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: Fri Aug 2 15:53:30 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy