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Fluorine in PDB 8wb1: Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D)

Protein crystallography data

The structure of Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D), PDB code: 8wb1 was solved by L.Zhou, R.Zhang, T.B.Shuai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.98 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.099, 51.955, 90.475, 90, 90, 90
R / Rfree (%) 19.2 / 21.2

Other elements in 8wb1:

The structure of Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D) (pdb code 8wb1). 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 Small Molecule KN2H Covalently Bound to K- Ras(G12D), PDB code: 8wb1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8wb1

Go back to Fluorine Binding Sites List in 8wb1
Fluorine binding site 1 out of 3 in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D)


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 Small Molecule KN2H Covalently Bound to K- Ras(G12D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F204

b:34.5
occ:1.00
F01 A:W3T204 0.0 34.5 1.0
C02 A:W3T204 1.4 33.6 1.0
C55 A:W3T204 2.2 30.9 1.0
C03 A:W3T204 2.4 30.1 1.0
N51 A:W3T204 2.8 30.7 1.0
C04 A:W3T204 2.9 28.6 1.0
C54 A:W3T204 3.2 31.4 1.0
C52 A:W3T204 3.4 31.7 1.0
O A:HOH328 3.5 39.6 1.0
C53 A:W3T204 3.8 31.1 1.0
OD1 A:ASP92 3.9 32.4 1.0
NZ A:LYS88 4.2 37.7 1.0
C05 A:W3T204 4.5 30.3 1.0
CG A:ASP92 4.6 34.1 1.0
O06 A:W3T204 4.7 28.2 1.0
CG A:HIS95 4.9 29.4 1.0
OD2 A:ASP92 5.0 31.3 1.0

Fluorine binding site 2 out of 3 in 8wb1

Go back to Fluorine Binding Sites List in 8wb1
Fluorine binding site 2 out of 3 in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D)


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 Small Molecule KN2H Covalently Bound to K- Ras(G12D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F204

b:28.6
occ:1.00
F32 A:W3T204 0.0 28.6 1.0
C31 A:W3T204 1.4 27.5 1.0
C30 A:W3T204 2.4 27.0 1.0
C33 A:W3T204 2.5 28.2 1.0
N50 A:W3T204 2.8 25.9 1.0
C34 A:W3T204 2.8 26.8 1.0
C35 A:W3T204 3.1 26.5 1.0
C37 A:W3T204 3.2 25.4 1.0
CE1 A:TYR64 3.3 28.5 1.0
C36 A:W3T204 3.3 22.6 1.0
NE2 A:HIS95 3.3 27.9 1.0
OH A:TYR64 3.5 27.9 1.0
C47 A:W3T204 3.5 26.3 1.0
C29 A:W3T204 3.6 24.8 1.0
C38 A:W3T204 3.6 28.2 1.0
N48 A:W3T204 3.7 27.7 1.0
CG A:GLN99 3.7 24.6 1.0
CZ A:TYR64 3.7 28.7 1.0
CE1 A:HIS95 4.0 29.0 1.0
C07 A:W3T204 4.1 27.3 1.0
C49 A:W3T204 4.1 26.9 1.0
C43 A:W3T204 4.1 24.4 1.0
CB A:GLN99 4.2 25.0 1.0
CD2 A:HIS95 4.2 27.2 1.0
CD1 A:TYR64 4.3 29.5 1.0
C39 A:W3T204 4.4 25.9 1.0
CE1 A:TYR96 4.4 24.2 1.0
C45 A:W3T204 4.5 27.3 1.0
CD1 A:TYR96 4.6 27.0 1.0
CD A:GLN99 4.6 30.3 1.0
C44 A:W3T204 4.7 26.2 1.0
OE1 A:GLN99 4.8 27.7 1.0
C09 A:W3T204 4.8 27.1 1.0
N08 A:W3T204 4.9 25.3 1.0
O06 A:W3T204 5.0 28.2 1.0
CE2 A:TYR64 5.0 29.4 1.0

Fluorine binding site 3 out of 3 in 8wb1

Go back to Fluorine Binding Sites List in 8wb1
Fluorine binding site 3 out of 3 in the Crystal Structure of Small Molecule KN2H Covalently Bound to K- Ras(G12D)


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 Small Molecule KN2H Covalently Bound to K- Ras(G12D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F204

b:25.7
occ:1.00
F40 A:W3T204 0.0 25.7 1.0
C39 A:W3T204 1.4 25.9 1.0
C36 A:W3T204 2.4 22.6 1.0
C41 A:W3T204 2.4 25.2 1.0
C37 A:W3T204 2.7 25.4 1.0
C38 A:W3T204 3.4 28.2 1.0
CG1 A:VAL9 3.4 23.6 1.0
CG1 A:ILE100 3.6 23.3 1.0
C42 A:W3T204 3.7 27.4 1.0
C35 A:W3T204 3.7 26.5 1.0
CB A:VAL9 3.8 21.3 1.0
CG2 A:VAL9 4.0 21.4 1.0
C43 A:W3T204 4.1 24.4 1.0
O A:TYR96 4.2 25.0 1.0
CD1 A:ILE100 4.2 24.6 1.0
CD1 A:TYR96 4.3 27.0 1.0
SD A:MET72 4.5 33.2 1.0
CE2 A:PHE78 4.6 21.8 1.0
CD2 A:PHE78 4.6 22.6 1.0
CB A:GLN99 4.6 25.0 1.0
N A:ILE100 4.7 26.1 1.0
CB A:TYR96 4.7 27.2 1.0
CA A:TYR96 4.8 24.5 1.0
C A:TYR96 4.9 26.8 1.0
C34 A:W3T204 4.9 26.8 1.0
CB A:ILE100 4.9 27.3 1.0
CG A:TYR96 5.0 23.8 1.0

Reference:

L.Zhou, R.Zhang, T.B.Shuai. Crystal Structure of Small Molecule KN2H Covalently Bound to K-Ras(G12D) To Be Published.
Page generated: Wed Jul 16 09:59:56 2025

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