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Magnesium 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:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 6vrf

Go back to Magnesium Binding Sites List in 6vrf
Magnesium binding site 1 out of 2 in the Adp Bound TTBK2 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adp Bound TTBK2 Kinase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:24.7
occ:1.00
O1B A:ADP301 2.0 35.0 1.0
O1A A:ADP301 2.0 29.6 1.0
O A:HOH584 2.1 26.6 1.0
OD1 A:ASN146 2.2 18.6 1.0
OD2 A:ASP163 2.2 27.8 1.0
O A:HOH565 2.2 31.3 1.0
CG A:ASN146 3.2 16.5 1.0
CG A:ASP163 3.2 26.0 1.0
PA A:ADP301 3.2 29.8 1.0
PB A:ADP301 3.3 37.8 1.0
O3A A:ADP301 3.4 35.4 1.0
ND2 A:ASN146 3.6 16.5 1.0
CB A:ASP163 3.6 19.8 1.0
O A:HOH401 3.8 42.4 1.0
O A:HOH409 4.0 18.7 1.0
O A:HOH411 4.0 55.6 1.0
O2B A:ADP301 4.1 40.5 1.0
C5' A:ADP301 4.2 22.8 1.0
O A:HOH674 4.2 41.9 1.0
O5' A:ADP301 4.3 26.6 1.0
O2A A:ADP301 4.3 27.0 1.0
OD1 A:ASP163 4.3 25.9 1.0
O3B A:ADP301 4.4 45.8 1.0
CE A:LYS143 4.6 28.6 1.0
CB A:ASN146 4.6 13.2 1.0
OG A:SER145 4.6 19.2 1.0
O3' A:ADP301 4.8 30.5 1.0
CA A:ASN146 4.9 14.4 1.0
O A:SER145 4.9 15.9 1.0
C3' A:ADP301 5.0 22.6 1.0

Magnesium binding site 2 out of 2 in 6vrf

Go back to Magnesium Binding Sites List in 6vrf
Magnesium binding site 2 out of 2 in the Adp Bound TTBK2 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adp Bound TTBK2 Kinase Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:23.6
occ:1.00
O B:HOH581 2.0 23.8 1.0
O1B B:ADP301 2.0 27.1 1.0
O1A B:ADP301 2.0 24.0 1.0
O B:HOH500 2.1 28.8 1.0
OD1 B:ASN146 2.2 17.8 1.0
OD2 B:ASP163 2.2 24.5 1.0
CG B:ASN146 3.2 17.2 1.0
CG B:ASP163 3.3 19.9 1.0
PA B:ADP301 3.3 22.9 1.0
PB B:ADP301 3.3 31.6 1.0
O3A B:ADP301 3.5 27.4 1.0
ND2 B:ASN146 3.6 17.2 1.0
CB B:ASP163 3.7 16.2 1.0
O B:HOH427 3.8 46.4 1.0
O B:HOH408 3.9 29.6 1.0
O B:HOH519 4.0 45.4 1.0
O2B B:ADP301 4.2 36.6 1.0
O2A B:ADP301 4.3 20.2 1.0
O5' B:ADP301 4.3 19.8 1.0
OD1 B:ASP163 4.4 21.7 1.0
C5' B:ADP301 4.4 21.0 1.0
O3B B:ADP301 4.4 33.6 1.0
CB B:ASN146 4.5 15.1 1.0
OG B:SER145 4.6 18.7 1.0
CE B:LYS143 4.6 23.4 1.0
CA B:ASN146 4.8 15.3 1.0
O B:SER145 4.9 17.7 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 1 22:14:30 2024

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