9 1.0 CE1 A:TYR790 3.7 53.2 1.0 CZ A:TYR790 3.8 56.4 1.0 N A:LYS625 3.8 52.4 1.0 CG A:ARG624 3.8 59.3 1.0 CD A:ARG624 4.0 61.7 1.0 CD2 A:LEU764 4.1 51.7 1.0 CB A:LYS625 4.1 58.1 1.0 CA A:LYS625 4.4 56.7 1.0 C A:ARG624 4.5 54.5 1.0 CE A:LYS625 4.5 59.8 1.0 N A:TRP622 4.6 60.3 1.0 CA A:ARG624 4.7 51.7 1.0 N A:PRO621 4.8 71.6 1.0 CG A:GLU761 5.0 60.1 1.0

Sodium binding site 2 out of 5 in the Ttk Kinase Domain in Complex with Mps-BAY2B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ttk Kinase Domain in Complex with Mps-BAY2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:58.8 occ:1.00 O A:LEU785 2.9 42.9 1.0 NE1 A:TRP628 3.1 48.9 1.0 CG2 A:VAL791 3.5 48.5 1.0 CB A:HIS788 3.7 57.9 1.0 C A:LEU785 3.7 43.8 1.0 CD2 A:LEU785 3.8 48.7 1.0 CD1 A:LEU632 3.8 44.5 1.0 CG1 A:VAL791 3.9 58.0 1.0 CD1 A:TRP628 3.9 54.7 1.0 CG2 A:VAL767 4.0 54.2 1.0 CB A:LEU785 4.0 41.7 1.0 CA A:LEU785 4.0 41.3 1.0 CD2 A:TYR790 4.2 50.5 1.0 CE2 A:TRP628 4.2 44.1 1.0 CB A:VAL791 4.2 51.5 1.0 CG A:HIS788 4.3 55.8 1.0 N A:VAL791 4.4 54.7 1.0 CB A:TYR790 4.5 49.2 1.0 ND1 A:HIS788 4.5 61.0 1.0 CG A:LEU785 4.5 44.2 1.0 CZ2 A:TRP628 4.7 42.0 1.0 CG1 A:VAL767 4.7 50.0 1.0 CA A:HIS788 4.8 51.7 1.0 CG A:TYR790 4.9 52.7 1.0 N A:LEU786 4.9 46.4 1.0 CA A:VAL791 4.9 46.4 1.0 N A:HIS788 4.9 52.0 1.0 O A:HIS788 5.0 51.3 1.0 CB A:VAL767 5.0 46.5 1.0 C A:TYR790 5.0 51.5 1.0

Sodium binding site 3 out of 5 in the Ttk Kinase Domain in Complex with Mps-BAY2B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ttk Kinase Domain in Complex with Mps-BAY2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:72.8 occ:1.00 OD2 A:ASP664 2.6 59.8 1.0 OE1 A:GLU571 2.7 65.0 1.0 O A:HOH1023 2.8 72.0 1.0 O A:HOH1011 3.0 84.5 1.0 CG A:ASP664 3.5 52.6 1.0 CD A:GLU571 3.5 70.3 1.0 OE2 A:GLU571 3.7 67.9 1.0 CB A:ASP664 3.7 52.3 1.0 N A:GLY666 3.8 51.4 1.0 O A:HOH1003 3.8 57.7 1.0 N A:ILE667 4.0 46.3 1.0 CA A:GLY666 4.0 42.9 1.0 CB A:ALA668 4.1 49.5 1.0 N A:ALA668 4.1 49.3 1.0 C A:GLY666 4.2 48.1 1.0 O A:ALA668 4.4 56.5 1.0 N A:PHE665 4.5 43.5 1.0 CA A:ALA668 4.6 53.7 1.0 OD1 A:ASP664 4.7 64.2 1.0 CG A:GLU571 4.8 62.0 1.0 CA A:ASP664 4.9 48.6 1.0 C A:PHE665 4.9 45.1 1.0 C A:ALA668 5.0 58.7 1.0 C A:ILE667 5.0 45.3 1.0

