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Sodium in PDB 3k2l: Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2)

Enzymatic activity of Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2)

All present enzymatic activity of Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2):
2.7.12.1;

Protein crystallography data

The structure of Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2), PDB code: 3k2l was solved by P.Filippakopoulos, V.Myrianthopoulos, M.Soundararajan, T.Krojer, E.Hapka, O.Fedorov, G.Berridge, J.Wang, L.Shrestha, A.C.W.Pike, E.Ugochukwu, F.Vondelft, C.H.Arrowsmith, A.Edwards, J.Weigelt, C.Bountra, E.Mikros, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.54 / 2.36
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.285, 84.285, 148.505, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 28.8

Other elements in 3k2l:

The structure of Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2) (pdb code 3k2l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2), PDB code: 3k2l:

Sodium binding site 1 out of 1 in 3k2l

Go back to Sodium Binding Sites List in 3k2l
Sodium binding site 1 out of 1 in the Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dual-Specificity Tyrosine Phosphorylation Regulated Kinase 2 (DYRK2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na480

b:41.4
occ:1.00
 O A:GLY290 2.5 33.1 1.0
O A:ARG288 2.7 27.4 1.0
N A:GLN285 2.9 27.9 1.0
O A:GLN285 3.0 31.9 1.0
N A:LYS284 3.0 30.2 1.0
C A:ARG288 3.2 26.9 1.0
N A:GLY290 3.3 23.7 1.0
C A:GLY290 3.4 29.3 1.0
CA A:LYS284 3.6 30.8 1.0
C A:LYS284 3.7 30.1 1.0
CA A:GLY290 3.7 25.8 1.0
CB A:ARG288 3.7 19.8 1.0
CB A:LYS284 3.7 23.9 1.0
CA A:GLN285 3.7 30.0 1.0
C A:LEU283 3.8 24.7 1.0
C A:GLN285 3.8 29.1 1.0
N A:SER289 3.8 25.7 1.0
C A:SER289 3.8 25.7 1.0
CB A:GLN285 3.9 26.9 1.0
CA A:ARG288 4.0 24.5 1.0
CB A:LEU283 4.0 27.8 1.0
CA A:LEU283 4.0 28.2 1.0
CA A:SER289 4.3 28.4 1.0
N A:ARG288 4.4 27.6 1.0
O A:HOH36 4.5 24.6 1.0
CD2 A:LEU283 4.5 16.6 1.0
O A:SER289 4.5 25.0 1.0
N A:ILE291 4.7 33.6 1.0
CG A:LEU283 4.7 22.5 1.0
CG A:LYS284 4.7 39.2 1.0
O A:LEU283 4.8 29.6 1.0
CG A:GLN285 4.8 32.8 1.0
O A:LYS284 4.9 36.2 1.0
CG A:ARG288 4.9 24.1 1.0
CD1 A:LEU283 4.9 22.1 1.0
CD A:LYS284 5.0 41.1 1.0

Reference:

M.Soundararajan, A.K.Roos, P.Savitsky, P.Filippakopoulos, A.N.Kettenbach, J.V.Olsen, S.A.Gerber, J.Eswaran, S.Knapp, J.M.Elkins. Structures of Down Syndrome Kinases, Dyrks, Reveal Mechanisms of Kinase Activation and Substrate Recognition. Structure V. 21 986 2013.
ISSN: ISSN 0969-2126
PubMed: 23665168
DOI: 10.1016/J.STR.2013.03.012
Page generated: Sun Aug 17 15:56:12 2025

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