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Sodium in PDB 6zl3: Crystal Structure of Hras in Complex with Compound 18 and Gdp

Protein crystallography data

The structure of Crystal Structure of Hras in Complex with Compound 18 and Gdp, PDB code: 6zl3 was solved by D.Kessler, G.Fischer, J.Boettcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.53 / 2.03
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.067, 93.067, 55.441, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 22.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hras in Complex with Compound 18 and Gdp (pdb code 6zl3). 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 Hras in Complex with Compound 18 and Gdp, PDB code: 6zl3:

Sodium binding site 1 out of 1 in 6zl3

Go back to Sodium Binding Sites List in 6zl3
Sodium binding site 1 out of 1 in the Crystal Structure of Hras in Complex with Compound 18 and Gdp


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 Hras in Complex with Compound 18 and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:36.6
occ:1.00
O2B A:GDP202 2.2 37.5 1.0
OG A:SER17 2.2 38.7 1.0
O A:HOH301 2.2 35.4 1.0
O A:HOH327 2.2 47.7 1.0
O A:HOH307 2.3 36.9 1.0
O A:HOH319 2.3 54.4 1.0
CB A:SER17 3.3 36.4 1.0
PB A:GDP202 3.5 39.0 1.0
O3B A:GDP202 3.7 40.0 1.0
N A:SER17 4.1 34.6 1.0
OD1 A:ASP57 4.2 45.2 1.0
O2A A:GDP202 4.2 42.3 1.0
CD2 A:TYR32 4.2 62.0 1.0
CA A:SER17 4.2 35.3 1.0
CA A:PRO34 4.3 60.6 1.0
OD2 A:ASP57 4.3 49.7 1.0
O A:ASP33 4.3 60.9 1.0
O A:THR58 4.4 42.4 1.0
O A:ILE36 4.5 55.1 1.0
O3A A:GDP202 4.5 40.0 1.0
CE2 A:TYR32 4.5 63.0 1.0
O1B A:GDP202 4.5 38.0 1.0
O A:PRO34 4.6 60.5 1.0
CG A:ASP57 4.6 45.7 1.0
C A:PRO34 4.7 60.3 1.0
PA A:GDP202 4.8 41.7 1.0
O1A A:GDP202 4.8 42.6 1.0
O A:HOH346 4.9 51.3 1.0

Reference:

D.Kessler, A.Bergner, J.Bottcher, G.Fischer, S.Dobel, M.Hinkel, B.Mullauer, A.Weiss-Puxbaum, D.B.Mcconnell. Drugging All Ras Isoforms with One Pocket. Future Med Chem V. 12 1911 2020.
ISSN: ISSN 1756-8927
PubMed: 32779487
DOI: 10.4155/FMC-2020-0221
Page generated: Tue Dec 15 17:09:29 2020

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