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Fluorine in PDB 9bhp: Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977

Enzymatic activity of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977

All present enzymatic activity of Crystal Structure of Kras G12C 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 G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977, PDB code: 9bhp 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) 29.81 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.456, 82.648, 127.829, 90, 90, 90
R / Rfree (%) 21 / 25.3

Other elements in 9bhp:

The structure of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 (pdb code 9bhp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977, PDB code: 9bhp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9bhp

Go back to Fluorine Binding Sites List in 9bhp
Fluorine binding site 1 out of 6 in the Crystal Structure of Kras G12C 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 G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:28.8
occ:1.00
F1 A:AF3201 0.0 28.8 1.0
AL A:AF3201 1.8 28.9 1.0
O A:HOH342 2.5 24.9 1.0
OH A:TYR32 2.6 33.1 1.0
SG A:CYS12 2.6 46.6 1.0
O3B A:GDP202 2.9 25.0 1.0
F2 A:AF3201 3.0 26.3 1.0
F3 A:AF3201 3.0 26.0 1.0
NE2 A:GLN61 3.5 32.4 1.0
CZ A:TYR32 3.5 33.5 1.0
CE2 A:TYR32 3.6 28.4 1.0
CB A:PRO34 3.6 28.3 1.0
CA A:PRO34 3.8 28.2 1.0
CB A:CYS12 3.9 28.5 1.0
OE1 A:GLN61 4.0 29.7 1.0
N A:GLY13 4.0 27.9 1.0
CA A:CYS12 4.1 27.8 1.0
CD A:GLN61 4.2 30.3 1.0
N A:THR35 4.3 25.4 1.0
PB A:GDP202 4.4 25.5 1.0
C A:PRO34 4.5 26.2 1.0
C A:CYS12 4.5 28.6 1.0
CE1 A:TYR32 4.8 30.5 1.0
O A:HOH313 4.8 24.7 1.0
MG A:MG203 4.8 22.8 1.0
CA A:GLY13 4.9 25.4 1.0
O1B A:GDP202 4.9 22.3 1.0
CD2 A:TYR32 5.0 30.4 1.0

Fluorine binding site 2 out of 6 in 9bhp

Go back to Fluorine Binding Sites List in 9bhp
Fluorine binding site 2 out of 6 in the Crystal Structure of Kras G12C 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 G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:26.3
occ:1.00
F2 A:AF3201 0.0 26.3 1.0
AL A:AF3201 1.8 28.9 1.0
MG A:MG203 1.9 22.8 1.0
O3B A:GDP202 2.6 25.0 1.0
O A:HOH313 2.8 24.7 1.0
N A:THR35 2.8 25.4 1.0
O A:HOH342 2.8 24.9 1.0
O1B A:GDP202 2.9 22.3 1.0
F1 A:AF3201 3.0 28.8 1.0
OG1 A:THR35 3.0 25.9 1.0
O A:HOH307 3.0 25.1 1.0
F3 A:AF3201 3.1 26.0 1.0
CB A:THR35 3.2 25.4 1.0
PB A:GDP202 3.3 25.5 1.0
CA A:THR35 3.6 25.3 1.0
C A:PRO34 3.8 26.2 1.0
CA A:PRO34 3.8 28.2 1.0
OG A:SER17 3.9 23.8 1.0
O A:THR58 4.3 24.3 1.0
O A:THR35 4.3 23.8 1.0
O2B A:GDP202 4.4 21.8 1.0
C A:THR35 4.5 25.1 1.0
O3A A:GDP202 4.5 25.7 1.0
O A:ASP33 4.5 26.9 1.0
NZ A:LYS16 4.5 24.3 1.0
O2A A:GDP202 4.6 24.9 1.0
CG2 A:THR35 4.6 25.0 1.0
CB A:PRO34 4.7 28.3 1.0
CE A:LYS16 4.8 26.4 1.0
CE2 A:TYR32 4.9 28.4 1.0
CB A:SER17 4.9 23.6 1.0
O A:PRO34 5.0 26.1 1.0
N A:PRO34 5.0 27.8 1.0

