Fluorine in PDB 9bgh: Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977

Enzymatic activity of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977

All present enzymatic activity of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977:
3.6.5.2; 5.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977, PDB code: 9bgh was solved by Y.Pourfarjam, Y.Goldgur, A.Cuevas-Navarro, P.Lito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.48 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.483, 81.787, 127.832, 90, 90, 90
R / Rfree (%) 21.8 / 25.1

Other elements in 9bgh:

The structure of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 also contains other interesting chemical elements:

Aluminium (Al) 1 atom
Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 (pdb code 9bgh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977, PDB code: 9bgh:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 9bgh

Go back to Fluorine Binding Sites List in 9bgh
Fluorine binding site 1 out of 3 in the Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F203

b:55.6
occ:1.00
 F1 C:AF3203 0.0 55.6 1.0
AL C:AF3203 1.8 43.9 1.0
O C:HOH307 2.5 52.0 1.0
O C:ALA11 2.6 51.1 1.0
CG C:LYS16 2.6 48.3 1.0
CD C:LYS16 2.7 49.3 1.0
O3B C:GDP201 2.8 44.8 1.0
CG2 C:VAL14 2.8 47.7 1.0
CE C:LYS16 3.1 50.4 1.0
F2 C:AF3203 3.1 48.8 1.0
F3 C:AF3203 3.1 45.3 1.0
NZ C:LYS16 3.2 54.0 1.0
O C:GLY10 3.3 51.2 1.0
CB C:LYS16 3.4 46.1 1.0
C C:GLY10 3.5 50.8 1.0
C C:ALA11 3.6 49.9 1.0
CA C:GLY10 3.8 50.5 1.0
N C:LYS16 4.0 50.1 1.0
PB C:GDP201 4.1 44.0 1.0
N C:ALA11 4.1 50.1 1.0
CB C:VAL14 4.1 51.3 1.0
N C:GLY10 4.2 49.4 1.0
CA C:ASP12 4.3 51.7 1.0
CA C:LYS16 4.3 47.0 1.0
N C:VAL14 4.4 49.9 1.0
N C:ASP12 4.4 50.3 1.0
CA C:ALA11 4.5 51.0 1.0
CG1 C:VAL14 4.5 52.0 1.0
O1B C:GDP201 4.5 42.6 1.0
O2B C:GDP201 4.6 44.7 1.0
N C:GLY15 4.6 46.5 1.0
C C:VAL9 4.7 46.1 1.0
OD1 C:ASP12 4.7 45.2 1.0
CA C:VAL14 4.7 50.2 1.0
N C:GLY13 4.8 49.6 1.0
C C:ASP12 4.8 51.4 1.0
O C:VAL9 4.8 44.6 1.0
O C:HOH320 4.9 30.6 1.0
O C:VAL81 5.0 49.7 1.0

Fluorine binding site 2 out of 3 in 9bgh

Go back to Fluorine Binding Sites List in 9bgh
Fluorine binding site 2 out of 3 in the Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F203

b:48.8
occ:1.00
 F2 C:AF3203 0.0 48.8 1.0
AL C:AF3203 1.8 43.9 1.0
OD1 C:ASP12 1.9 45.2 1.0
O C:HOH307 2.2 52.0 1.0
CA C:ASP12 2.2 51.7 1.0
CG C:ASP12 2.6 49.1 1.0
CB C:ASP12 2.8 56.0 1.0
O2B C:GDP201 2.9 44.7 1.0
O C:ALA11 3.0 51.1 1.0
N C:ASP12 3.0 50.3 1.0
F3 C:AF3203 3.1 45.3 1.0
F1 C:AF3203 3.1 55.6 1.0
O C:HOH327 3.1 33.5 1.0
O3B C:GDP201 3.2 44.8 1.0
C C:ASP12 3.2 51.4 1.0
C C:ALA11 3.3 49.9 1.0
N C:GLY13 3.3 49.6 1.0
PB C:GDP201 3.5 44.0 1.0
OD2 C:ASP12 3.8 52.0 1.0
O C:GLY10 4.0 51.2 1.0
O1B C:GDP201 4.2 42.6 1.0
O C:HOH320 4.3 30.6 1.0
O C:ASP12 4.4 53.0 1.0
N C:GLY60 4.4 48.8 1.0
NZ C:LYS16 4.5 54.0 1.0
CA C:ALA11 4.6 51.0 1.0
MG C:MG202 4.6 39.6 1.0
CA C:GLY13 4.7 51.0 1.0
N C:VAL14 4.8 49.9 1.0
C C:GLY10 4.8 50.8 1.0
CE C:LYS16 4.8 50.4 1.0
CA C:GLY60 4.9 49.2 1.0
O3A C:GDP201 4.9 46.0 1.0

Fluorine binding site 3 out of 3 in 9bgh

Go back to Fluorine Binding Sites List in 9bgh
Fluorine binding site 3 out of 3 in the Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F203

b:45.3
occ:1.00
 F3 C:AF3203 0.0 45.3 1.0
AL C:AF3203 1.8 43.9 1.0
O C:HOH320 2.0 30.6 1.0
O1B C:GDP201 2.2 42.6 1.0
O C:HOH307 2.6 52.0 1.0
O3B C:GDP201 2.7 44.8 1.0
MG C:MG202 2.7 39.6 1.0
PB C:GDP201 2.7 44.0 1.0
O C:HOH327 2.8 33.5 1.0
CB C:LYS16 3.0 46.1 1.0
F2 C:AF3203 3.1 48.8 1.0
F1 C:AF3203 3.1 55.6 1.0
O2B C:GDP201 3.1 44.7 1.0
CE C:LYS16 3.4 50.4 1.0
OG C:SER17 3.6 37.4 1.0
CG C:LYS16 3.6 48.3 1.0
N C:SER17 3.7 38.8 1.0
CA C:LYS16 3.9 47.0 1.0
N C:LYS16 3.9 50.1 1.0
CD C:LYS16 4.0 49.3 1.0
NZ C:LYS16 4.0 54.0 1.0
O C:THR58 4.1 40.6 1.0
OD1 C:ASP12 4.2 45.2 1.0
OD1 C:ASP57 4.2 36.1 1.0
C C:LYS16 4.2 41.1 1.0
O3A C:GDP201 4.2 46.0 1.0
OG1 C:THR35 4.3 37.5 1.0
CB C:SER17 4.6 37.3 1.0
O C:HOH310 4.6 33.9 1.0
CA C:SER17 4.7 38.9 1.0
CB C:THR35 4.9 37.5 1.0
O C:ALA11 5.0 51.1 1.0
C C:GLY15 5.0 45.2 1.0

Reference:

Y.Pourfarjam, Y.Goldgur, A.Cuevas-Navarro, P.Lito. Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 To Be Published.
Page generated: Wed Nov 13 08:39:06 2024

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