Atomistry » Cobalt » PDB 5nrb-5vsa » 5ufe
Atomistry »
  Cobalt »
    PDB 5nrb-5vsa »
      5ufe »

Cobalt 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:

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

Cobalt Binding Sites:

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 5ufe

Go back to Cobalt Binding Sites List in 5ufe
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 5ufe

Go back to Cobalt Binding Sites List in 5ufe
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 5ufe

Go back to Cobalt Binding Sites List in 5ufe
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

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: Sun Dec 13 10:48:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy