Calcium in PDB 5wha: Kras G12V, Bound to Gdp and Miniprotein 225-11

The structure of Kras G12V, Bound to Gdp and Miniprotein 225-11, PDB code: 5wha was solved by S.Y.Shim, J.H.Mcgee, S.-J.Lee, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	115.45 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.003, 40.328, 230.939, 90.00, 90.99, 90.00
R / Rfree (%)	23.8 / 27.7

The structure of Kras G12V, Bound to Gdp and Miniprotein 225-11 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Kras G12V, Bound to Gdp and Miniprotein 225-11 (pdb code 5wha). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Kras G12V, Bound to Gdp and Miniprotein 225-11, PDB code: 5wha:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:21.7 occ:1.00 O A:TYR64 2.4 20.2 1.0 OE1 A:GLU63 3.2 33.4 1.0 C A:TYR64 3.6 20.3 1.0 CD A:GLU63 3.7 28.1 1.0 CG A:GLU63 4.2 23.5 1.0 OXT B:ALA32 4.2 30.7 1.0 CB A:SER65 4.2 33.2 1.0 CA A:CA204 4.2 23.6 1.0 CA A:SER65 4.3 28.4 1.0 N A:SER65 4.4 20.1 1.0 OE2 A:GLU63 4.4 29.8 1.0 O A:HOH325 4.5 22.2 1.0 CA A:TYR64 4.6 30.0 1.0 N A:TYR64 4.7 29.5 1.0 OG A:SER65 4.8 34.9 1.0 CB A:GLU63 4.8 22.7 1.0 CD2 A:TYR64 4.9 38.2 1.0

Calcium binding site 2 out of 8 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:23.6 occ:1.00 OE1 A:GLU63 2.4 33.4 1.0 OE2 A:GLU63 2.5 29.8 1.0 O B:ALA32 2.7 20.6 1.0 CD A:GLU63 2.8 28.1 1.0 OXT B:ALA32 2.9 30.7 1.0 C B:ALA32 3.2 26.1 1.0 CA A:CA203 4.2 21.7 1.0 CG A:GLU63 4.3 23.5 1.0 O A:HOH312 4.6 19.7 1.0 CA B:ALA32 4.7 22.9 1.0

Calcium binding site 3 out of 8 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca203 b:29.5 occ:1.00 O E:ALA32 2.4 33.9 1.0 OE2 D:GLU63 2.5 29.4 1.0 OXT E:ALA32 2.6 30.9 1.0 OE1 D:GLU63 2.8 39.3 1.0 C E:ALA32 2.9 34.0 1.0 CD D:GLU63 3.0 32.3 1.0 O D:HOH319 3.9 30.0 1.0 CA D:CA204 4.4 19.7 1.0 CA E:ALA32 4.4 32.2 1.0 CG D:GLU63 4.5 31.6 1.0

Calcium binding site 4 out of 8 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca204 b:19.7 occ:1.00 O D:TYR64 2.4 24.9 1.0 OE2 D:GLU63 2.8 29.4 1.0 O D:HOH319 3.1 30.0 1.0 C D:TYR64 3.6 20.7 1.0 CD D:GLU63 3.7 32.3 1.0 CG D:GLU63 4.1 31.6 1.0 OXT E:ALA32 4.2 30.9 1.0 CB D:SER65 4.2 17.5 1.0 CA D:SER65 4.3 25.1 1.0 CA D:CA203 4.4 29.5 1.0 N D:SER65 4.4 21.8 1.0 CA D:TYR64 4.6 26.2 1.0 N D:TYR64 4.7 29.0 1.0 OE1 D:GLU63 4.7 39.3 1.0 OG D:SER65 4.8 20.7 1.0 CB D:GLU63 4.8 36.3 1.0 O D:HOH317 4.8 25.9 1.0 CD2 D:TYR64 4.9 45.3 1.0 CB D:TYR64 5.0 38.4 1.0

Calcium binding site 5 out of 8 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca203 b:43.8 occ:1.00 OD2 L:ASP16 2.5 20.6 1.0 OE1 G:GLU63 2.6 29.1 1.0 OE2 G:GLU63 2.6 21.2 1.0 CD G:GLU63 2.9 25.3 1.0 OD1 L:ASP16 2.9 14.8 1.0 OXT H:ALA32 2.9 37.7 1.0 CG L:ASP16 3.0 14.9 1.0 O H:ALA32 3.2 36.0 1.0 C H:ALA32 3.5 33.1 1.0 CA G:CA204 4.3 25.7 1.0 OG L:SER13 4.4 19.8 1.0 CG G:GLU63 4.4 24.0 1.0 O G:HOH305 4.4 20.9 1.0 CB L:ASP16 4.5 23.6 1.0 O H:HOH105 4.5 14.9 1.0 CB G:GLU63 5.0 23.7 1.0

