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Sodium in PDB 6e6g: Kras G13D Bound to Gdp (K13GDP)

Protein crystallography data

The structure of Kras G13D Bound to Gdp (K13GDP), PDB code: 6e6g was solved by C.W.Johnson, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.00 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.096, 37.829, 100.171, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 22.5

Other elements in 6e6g:

The structure of Kras G13D Bound to Gdp (K13GDP) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Kras G13D Bound to Gdp (K13GDP) (pdb code 6e6g). 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 Kras G13D Bound to Gdp (K13GDP), PDB code: 6e6g:

Sodium binding site 1 out of 1 in 6e6g

Go back to Sodium Binding Sites List in 6e6g
Sodium binding site 1 out of 1 in the Kras G13D Bound to Gdp (K13GDP)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kras G13D Bound to Gdp (K13GDP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:40.4
occ:1.00
OD1 A:ASP13 2.4 28.3 1.0
O A:HOH373 2.5 38.5 1.0
O A:HOH424 2.9 35.9 1.0
O3B A:GDP201 2.9 19.7 1.0
O A:HOH345 3.6 21.1 1.0
CG A:ASP13 3.6 34.7 1.0
N A:ASP13 3.9 17.3 1.0
O2A A:GDP201 3.9 16.1 1.0
O A:HOH362 4.1 17.0 1.0
CA A:ASP13 4.1 16.1 1.0
PB A:GDP201 4.2 15.2 1.0
CB A:ASP13 4.3 22.5 1.0
O3A A:GDP201 4.4 15.9 1.0
OD2 A:ASP13 4.5 46.6 1.0
C5' A:GDP201 4.6 17.3 1.0
PA A:GDP201 4.7 14.9 1.0
O A:HOH411 4.9 20.2 1.0
C A:GLY12 4.9 17.1 1.0

Reference:

C.W.Johnson, Y.J.Lin, D.Reid, J.Parker, S.Pavlopoulos, P.Dischinger, C.Graveel, A.J.Aguirre, M.Steensma, K.M.Haigis, C.Mattos. Isoform-Specific Destabilization of the Active Site Reveals A Molecular Mechanism of Intrinsic Activation of Kras G13D. Cell Rep V. 28 1538 2019.
ISSN: ESSN 2211-1247
PubMed: 31390567
DOI: 10.1016/J.CELREP.2019.07.026
Page generated: Tue Dec 15 12:09:30 2020

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