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Sodium in PDB 4d9u: RSK2 C-Terminal Kinase Domain, (E)-Tert-Butyl 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, (E)-Tert-Butyl 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, (E)-Tert-Butyl 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, (E)-Tert-Butyl 3-(4-Amino-7-(3- Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate, PDB code: 4d9u 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) 46.10 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 46.700, 46.700, 293.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 27.6

Sodium Binding Sites:

The binding sites of Sodium atom in the RSK2 C-Terminal Kinase Domain, (E)-Tert-Butyl 3-(4-Amino-7-(3- Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate (pdb code 4d9u). 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, (E)-Tert-Butyl 3-(4-Amino-7-(3- Hydroxypropyl)-5-P-Tolyl-7H-Pyrrolo[2,3-D]Pyrimidin-6-Yl)-2- Cyanoacrylate, PDB code: 4d9u:

Sodium binding site 1 out of 1 in 4d9u

Go back to Sodium Binding Sites List in 4d9u
Sodium binding site 1 out of 1 in the RSK2 C-Terminal Kinase Domain, (E)-Tert-Butyl 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, (E)-Tert-Butyl 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:58.8
occ:1.00
 O A:HIS473 2.3 47.2 1.0
O A:ILE476 2.3 47.5 1.0
O A:GLY471 2.4 64.9 1.0
OG1 A:THR478 2.4 48.8 1.0
C A:HIS473 3.4 46.2 1.0
C A:GLY471 3.4 60.0 1.0
C A:ILE476 3.4 46.6 1.0
CB A:THR478 3.7 48.9 1.0
C A:GLN472 3.9 54.8 1.0
N A:HIS473 3.9 50.1 1.0
N A:ILE476 4.0 45.9 1.0
CA A:THR478 4.0 46.8 1.0
C A:ILE477 4.1 45.1 1.0
O A:GLN472 4.1 52.4 1.0
N A:THR478 4.1 43.6 1.0
CA A:ILE476 4.1 46.6 1.0
N A:GLN472 4.2 57.4 1.0
O A:ILE477 4.2 52.2 1.0
N A:PRO474 4.2 45.7 1.0
CA A:GLN472 4.2 59.8 1.0
CA A:HIS473 4.3 45.5 1.0
CA A:PRO474 4.3 48.8 1.0
C A:PRO474 4.3 46.5 1.0
CA A:GLY471 4.3 58.5 1.0
CB A:ILE476 4.4 46.7 1.0
CG2 A:THR478 4.4 52.3 1.0
O A:PRO474 4.4 47.5 1.0
N A:ILE477 4.5 46.2 1.0
OE2 A:GLU494 4.5 48.2 1.0
N A:ASN475 4.7 45.9 1.0
CA A:ILE477 4.7 42.9 1.0
NE A:ARG558 4.8 50.0 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 18:55:31 2025

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