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Cadmium in PDB 5ufq: K-RASG12D(Gnp)/R11.1.6 Complex

Protein crystallography data

The structure of K-RASG12D(Gnp)/R11.1.6 Complex, PDB code: 5ufq 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) 45.17 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.717, 42.707, 100.235, 90.00, 113.33, 90.00
R / Rfree (%) 20 / 26.3

Other elements in 5ufq:

The structure of K-RASG12D(Gnp)/R11.1.6 Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the K-RASG12D(Gnp)/R11.1.6 Complex (pdb code 5ufq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the K-RASG12D(Gnp)/R11.1.6 Complex, PDB code: 5ufq:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 5ufq

Go back to Cadmium Binding Sites List in 5ufq
Cadmium binding site 1 out of 2 in the K-RASG12D(Gnp)/R11.1.6 Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of K-RASG12D(Gnp)/R11.1.6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:34.9
occ:1.00
OD1 A:ASP33 2.4 35.5 1.0
OD1 A:ASP30 2.5 37.7 1.0
CL A:CL204 2.5 39.1 1.0
OD2 A:ASP30 2.6 33.9 1.0
OD2 A:ASP33 2.9 34.9 1.0
CG A:ASP30 2.9 32.8 1.0
CG A:ASP33 3.0 33.9 1.0
CB A:TYR32 4.3 40.2 1.0
CB A:ASP30 4.4 38.0 1.0
CB A:ASP33 4.4 31.0 1.0
N A:ASP33 4.6 28.0 1.0
C A:TYR32 4.8 33.4 1.0
CA A:ASP33 4.9 31.8 1.0
CA A:TYR32 4.9 38.1 1.0

Cadmium binding site 2 out of 2 in 5ufq

Go back to Cadmium Binding Sites List in 5ufq
Cadmium binding site 2 out of 2 in the K-RASG12D(Gnp)/R11.1.6 Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of K-RASG12D(Gnp)/R11.1.6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd205

b:32.9
occ:1.00
OD1 B:ASP33 2.4 28.6 1.0
OD2 B:ASP30 2.5 32.4 1.0
CL D:CL101 2.5 31.9 1.0
OD1 B:ASP30 2.6 27.7 1.0
CG B:ASP30 2.9 34.0 1.0
OD2 B:ASP33 3.0 29.5 1.0
CG B:ASP33 3.0 32.7 1.0
NZ D:LYS20 3.9 29.8 1.0
CB B:TYR32 4.2 33.3 1.0
CE D:LYS40 4.2 44.2 1.0
CB B:ASP30 4.4 24.8 1.0
CB B:ASP33 4.4 30.7 1.0
CD D:LYS32 4.5 35.8 1.0
N B:ASP33 4.6 28.5 1.0
CD D:LYS40 4.8 40.8 1.0
C B:TYR32 4.8 33.4 1.0
CD D:LYS20 4.8 35.8 1.0
NZ D:LYS32 4.8 30.9 1.0
CE D:LYS20 4.9 35.0 1.0
CA B:TYR32 4.9 36.6 1.0
CA B:ASP33 4.9 31.3 1.0
N B:ASP30 5.0 29.5 1.0

Reference:

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
Page generated: Sat Dec 12 08:27:43 2020

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