Calcium binding site 6 out of 8 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca204 b:25.7 occ:1.00 O G:TYR64 2.4 30.9 1.0 OD1 L:ASP16 2.4 14.8 1.0 O H:HOH105 2.5 14.9 1.0 OE2 L:GLU19 2.5 29.2 1.0 OE1 L:GLU19 2.5 22.0 1.0 OE1 G:GLU63 2.6 29.1 1.0 CD L:GLU19 2.8 25.6 1.0 C G:TYR64 3.6 26.6 1.0 CG L:ASP16 3.7 14.9 1.0 CD G:GLU63 3.8 25.3 1.0 OXT H:ALA32 4.2 37.7 1.0 CA L:ASP16 4.2 14.8 1.0 CG L:GLU19 4.3 20.8 1.0 CA G:CA203 4.3 43.8 1.0 CB G:SER65 4.3 19.9 1.0 CG G:GLU63 4.4 24.0 1.0 CA G:SER65 4.4 23.9 1.0 N G:SER65 4.4 28.9 1.0 CB L:ASP16 4.4 23.6 1.0 OD2 L:ASP16 4.6 20.6 1.0 N L:ASP16 4.6 16.9 1.0 CA G:TYR64 4.6 23.0 1.0 N G:TYR64 4.6 19.0 1.0 O G:HOH331 4.8 16.6 1.0 CB G:GLU63 4.8 23.7 1.0 OE2 G:GLU63 4.8 21.2 1.0 CD2 G:TYR64 4.9 44.4 1.0 OG G:SER65 4.9 23.3 1.0 CB G:TYR64 5.0 25.2 1.0

Calcium binding site 7 out of 8 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca101 b:36.3 occ:1.00 OE1 J:GLU63 2.5 23.3 1.0 OD2 I:ASP16 2.5 33.7 1.0 OE2 J:GLU63 2.5 33.0 1.0 O I:HOH202 2.5 22.7 1.0 OD1 I:ASP16 2.6 20.2 1.0 O K:ALA32 2.6 48.4 1.0 OXT K:ALA32 2.7 44.5 1.0 CD J:GLU63 2.8 27.5 1.0 CG I:ASP16 2.9 28.1 1.0 C K:ALA32 3.1 42.3 1.0 CA I:CA102 3.9 29.2 1.0 OG I:SER13 4.1 33.0 1.0 CG J:GLU63 4.3 26.9 1.0 CB I:ASP16 4.4 24.6 1.0 CA K:ALA32 4.6 34.2 1.0 O J:HOH313 4.8 41.1 1.0 CB J:GLU63 4.9 27.5 1.0

Calcium binding site 8 out of 8 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca102 b:29.2 occ:1.00 O J:TYR64 2.4 30.4 1.0 OD1 I:ASP16 2.5 20.2 1.0 OE1 I:GLU19 2.5 16.4 1.0 OE1 J:GLU63 2.6 23.3 1.0 OE2 I:GLU19 2.7 20.4 1.0 CD I:GLU19 2.9 17.9 1.0 CD J:GLU63 3.6 27.5 1.0 C J:TYR64 3.6 39.7 1.0 CG I:ASP16 3.7 28.1 1.0 O I:HOH202 3.8 22.7 1.0 OXT K:ALA32 3.8 44.5 1.0 CA I:CA101 3.9 36.3 1.0 CB J:SER65 4.1 36.1 1.0 CG J:GLU63 4.1 26.9 1.0 CA J:SER65 4.2 32.4 1.0 CA I:ASP16 4.3 20.4 1.0 CG I:GLU19 4.4 16.6 1.0 N J:SER65 4.4 33.6 1.0 N I:ASP16 4.5 22.5 1.0 OD2 I:ASP16 4.6 33.7 1.0 CB I:ASP16 4.6 24.6 1.0 OE2 J:GLU63 4.6 33.0 1.0 OE1 I:GLU15 4.6 33.7 1.0 CD I:GLU15 4.6 29.3 1.0 N J:TYR64 4.7 48.4 1.0 CA J:TYR64 4.7 52.9 1.0 OG J:SER65 4.7 37.4 1.0 CG I:GLU15 4.7 28.3 1.0 C K:ALA32 4.8 42.3 1.0 CB J:GLU63 4.8 27.5 1.0 C I:GLU15 4.9 16.4 1.0 O I:GLU15 4.9 19.9 1.0 O J:HOH320 5.0 25.4 1.0

J.H.Mcgee, S.Y.Shim, S.J.Lee, P.K.Swanson, S.Y.Jiang, M.A.Durney, G.L.Verdine. Exceptionally High-Affinity Ras Binders That Remodel Its Effector Domain. J. Biol. Chem. V. 293 3265 2018.
ISSN: ESSN 1083-351X
PubMed: 29282294
DOI: 10.1074/JBC.M117.816348