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Sodium in PDB 4d9t: RSK2 C-Terminal Kinase Domain with Inhibitor (E)-Methyl 3-(4-Amino-7- (3-Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate

Enzymatic activity of RSK2 C-Terminal Kinase Domain with Inhibitor (E)-Methyl 3-(4-Amino-7- (3-Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate

All present enzymatic activity of RSK2 C-Terminal Kinase Domain with Inhibitor (E)-Methyl 3-(4-Amino-7- (3-Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate:
2.7.11.1;

Protein crystallography data

The structure of RSK2 C-Terminal Kinase Domain with Inhibitor (E)-Methyl 3-(4-Amino-7- (3-Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate, PDB code: 4d9t was solved by I.M.Serafimova, M.A.Pufall, S.Krishnan, K.Duda, M.S.Cohen, R.L.Maglathlin, J.M.Mcfarland, R.M.Miller, M.Frodin, J.Taunton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.57 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 46.700, 46.700, 294.100, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 26.7

Sodium Binding Sites:

The binding sites of Sodium atom in the RSK2 C-Terminal Kinase Domain with Inhibitor (E)-Methyl 3-(4-Amino-7- (3-Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate (pdb code 4d9t). 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 RSK2 C-Terminal Kinase Domain with Inhibitor (E)-Methyl 3-(4-Amino-7- (3-Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate, PDB code: 4d9t:

Sodium binding site 1 out of 1 in 4d9t

Go back to Sodium Binding Sites List in 4d9t
Sodium binding site 1 out of 1 in the RSK2 C-Terminal Kinase Domain with Inhibitor (E)-Methyl 3-(4-Amino-7- (3-Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of RSK2 C-Terminal Kinase Domain with Inhibitor (E)-Methyl 3-(4-Amino-7- (3-Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:51.4
occ:1.00
 O A:GLY471 2.3 60.0 1.0
O A:ILE476 2.3 48.4 1.0
OG1 A:THR478 2.5 62.5 1.0
O A:HIS473 2.5 43.6 1.0
O A:HOH1007 2.9 50.7 1.0
C A:GLY471 3.2 58.0 1.0
CB A:THR478 3.4 64.3 1.0
C A:ILE476 3.4 51.4 1.0
C A:HIS473 3.6 53.1 1.0
CA A:THR478 3.7 57.7 1.0
CG2 A:THR478 3.7 68.1 1.0
N A:THR478 3.8 53.9 1.0
C A:ILE477 3.8 56.6 1.0
C A:GLN472 3.8 65.9 1.0
N A:HIS473 4.0 58.7 1.0
O A:ILE477 4.0 56.4 1.0
N A:GLN472 4.0 61.6 1.0
CA A:GLY471 4.1 61.5 1.0
CA A:GLN472 4.1 66.2 1.0
O A:GLN472 4.2 68.9 1.0
N A:ILE476 4.3 44.1 1.0
CA A:ILE476 4.3 49.2 1.0
N A:ILE477 4.3 57.9 1.0
OE2 A:GLU494 4.4 68.2 1.0
CA A:ILE477 4.4 53.3 1.0
CA A:HIS473 4.4 50.0 1.0
N A:PRO474 4.5 58.8 1.0
O A:PRO474 4.5 44.4 1.0
C A:PRO474 4.5 50.8 1.0
CA A:PRO474 4.6 51.8 1.0
CB A:ILE476 4.7 51.9 1.0
NE A:ARG558 4.9 52.4 1.0
CG2 A:ILE476 5.0 57.1 1.0

Reference:

I.M.Serafimova, M.A.Pufall, S.Krishnan, K.Duda, M.S.Cohen, R.L.Maglathlin, J.M.Mcfarland, R.M.Miller, M.Frodin, J.Taunton. Reversible Targeting of Noncatalytic Cysteines with Chemically Tuned Electrophiles. Nat.Chem.Biol. V. 8 471 2012.
ISSN: ISSN 1552-4450
PubMed: 22466421
DOI: 10.1038/NCHEMBIO.925
Page generated: Sun Aug 17 18:55:22 2025

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