Sodium in PDB 6vrf: Adp Bound TTBK2 Kinase Domain

All present enzymatic activity of Adp Bound TTBK2 Kinase Domain:
2.7.11.1;

The structure of Adp Bound TTBK2 Kinase Domain, PDB code: 6vrf was solved by J.V.Chodaparambil, D.J.Marcotte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.53 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.223, 114.625, 120.005, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.9

The structure of Adp Bound TTBK2 Kinase Domain also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Adp Bound TTBK2 Kinase Domain (pdb code 6vrf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Adp Bound TTBK2 Kinase Domain, PDB code: 6vrf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Adp Bound TTBK2 Kinase Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Adp Bound TTBK2 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:71.3 occ:1.00 NA A:NA304 2.7 32.6 1.0 O A:HOH821 2.8 44.6 1.0 O A:HOH415 2.9 41.9 1.0 CG A:LYS62 3.5 44.2 1.0 NZ A:LYS62 3.6 58.8 1.0 CE A:LYS62 3.7 57.3 1.0 CB A:ALA66 4.0 20.3 1.0 CD A:LYS62 4.1 47.2 1.0 O A:HOH717 4.2 31.8 1.0 O A:LYS62 4.2 25.1 1.0 O A:HOH789 4.7 30.1 1.0 O A:HOH805 4.8 32.1 1.0 C A:LYS62 4.8 31.4 1.0 O A:HOH787 4.8 41.1 1.0 O A:HOH810 4.8 31.0 1.0 CB A:LYS62 4.9 30.4 1.0

Sodium binding site 2 out of 4 in the Adp Bound TTBK2 Kinase Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Adp Bound TTBK2 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:32.6 occ:1.00 O A:LYS62 2.7 25.1 1.0 NA A:NA303 2.7 71.3 1.0 O A:HOH717 2.8 31.8 1.0 O A:HOH787 2.9 41.1 1.0 C A:LYS62 3.6 31.4 1.0 CG A:LYS62 3.6 44.2 1.0 N A:ALA66 3.6 17.4 1.0 CB A:ALA66 3.7 20.3 1.0 CA A:LYS62 3.8 25.3 1.0 CB A:VAL65 4.0 18.5 1.0 CA A:ALA66 4.0 19.6 1.0 CG1 A:VAL65 4.1 21.0 1.0 O A:HOH500 4.1 46.7 1.0 CB A:LYS62 4.3 30.4 1.0 C A:VAL65 4.4 18.4 1.0 O A:HOH821 4.6 44.6 1.0 O A:HOH415 4.6 41.9 1.0 CA A:VAL65 4.7 17.4 1.0 O A:HOH813 4.7 54.5 1.0 O A:HOH805 4.7 32.1 1.0 N A:MET63 4.8 28.4 1.0 CD A:LYS62 4.8 47.2 1.0 O A:HOH421 4.9 37.8 1.0 N A:VAL65 5.0 18.2 1.0

Sodium binding site 3 out of 4 in the Adp Bound TTBK2 Kinase Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Adp Bound TTBK2 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:63.3 occ:1.00 O1 A:PO4302 2.1 51.8 1.0 O A:GLY185 2.6 34.7 1.0 NH1 A:ARG140 3.2 20.9 1.0 NH2 A:ARG181 3.2 23.1 1.0 O A:HOH541 3.3 33.3 1.0 N A:GLY185 3.4 34.0 1.0 P A:PO4302 3.5 37.0 1.0 C A:GLY185 3.6 29.9 1.0 CB A:ALA184 3.7 24.6 1.0 NE A:ARG187 3.7 35.4 1.0 C A:ALA184 3.8 38.2 1.0 CA A:GLY185 3.9 32.2 1.0 O2 A:PO4302 3.9 52.5 1.0 O A:HOH576 3.9 21.8 1.0 O3 A:PO4302 4.0 37.0 1.0 CG A:ARG187 4.0 37.0 1.0 CZ A:ARG181 4.1 23.6 1.0 CA A:ALA184 4.1 27.6 1.0 CZ A:ARG187 4.1 44.0 1.0 NH1 A:ARG181 4.1 29.0 1.0 NH2 A:ARG187 4.2 43.5 1.0 CZ A:ARG140 4.2 17.6 1.0 O A:HOH608 4.3 37.4 1.0 NH2 A:ARG140 4.3 18.6 1.0 O4 A:PO4302 4.4 33.9 1.0 CD A:ARG187 4.4 42.5 1.0 O A:HOH567 4.4 43.0 1.0 O A:ALA184 4.6 30.4 1.0 N A:PHE186 4.8 33.0 1.0

Sodium binding site 4 out of 4 in the Adp Bound TTBK2 Kinase Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Adp Bound TTBK2 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:37.5 occ:1.00 OD1 A:ASP266 2.6 35.7 1.0 CG A:ASP266 3.2 38.5 1.0 O A:HOH562 3.2 47.0 1.0 OD2 A:ASP266 3.4 69.2 1.0 OG1 A:THR269 3.7 25.9 1.0 CB A:PHE268 3.7 25.2 1.0 O A:HOH537 4.1 38.5 1.0 C A:PHE268 4.4 24.2 1.0 CB A:ASP266 4.5 29.6 1.0 CA A:PHE268 4.5 20.1 1.0 CD2 A:PHE268 4.5 23.2 1.0 CG A:PHE268 4.6 22.2 1.0 O A:PHE268 4.6 26.7 1.0 N A:PHE268 4.7 22.7 1.0 O A:HOH485 4.7 50.5 1.0 N A:THR269 4.8 23.9 1.0

C.Bao, B.Bajrami, D.J.Marcotte, J.V.Chodaparambil, H.M.Kerns, J.Henderson, R.Wei, B.Gao, G.M.Dillon. Mechanisms of Regulation and Diverse Activities of Tau-Tubulin Kinase (Ttbk) Isoforms. Cell. Mol. Neurobiol. 2020.
ISSN: ISSN 1573-6830
PubMed: 32424773
DOI: 10.1007/S10571-020-00875-6