Fluorine binding site 3 out of 6 in 9bhp

Go back to Fluorine Binding Sites List in 9bhp
Fluorine binding site 3 out of 6 in the Crystal Structure of Kras G12C 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 G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:26.0
occ:1.00
F3 A:AF3201 0.0 26.0 1.0
AL A:AF3201 1.8 28.9 1.0
N A:GLY60 2.7 28.0 1.0
NZ A:LYS16 2.7 24.3 1.0
O A:HOH342 2.9 24.9 1.0
O3B A:GDP202 2.9 25.0 1.0
F1 A:AF3201 3.0 28.8 1.0
F2 A:AF3201 3.1 26.3 1.0
CA A:GLY60 3.3 27.8 1.0
CE A:LYS16 3.4 26.4 1.0
CA A:CYS12 3.6 27.8 1.0
C A:ALA59 3.7 28.0 1.0
CA A:ALA59 3.8 26.1 1.0
O A:THR58 3.9 24.3 1.0
PB A:GDP202 4.0 25.5 1.0
O2B A:GDP202 4.2 21.8 1.0
CB A:CYS12 4.2 28.5 1.0
OE1 A:GLN61 4.2 29.7 1.0
SG A:CYS12 4.2 46.6 1.0
O A:HOH307 4.2 25.1 1.0
N A:CYS12 4.3 27.0 1.0
O A:ALA11 4.3 27.5 1.0
N A:GLY13 4.3 27.9 1.0
C A:GLY60 4.3 30.4 1.0
O1B A:GDP202 4.4 22.3 1.0
MG A:MG203 4.5 22.8 1.0
N A:GLN61 4.5 30.1 1.0
C A:CYS12 4.6 28.6 1.0
C A:ALA11 4.6 28.4 1.0
O A:GLY10 4.7 26.7 1.0
C A:THR58 4.7 26.9 1.0
N A:ALA59 4.7 24.8 1.0
O A:ALA59 4.8 27.6 1.0
CD A:LYS16 4.8 27.4 1.0
CB A:ALA59 4.9 25.6 1.0
CD A:GLN61 4.9 30.3 1.0

Fluorine binding site 4 out of 6 in 9bhp

Go back to Fluorine Binding Sites List in 9bhp
Fluorine binding site 4 out of 6 in the Crystal Structure of Kras G12C 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 4 of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:56.9
occ:1.00
F1 C:AF3201 0.0 56.9 1.0
AL C:AF3201 1.8 56.5 1.0
O C:HOH328 2.4 50.0 1.0
N C:GLY60 2.7 55.1 1.0
NZ C:LYS16 2.9 59.8 1.0
F2 C:AF3201 3.0 57.4 1.0
O2B C:GDP202 3.0 56.2 1.0
F3 C:AF3201 3.0 49.8 1.0
CA C:ALA59 3.5 49.6 1.0
C C:ALA59 3.6 52.8 1.0
CA C:GLY60 3.6 59.9 1.0
CE C:LYS16 3.6 55.1 1.0
CA C:CYS12 3.7 70.6 1.0
O1B C:GDP202 3.8 57.4 1.0
PB C:GDP202 3.9 55.3 1.0
OE1 C:GLN61 4.0 53.1 1.0
O C:THR58 4.0 48.3 1.0
SG C:CYS12 4.1 71.0 1.0
CB C:CYS12 4.1 70.4 1.0
O3B C:GDP202 4.2 52.0 1.0
O C:ALA11 4.3 66.6 1.0
O C:HOH308 4.4 46.1 1.0
CB C:ALA59 4.4 48.0 1.0
N C:CYS12 4.4 72.7 1.0
C C:GLY60 4.4 59.8 1.0
N C:GLY13 4.5 65.5 1.0
MG C:MG203 4.5 47.6 1.0
C C:ALA11 4.6 69.5 1.0
N C:GLN61 4.6 58.8 1.0
N C:ALA59 4.6 47.9 1.0
NE2 C:GLN61 4.6 55.0 1.0
CD C:GLN61 4.6 54.8 1.0
C C:CYS12 4.7 72.1 1.0
C C:THR58 4.7 47.4 1.0
O C:ALA59 4.7 53.1 1.0
O C:GLY10 4.9 64.5 1.0

