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Fluorine in PDB 7yv1: Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab

Protein crystallography data

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab, PDB code: 7yv1 was solved by M.Irie, T.A.Fukami, A.Matsuo, K.Saka, M.Nishimura, H.Saito, T.Torizawa, M.Tanada, A.Ohta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.41 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.617, 90.373, 116.81, 90, 90, 90
R / Rfree (%) 23.8 / 27.7

Other elements in 7yv1:

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab (pdb code 7yv1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab, PDB code: 7yv1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 7yv1

Go back to Fluorine Binding Sites List in 7yv1
Fluorine binding site 1 out of 5 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F7

b:8.8
occ:1.00
 FZ1 I:7W27 0.0 8.8 1.0
CZ1 I:7W27 1.4 8.1 1.0
CE1 I:7W27 2.3 6.6 1.0
CH I:7W27 2.4 9.6 1.0
FT3 I:7W27 2.7 14.9 1.0
CT I:7W27 2.8 12.5 1.0
FT1 I:7W27 3.1 11.7 1.0
NE A:ARG68 3.2 8.8 1.0
CG2 A:THR58 3.4 5.5 1.0
CG A:ARG68 3.4 6.7 1.0
CZ2 I:7W27 3.6 9.2 1.0
CD I:7W27 3.6 6.4 1.0
CD A:ARG68 3.6 9.2 1.0
CD2 A:LEU56 3.7 5.4 1.0
CZ A:ARG68 3.8 7.8 1.0
OE2 A:GLU37 4.1 6.2 1.0
CE2 I:7W27 4.1 7.8 1.0
FT2 I:7W27 4.1 13.4 1.0
NH2 A:ARG68 4.1 7.2 1.0
OE1 A:GLU37 4.2 8.4 1.0
CB A:THR58 4.2 4.3 1.0
CD A:GLU37 4.4 7.8 1.0
CG1 A:VAL7 4.5 5.2 1.0
CB A:ARG68 4.6 5.7 1.0
NH1 A:ARG68 4.6 7.5 1.0
FZ2 I:7W27 4.7 10.2 1.0
CD2 I:7VN10 4.8 9.4 1.0
CG I:7W27 4.9 6.7 1.0
CG A:LEU56 4.9 4.8 1.0

Fluorine binding site 2 out of 5 in 7yv1

Go back to Fluorine Binding Sites List in 7yv1
Fluorine binding site 2 out of 5 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F7

b:10.2
occ:1.00
 FZ2 I:7W27 0.0 10.2 1.0
CZ2 I:7W27 1.4 9.2 1.0
CE2 I:7W27 2.3 7.8 1.0
CH I:7W27 2.4 9.6 1.0
FT2 I:7W27 2.5 13.4 1.0
CT I:7W27 2.9 12.5 1.0
CE2 A:PHE78 3.4 7.7 1.0
CD I:7W27 3.6 6.4 1.0
CZ1 I:7W27 3.6 8.1 1.0
FT1 I:7W27 3.6 11.7 1.0
CD2 I:7VN10 3.9 9.4 1.0
CZ A:PHE78 4.0 8.1 1.0
FT3 I:7W27 4.0 14.9 1.0
CE1 I:7W27 4.1 6.6 1.0
CG1 A:ILE100 4.1 10.6 1.0
CD1 I:7VN10 4.2 8.4 1.0
CG1 A:VAL103 4.3 15.2 1.0
CD2 A:PHE78 4.4 6.7 1.0
CG2 A:VAL103 4.5 14.4 1.0
O A:HOH345 4.5 9.3 1.0
CB A:VAL103 4.6 14.2 1.0
FZ1 I:7W27 4.7 8.8 1.0
CG I:7W27 4.8 6.7 1.0
CA A:ILE100 4.9 8.4 1.0

Fluorine binding site 3 out of 5 in 7yv1

Go back to Fluorine Binding Sites List in 7yv1
Fluorine binding site 3 out of 5 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F7

b:11.7
occ:1.00
 FT1 I:7W27 0.0 11.7 1.0
CT I:7W27 1.3 12.5 1.0
FT2 I:7W27 2.1 13.4 1.0
FT3 I:7W27 2.1 14.9 1.0
CH I:7W27 2.4 9.6 1.0
CZ1 I:7W27 3.0 8.1 1.0
FZ1 I:7W27 3.1 8.8 1.0
CZ2 I:7W27 3.3 9.2 1.0
CG A:ARG68 3.5 6.7 1.0
CB A:MET72 3.6 6.9 1.0
CD1 I:7VN10 3.6 8.4 1.0
CA A:MET72 3.6 6.0 1.0
FZ2 I:7W27 3.6 10.2 1.0
N A:MET72 3.7 5.8 1.0
O A:ARG68 3.7 5.3 1.0
CD2 I:7VN10 4.1 9.4 1.0
CD A:ARG68 4.2 9.2 1.0
CG A:MET72 4.2 8.2 1.0
CE1 I:7W27 4.3 6.6 1.0
C A:TYR71 4.4 6.4 1.0
CE2 I:7W27 4.5 7.8 1.0
C A:ARG68 4.5 4.9 1.0
CB A:TYR71 4.8 6.0 1.0
O A:TYR71 4.8 6.6 1.0
NE A:ARG68 4.8 8.8 1.0
CB A:ARG68 4.8 5.7 1.0
CD I:7W27 4.9 6.4 1.0

Fluorine binding site 4 out of 5 in 7yv1

Go back to Fluorine Binding Sites List in 7yv1
Fluorine binding site 4 out of 5 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F7

b:13.4
occ:1.00
 FT2 I:7W27 0.0 13.4 1.0
CT I:7W27 1.3 12.5 1.0
FT3 I:7W27 2.1 14.9 1.0
FT1 I:7W27 2.1 11.7 1.0
CH I:7W27 2.4 9.6 1.0
FZ2 I:7W27 2.5 10.2 1.0
CZ2 I:7W27 2.8 9.2 1.0
CE2 A:PHE78 3.5 7.7 1.0
CZ1 I:7W27 3.6 8.1 1.0
CA A:MET72 3.7 6.0 1.0
CZ A:PHE78 3.7 8.1 1.0
N A:MET72 4.0 5.8 1.0
O A:TYR71 4.0 6.6 1.0
FZ1 I:7W27 4.1 8.8 1.0
C A:TYR71 4.1 6.4 1.0
CE2 I:7W27 4.2 7.8 1.0
CB A:MET72 4.3 6.9 1.0
CG1 A:VAL7 4.5 5.2 1.0
CG2 A:VAL7 4.5 5.6 1.0
CG1 A:VAL103 4.6 15.2 1.0
CD1 I:7VN10 4.7 8.4 1.0
CG A:MET72 4.8 8.2 1.0
CE1 I:7W27 4.8 6.6 1.0
CD2 A:PHE78 4.8 6.7 1.0
CB A:TYR71 4.8 6.0 1.0
C A:MET72 4.9 6.9 1.0
CB A:VAL7 4.9 5.2 1.0
CD2 I:7VN10 5.0 9.4 1.0
O A:MET72 5.0 7.7 1.0

Fluorine binding site 5 out of 5 in 7yv1

Go back to Fluorine Binding Sites List in 7yv1
Fluorine binding site 5 out of 5 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F7

b:14.9
occ:1.00
 FT3 I:7W27 0.0 14.9 1.0
CT I:7W27 1.3 12.5 1.0
FT2 I:7W27 2.1 13.4 1.0
FT1 I:7W27 2.1 11.7 1.0
CH I:7W27 2.4 9.6 1.0
FZ1 I:7W27 2.7 8.8 1.0
CZ1 I:7W27 2.9 8.1 1.0
CG1 A:VAL7 3.5 5.2 1.0
CZ2 I:7W27 3.6 9.2 1.0
CB A:TYR71 3.6 6.0 1.0
CD2 A:LEU56 3.6 5.4 1.0
CG2 A:VAL7 3.8 5.6 1.0
FZ2 I:7W27 4.0 10.2 1.0
N A:MET72 4.1 5.8 1.0
C A:TYR71 4.1 6.4 1.0
O A:ARG68 4.2 5.3 1.0
CE1 I:7W27 4.3 6.6 1.0
CB A:VAL7 4.3 5.2 1.0
CG A:ARG68 4.4 6.7 1.0
O A:TYR71 4.4 6.6 1.0
CA A:TYR71 4.5 5.9 1.0
CA A:MET72 4.5 6.0 1.0
CE2 A:PHE78 4.6 7.7 1.0
CG2 A:THR58 4.7 5.5 1.0
CG A:TYR71 4.7 6.2 1.0
CE2 I:7W27 4.7 7.8 1.0
CG A:LEU56 4.9 4.8 1.0

Reference:

M.Tanada, A.Ohta. Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab To Be Published.
Page generated: Thu Dec 28 04:19:40 2023

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