Sodium binding site 4 out of 5 in the Ttk Kinase Domain in Complex with Mps-BAY2B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ttk Kinase Domain in Complex with Mps-BAY2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na905 b:89.2 occ:1.00 O A:ASN688 2.7 66.6 1.0 O A:MET690 3.0 72.5 1.0 NE1 A:TRP718 3.2 57.7 1.0 C A:ASN688 3.3 68.6 1.0 N A:MET690 3.5 64.5 1.0 CD1 A:ILE747 3.7 69.5 1.0 N A:TYR689 3.8 61.9 1.0 O A:VAL687 3.8 65.6 1.0 SG A:CYS722 3.8 51.9 1.0 CD2 A:PHE734 3.8 70.2 1.0 C A:TYR689 3.9 65.4 1.0 CE2 A:TRP718 3.9 56.9 1.0 CZ2 A:TRP718 3.9 55.6 1.0 CG1 A:ILE747 3.9 72.5 1.0 C A:MET690 3.9 62.9 1.0 CE2 A:PHE734 3.9 73.4 1.0 CA A:TYR689 4.0 65.3 1.0 CA A:ASN688 4.2 70.7 1.0 CD1 A:TRP718 4.3 57.2 1.0 CA A:MET690 4.3 70.0 1.0 CG2 A:ILE747 4.4 80.3 1.0 NA A:NA906 4.5 79.5 1.0 O A:TYR689 4.6 63.4 1.0 C A:VAL687 4.8 65.8 1.0 CB A:ILE747 4.8 71.8 1.0 N A:ASN688 5.0 61.0 1.0 CB A:MET690 5.0 71.4 1.0

Sodium binding site 5 out of 5 in the Ttk Kinase Domain in Complex with Mps-BAY2B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ttk Kinase Domain in Complex with Mps-BAY2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na906 b:79.5 occ:1.00 OG1 A:THR732 2.7 69.2 1.0 N A:PHE734 2.9 66.0 1.0 O A:ASN688 3.0 66.6 1.0 CB A:THR732 3.1 66.9 1.0 OD1 A:ASN688 3.2 82.0 1.0 N A:PRO733 3.4 66.5 1.0 CB A:ASN688 3.5 71.9 1.0 CB A:PHE734 3.5 61.6 1.0 CA A:PHE734 3.5 64.8 1.0 CA A:ASN688 3.5 70.7 1.0 C A:THR732 3.6 62.7 1.0 CD A:PRO733 3.7 66.5 1.0 C A:ASN688 3.7 68.6 1.0 CG A:ASN688 3.7 79.7 1.0 N A:GLN735 3.7 63.5 1.0 CD2 A:PHE734 3.7 70.2 1.0 C A:PHE734 3.8 74.8 1.0 C A:PRO733 3.9 71.3 1.0 CA A:THR732 3.9 64.3 1.0 CG A:PHE734 4.0 68.4 1.0 O A:THR732 4.1 69.9 1.0 CA A:PRO733 4.1 67.0 1.0 CG2 A:THR732 4.3 63.5 1.0 NA A:NA905 4.5 89.2 1.0 CA A:GLN735 4.5 72.2 1.0 O A:PHE734 4.5 82.3 1.0 CG A:PRO733 4.6 68.7 1.0 CB A:PRO733 4.7 65.0 1.0 N A:ASN688 4.9 61.0 1.0 CE2 A:PHE734 4.9 73.4 1.0 O A:PRO733 4.9 70.7 1.0 ND2 A:ASN688 5.0 79.2 1.0 CB A:GLN735 5.0 72.0 1.0

J.C.M.Uitdehaag, J.De Man, N.Willemsen-Seegers, M.B.W.Prinsen, M.A.A.Libouban, J.G.Sterrenburg, J.J.P.De Wit, J.R.F.De Vetter, J.A.D.M.De Roos, R.C.Buijsman, G.J.R.Zaman. Target Residence Time-Guided Optimization on Ttk Kinase Results in Inhibitors with Potent Anti-Proliferative Activity. J. Mol. Biol. V. 429 2211 2017.
ISSN: ESSN 1089-8638
PubMed: 28539250
DOI: 10.1016/J.JMB.2017.05.014