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Sodium in PDB 4m8t: RSK2 T493M C-Terminal Kinase Domain in Complex with 3-(3-(1H-Pyrazol- 4-Yl)Phenyl)-2-Cyanoacrylamide

Enzymatic activity of RSK2 T493M C-Terminal Kinase Domain in Complex with 3-(3-(1H-Pyrazol- 4-Yl)Phenyl)-2-Cyanoacrylamide

All present enzymatic activity of RSK2 T493M C-Terminal Kinase Domain in Complex with 3-(3-(1H-Pyrazol- 4-Yl)Phenyl)-2-Cyanoacrylamide:
2.7.11.1;

Protein crystallography data

The structure of RSK2 T493M C-Terminal Kinase Domain in Complex with 3-(3-(1H-Pyrazol- 4-Yl)Phenyl)-2-Cyanoacrylamide, PDB code: 4m8t was solved by R.M.Miller, J.Taunton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.39 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 46.990, 46.990, 291.100, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 31.1

Sodium Binding Sites:

The binding sites of Sodium atom in the RSK2 T493M C-Terminal Kinase Domain in Complex with 3-(3-(1H-Pyrazol- 4-Yl)Phenyl)-2-Cyanoacrylamide (pdb code 4m8t). 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 T493M C-Terminal Kinase Domain in Complex with 3-(3-(1H-Pyrazol- 4-Yl)Phenyl)-2-Cyanoacrylamide, PDB code: 4m8t:

Sodium binding site 1 out of 1 in 4m8t

Go back to Sodium Binding Sites List in 4m8t
Sodium binding site 1 out of 1 in the RSK2 T493M C-Terminal Kinase Domain in Complex with 3-(3-(1H-Pyrazol- 4-Yl)Phenyl)-2-Cyanoacrylamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of RSK2 T493M C-Terminal Kinase Domain in Complex with 3-(3-(1H-Pyrazol- 4-Yl)Phenyl)-2-Cyanoacrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:44.6
occ:1.00
 O A:HIS473 2.1 41.1 1.0
O A:ILE476 2.3 43.9 1.0
OG1 A:THR478 2.3 44.9 1.0
O A:GLY471 2.6 38.3 1.0
HA A:PRO474 3.1 48.5 1.0
C A:HIS473 3.1 41.4 1.0
H A:ILE476 3.3 50.5 1.0
O A:PRO474 3.4 50.2 1.0
C A:ILE476 3.4 41.2 1.0
C A:PRO474 3.6 48.3 1.0
CB A:THR478 3.6 39.5 1.0
CA A:PRO474 3.6 40.4 1.0
HA A:THR478 3.7 47.2 1.0
N A:PRO474 3.8 40.5 1.0
C A:GLY471 3.8 42.1 1.0
HE A:ARG558 3.8 48.4 1.0
HB A:ILE476 3.8 48.0 1.0
N A:THR478 3.9 45.4 1.0
N A:ILE476 3.9 42.1 1.0
CA A:THR478 3.9 39.4 1.0
HB A:THR478 4.0 47.4 1.0
H A:THR478 4.0 54.5 1.0
HD2 A:ARG558 4.1 43.3 1.0
CA A:ILE476 4.1 38.6 1.0
O A:GLN472 4.1 45.6 1.0
C A:GLN472 4.1 50.2 1.0
C A:ILE477 4.2 41.8 1.0
OE2 A:GLU494 4.2 42.8 1.0
N A:HIS473 4.2 47.6 1.0
CA A:HIS473 4.3 42.7 1.0
HA2 A:GLY471 4.3 50.6 1.0
NE A:ARG558 4.4 40.4 1.0
N A:ASN475 4.4 49.1 1.0
HG22 A:ILE476 4.4 44.1 1.0
CB A:ILE476 4.4 40.0 1.0
N A:ILE477 4.5 30.6 1.0
HB3 A:HIS473 4.5 49.8 1.0
O A:ILE477 4.5 37.9 1.0
HA A:ILE477 4.6 37.2 1.0
HG23 A:THR478 4.6 47.7 1.0
H A:HIS473 4.6 57.2 1.0
CG2 A:THR478 4.6 39.8 1.0
CA A:GLY471 4.6 42.2 1.0
CD A:ARG558 4.7 36.1 1.0
CA A:ILE477 4.7 31.0 1.0
HA A:GLN472 4.7 74.1 1.0
N A:GLN472 4.7 57.2 1.0
CA A:GLN472 4.8 61.8 1.0
HG21 A:THR478 4.8 47.7 1.0
H A:ASN475 4.8 58.9 1.0
C A:ASN475 4.9 40.4 1.0
HD3 A:ARG558 4.9 43.3 1.0
CG2 A:ILE476 5.0 36.8 1.0
HA3 A:GLY471 5.0 50.6 1.0
CB A:HIS473 5.0 41.5 1.0

Reference:

N.London, R.M.Miller, S.Krishnan, K.Uchida, J.J.Irwin, O.Eidam, L.Gibold, P.Cimermancic, R.Bonnet, B.K.Shoichet, J.Taunton. Covalent Docking of Large Libraries For the Discovery of Chemical Probes. Nat.Chem.Biol. 2014.
ISSN: ESSN 1552-4469
PubMed: 25344815
DOI: 10.1038/NCHEMBIO.1666
Page generated: Mon Oct 7 16:56:10 2024

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