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Sodium in PDB 6vrf: Adp Bound TTBK2 Kinase Domain

Enzymatic activity of Adp Bound TTBK2 Kinase Domain

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

Protein crystallography data

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

Other elements in 6vrf:

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

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

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 6vrf

Go back to Sodium Binding Sites List in 6vrf
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 6vrf

Go back to Sodium Binding Sites List in 6vrf
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 6vrf

Go back to Sodium Binding Sites List in 6vrf
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 6vrf

Go back to Sodium Binding Sites List in 6vrf
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

Reference:

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
Page generated: Tue Oct 8 14:25:43 2024

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