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

Protein crystallography data

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

Other elements in 5ufe:

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
Calcium (Ca) 3 atoms
Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Wild-Type K-Ras(Gnp)/R11.1.6 Complex, PDB code: 5ufe:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 5ufe

Go back to Cadmium Binding Sites List in 5ufe
Cadmium binding site 1 out of 4 in the Wild-Type K-Ras(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 Wild-Type K-Ras(Gnp)/R11.1.6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:24.0
occ:1.00
OE1 A:GLU62 2.6 18.4 1.0
O A:HOH367 2.6 8.7 1.0
OE2 A:GLU37 2.6 15.9 1.0
OE2 A:GLU62 2.6 17.4 1.0
NZ B:LYS32 2.7 22.2 1.0
OE1 A:GLU37 2.7 14.9 1.0
CD A:GLU62 2.9 17.5 1.0
CD A:GLU37 3.0 15.4 1.0
CE B:LYS32 3.3 19.7 1.0
CD1 A:ILE36 3.7 20.1 1.0
SD A:MET67 3.8 17.6 1.0
CG A:GLU62 4.4 15.2 1.0
O A:HOH325 4.5 20.4 1.0
CG A:GLU37 4.5 15.3 1.0
CG1 A:ILE36 4.6 22.7 1.0
N A:GLU63 4.6 17.0 1.0
CD B:LYS32 4.7 15.3 1.0
CG A:MET67 4.8 15.8 1.0
CE A:MET67 4.8 15.2 1.0
CE2 A:TYR71 4.9 15.0 1.0
OH A:TYR71 4.9 13.9 1.0
CA A:GLU62 4.9 17.9 1.0

Cadmium binding site 2 out of 4 in 5ufe

Go back to Cadmium Binding Sites List in 5ufe
Cadmium binding site 2 out of 4 in the Wild-Type K-Ras(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 Wild-Type K-Ras(Gnp)/R11.1.6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:20.7
occ:1.00
CL A:CL209 2.6 18.9 1.0
SG A:CYS118 2.7 21.3 1.0
O A:CYS118 3.0 13.4 1.0
C A:CYS118 3.4 15.7 1.0
CB A:CYS118 3.7 23.3 1.0
N A:ASP119 4.0 14.1 1.0
CG A:GLN150 4.2 14.5 1.0
CA A:CYS118 4.2 19.6 1.0
CA A:ASP119 4.4 20.9 1.0
CB A:GLN150 4.6 13.9 1.0
CD A:GLN150 4.9 12.5 1.0

Cadmium binding site 3 out of 4 in 5ufe

Go back to Cadmium Binding Sites List in 5ufe
Cadmium binding site 3 out of 4 in the Wild-Type K-Ras(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 3 of Wild-Type K-Ras(Gnp)/R11.1.6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:28.4
occ:1.00
O2G A:GNP201 2.5 17.2 1.0
OD1 A:ASP33 2.5 27.4 1.0
O A:HOH368 2.6 21.4 1.0
OD2 A:ASP33 2.8 26.0 1.0
CG A:ASP33 3.0 32.6 1.0
PG A:GNP201 3.3 17.5 1.0
N3B A:GNP201 3.6 12.6 1.0
O3G A:GNP201 3.7 11.6 1.0
O A:HOH305 3.8 16.0 1.0
O A:HOH330 3.9 19.0 1.0
O A:HOH302 4.2 24.1 1.0
O2A A:GNP201 4.4 22.9 1.0
CB A:ASP33 4.5 26.2 1.0
O1G A:GNP201 4.7 18.1 1.0
O A:PRO34 4.8 28.2 1.0
MG A:MG211 4.9 1.9 1.0

Cadmium binding site 4 out of 4 in 5ufe

Go back to Cadmium Binding Sites List in 5ufe
Cadmium binding site 4 out of 4 in the Wild-Type K-Ras(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 4 of Wild-Type K-Ras(Gnp)/R11.1.6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:24.8
occ:1.00
OE1 A:GLU91 2.6 18.1 1.0
O A:HOH371 2.6 8.6 1.0
O A:HOH356 2.6 6.5 1.0
OE2 A:GLU91 2.7 16.6 1.0
CD A:GLU91 3.0 16.9 1.0
CG A:GLU91 4.4 12.6 1.0
CD A:LYS88 4.5 29.0 1.0
NZ A:LYS88 4.5 21.4 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 08:27:42 2020

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