Sodium in PDB 8hv1: Crystal Structure of EGFR_DMX in Complex with Covalently Bound Fragment 1

Enzymatic activity of Crystal Structure of EGFR_DMX in Complex with Covalently Bound Fragment 1

All present enzymatic activity of Crystal Structure of EGFR_DMX in Complex with Covalently Bound Fragment 1:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of EGFR_DMX in Complex with Covalently Bound Fragment 1, PDB code: 8hv1 was solved by P.Dokurno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.40
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 144.91, 144.91, 144.91, 90, 90, 90
R / Rfree (%) 18.9 / 21.9

Other elements in 8hv1:

The structure of Crystal Structure of EGFR_DMX in Complex with Covalently Bound Fragment 1 also contains other interesting chemical elements:

Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of EGFR_DMX in Complex with Covalently Bound Fragment 1 (pdb code 8hv1). 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 EGFR_DMX in Complex with Covalently Bound Fragment 1, PDB code: 8hv1:

Sodium binding site 1 out of 1 in 8hv1

Go back to Sodium Binding Sites List in 8hv1
Sodium binding site 1 out of 1 in the Crystal Structure of EGFR_DMX in Complex with Covalently Bound Fragment 1


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 EGFR_DMX in Complex with Covalently Bound Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1103

b:77.2
occ:1.00
 O A:HOH1241 2.3 59.0 1.0
O A:HOH1216 2.4 45.9 1.0
O A:HOH1251 2.7 55.9 1.0
OG A:SER899 2.9 48.8 1.0
O A:HOH1227 3.0 40.1 1.0
O A:SER895 3.6 44.2 1.0
CA A:ARG836 3.9 47.9 1.0
OD1 A:ASP896 4.0 46.6 1.0
CB A:SER899 4.0 45.1 1.0
O A:ARG836 4.1 51.5 1.0
C A:ARG836 4.1 46.9 1.0
C A:SER895 4.2 43.1 1.0
OG A:SER895 4.3 59.8 1.0
CE2 A:TYR891 4.3 54.2 1.0
CD2 A:TYR891 4.3 45.2 1.0
O A:TRP880 4.4 52.5 1.0
CA A:MET881 4.4 52.7 1.0
CG A:MET881 4.4 65.4 1.0
N A:ASP896 4.6 41.8 1.0
CA A:ASP896 4.6 49.3 1.0
N A:ASP837 4.8 42.7 1.0
CB A:SER895 4.8 47.1 1.0
N A:ARG836 4.8 51.1 1.0
N A:ALA882 4.8 45.4 1.0
CB A:MET881 4.9 60.7 1.0
CB A:ARG836 4.9 56.3 1.0

Reference:

N.Kuki, D.L.Walmsley, K.Kanai, S.Takechi, M.Yoshida, R.Murakami, K.Takano, Y.Tominaga, M.Takahashi, S.Ito, N.Nakao, H.Angove, L.M.Baker, E.Carter, P.Dokurno, L.L.Strat, A.T.Macias, C.A.Molyneaux, J.B.Murray, A.E.Surgenor, T.Hamada, R.E.Hubbard. A Covalent Fragment-Based Strategy Targeting A Novel Cysteine to Inhibit Activity of Mutant Egfr Kinase. Rsc Med Chem 2023.
ISSN: ESSN 2632-8682
DOI: 10.1039/D3MD00439B
Page generated: Wed Oct 9 12:17:32 2024

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