Fluorine binding site 5 out of 6 in 9bhp

Go back to Fluorine Binding Sites List in 9bhp
Fluorine binding site 5 out of 6 in the Crystal Structure of Kras G12C 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 5 of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:57.4
occ:1.00
F2 C:AF3201 0.0 57.4 1.0
AL C:AF3201 1.8 56.5 1.0
OH C:TYR32 2.4 62.4 1.0
O C:HOH328 2.4 50.0 1.0
O2B C:GDP202 2.6 56.2 1.0
F1 C:AF3201 3.0 56.9 1.0
F3 C:AF3201 3.1 49.8 1.0
CZ C:TYR32 3.4 60.9 1.0
NE2 C:GLN61 3.5 55.0 1.0
CE1 C:TYR32 3.5 57.8 1.0
CB C:CYS12 3.6 70.4 1.0
N C:GLY13 3.7 65.5 1.0
CB C:PRO34 3.8 48.9 1.0
CA C:CYS12 3.9 70.6 1.0
CA C:PRO34 4.1 50.1 1.0
PB C:GDP202 4.1 55.3 1.0
SG C:CYS12 4.2 71.0 1.0
C C:CYS12 4.3 72.1 1.0
CD C:GLN61 4.4 54.8 1.0
OE1 C:GLN61 4.4 53.1 1.0
N C:THR35 4.6 44.6 1.0
CA C:GLY13 4.7 66.3 1.0
CE2 C:TYR32 4.7 61.0 1.0
O3B C:GDP202 4.8 52.0 1.0
C C:PRO34 4.8 47.1 1.0
O1B C:GDP202 4.8 57.4 1.0
CD1 C:TYR32 4.9 59.0 1.0
O2A C:GDP202 4.9 52.9 1.0
MG C:MG203 5.0 47.6 1.0
O C:HOH311 5.0 47.2 1.0

Fluorine binding site 6 out of 6 in 9bhp

Go back to Fluorine Binding Sites List in 9bhp
Fluorine binding site 6 out of 6 in the Crystal Structure of Kras G12C 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 6 of Crystal Structure of Kras G12C in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:49.8
occ:1.00
F3 C:AF3201 0.0 49.8 1.0
AL C:AF3201 1.8 56.5 1.0
MG C:MG203 2.0 47.6 1.0
O C:HOH328 2.5 50.0 1.0
O2B C:GDP202 2.5 56.2 1.0
O3B C:GDP202 2.7 52.0 1.0
O C:HOH311 2.8 47.2 1.0
N C:THR35 2.9 44.6 1.0
O C:HOH308 3.0 46.1 1.0
F1 C:AF3201 3.0 56.9 1.0
F2 C:AF3201 3.1 57.4 1.0
OG1 C:THR35 3.1 45.0 1.0
PB C:GDP202 3.1 55.3 1.0
CB C:THR35 3.3 42.7 1.0
CA C:THR35 3.7 42.6 1.0
CA C:PRO34 3.9 50.1 1.0
C C:PRO34 3.9 47.1 1.0
OG C:SER17 3.9 47.5 1.0
O2A C:GDP202 4.0 52.9 1.0
O1B C:GDP202 4.1 57.4 1.0
O C:THR58 4.3 48.3 1.0
O C:THR35 4.3 44.1 1.0
O3A C:GDP202 4.4 56.8 1.0
C C:THR35 4.5 42.0 1.0
O C:ASP33 4.6 50.5 1.0
NZ C:LYS16 4.6 59.8 1.0
CB C:PRO34 4.6 48.9 1.0
CG2 C:THR35 4.7 40.2 1.0
PA C:GDP202 4.8 54.9 1.0
CE1 C:TYR32 4.9 57.8 1.0
CE C:LYS16 4.9 55.1 1.0
CA C:ALA59 5.0 49.6 1.0
CB C:SER17 5.0 47.4 1.0

Reference:

Y.Pourfarjam, Y.Goldgur, A.Cuevas-Navarro, P.Lito. Crystal Structure of Kras G12S in A Transition State Mimetic Complex with Cypa and Rmc-7977 To Be Published.
Page generated: Wed Jul 16 10:32:15 2025

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