Calcium in PDB 5ufe: Wild-Type K-Ras(Gnp)/R11.1.6 Complex

The structure of Wild-Type K-Ras(Gnp)/R11.1.6 Complex, PDB code: 5ufe was solved by J.A.Parker, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.77 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.713, 64.648, 74.506, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 24.1

The structure of Wild-Type K-Ras(Gnp)/R11.1.6 Complex also contains other interesting chemical elements:

Cobalt	(Co)	3 atoms
Magnesium	(Mg)	1 atom
Cadmium	(Cd)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Calcium atom in the Wild-Type K-Ras(Gnp)/R11.1.6 Complex (pdb code 5ufe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Wild-Type K-Ras(Gnp)/R11.1.6 Complex, PDB code: 5ufe:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Wild-Type K-Ras(Gnp)/R11.1.6 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Wild-Type K-Ras(Gnp)/R11.1.6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:13.1 occ:1.00 O A:HOH317 2.2 24.6 1.0 OE2 A:GLU31 2.3 35.0 1.0 O A:HOH306 2.3 26.1 1.0 O A:HOH365 2.5 24.7 1.0 CL A:CL208 2.5 26.9 1.0 CD A:GLU31 3.3 37.1 1.0 OE1 A:GLU31 3.6 35.5 1.0 O3' A:GNP201 4.1 17.2 1.0 O A:HOH334 4.3 24.7 1.0 OD1 A:ASP30 4.5 40.9 1.0 CG A:GLU31 4.6 39.2 1.0 OD2 A:ASP30 4.8 51.5 1.0 CG A:ASP30 5.0 46.6 1.0

Calcium binding site 2 out of 3 in the Wild-Type K-Ras(Gnp)/R11.1.6 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Wild-Type K-Ras(Gnp)/R11.1.6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:34.5 occ:1.00 O A:HOH308 2.2 23.9 1.0 OD1 A:ASP108 2.4 31.0 1.0 O A:HOH338 2.4 29.5 1.0 O A:HOH351 2.7 28.3 1.0 OD2 A:ASP108 3.0 40.0 1.0 CG A:ASP108 3.0 35.4 1.0 O A:HOH359 3.3 29.4 1.0 O A:HOH339 4.1 23.3 1.0 O A:GLY138 4.4 26.2 1.0 CB A:ASP108 4.5 39.6 1.0 NZ A:LYS165 5.0 40.6 1.0

Calcium binding site 3 out of 3 in the Wild-Type K-Ras(Gnp)/R11.1.6 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Wild-Type K-Ras(Gnp)/R11.1.6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:38.8 occ:1.00 O B:HOH215 2.4 54.2 1.0 O B:HOH213 2.6 19.9 1.0 O B:HOH208 2.7 23.2 1.0 O B:HOH209 3.5 26.3 1.0 NE1 B:TRP42 4.6 21.0 1.0 CD1 B:TRP42 4.9 18.1 1.0

M.J.Kauke, M.W.Traxlmayr, J.A.Parker, J.D.Kiefer, R.Knihtila, J.Mcgee, G.Verdine, C.Mattos, K.D.Wittrup. An Engineered Protein Antagonist of K-Ras/B-Raf Interaction. Sci Rep V. 7 5831 2017.
ISSN: ESSN 2045-2322
PubMed: 28724936
DOI: 10.1038/S41598-017-05889-7