Cobalt 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:

Magnesium	(Mg)	1 atom
Cadmium	(Cd)	4 atoms
Calcium	(Ca)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Wild-Type K-Ras(Gnp)/R11.1.6 Complex, PDB code: 5ufe:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt 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 Cobalt with other atoms in the Co 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:Co212 b:16.4 occ:1.00 O A:HOH336 2.1 20.0 1.0 O A:HOH341 2.1 18.0 1.0 OE2 A:GLU76 2.2 27.0 1.0 O A:GLU3 2.3 26.8 1.0 OE1 A:GLU76 2.7 15.3 1.0 CD A:GLU76 2.7 25.8 1.0 C A:GLU3 3.5 25.9 1.0 NZ A:LYS5 3.8 33.0 1.0 CA A:TYR4 4.1 19.3 1.0 N A:TYR4 4.2 26.0 1.0 CG A:GLU76 4.2 18.7 1.0 N A:MET1 4.4 43.5 1.0 CA A:GLU3 4.5 26.3 1.0 N A:LYS5 4.7 16.5 1.0 CB A:GLU3 4.7 37.3 1.0 N A:GLU3 4.8 24.2 1.0 C A:TYR4 4.9 17.2 1.0

Cobalt 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 Cobalt with other atoms in the Co 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:Co213 b:47.5 occ:1.00 NE2 A:HIS27 1.8 45.2 1.0 CD2 A:HIS27 1.9 42.7 1.0 O A:HOH304 2.1 12.1 1.0 CE1 A:HIS27 2.7 38.8 1.0 CG A:HIS27 2.9 37.8 1.0 ND1 A:HIS27 3.3 37.0 1.0 O A:HOH303 3.7 42.6 1.0 CB A:HIS27 4.1 33.5 1.0 O A:GLN25 4.5 39.5 1.0

Cobalt 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 Cobalt with other atoms in the Co 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 A:Co214 b:13.7 occ:1.00 ND1 A:HIS95 2.2 16.2 1.0 OE2 A:GLU98 2.2 19.4 1.0 O A:HOH310 2.3 17.4 1.0 CE1 A:HIS95 2.9 18.6 1.0 CL A:CL210 3.2 24.5 1.0 CD A:GLU98 3.4 25.1 1.0 CG A:HIS95 3.4 19.5 1.0 CB A:HIS95 4.0 14.5 1.0 NE2 A:HIS95 4.2 20.4 1.0 CG A:GLU98 4.2 18.5 1.0 OE1 A:GLU98 4.3 21.8 1.0 CA A:HIS95 4.3 17.2 1.0 CD2 A:HIS95 4.4 18.5 1.0 CD2 A:HIS94 4.5 14.4 1.0 NE2 A:HIS94 4.9 15.2 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