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Fluorine in PDB 6b9l: Crystal Structure of EPHA2 with Peptide 135E2

Enzymatic activity of Crystal Structure of EPHA2 with Peptide 135E2

All present enzymatic activity of Crystal Structure of EPHA2 with Peptide 135E2:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of EPHA2 with Peptide 135E2, PDB code: 6b9l was solved by J.Song, X.Tan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.08 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.268, 94.153, 134.464, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 27.4

Other elements in 6b9l:

The structure of Crystal Structure of EPHA2 with Peptide 135E2 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of EPHA2 with Peptide 135E2 (pdb code 6b9l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of EPHA2 with Peptide 135E2, PDB code: 6b9l:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6b9l

Go back to Fluorine Binding Sites List in 6b9l
Fluorine binding site 1 out of 4 in the Crystal Structure of EPHA2 with Peptide 135E2


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 EPHA2 with Peptide 135E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1

b:20.0
occ:1.00
 F E:DUG1 0.0 20.0 1.0
C02 E:DUG1 1.4 20.0 1.0
C12 E:DUG1 2.4 20.0 1.0
C03 E:DUG1 2.4 20.0 1.0
CL E:DUG1 3.0 20.0 1.0
CG G:ASP616 3.5 47.6 1.0
CB G:ASP616 3.5 46.2 1.0
OD1 G:ASP616 3.6 48.1 1.0
O A:SER107 3.6 45.4 1.0
C11 E:DUG1 3.7 20.0 1.0
C05 E:DUG1 3.7 20.0 1.0
CD A:PRO109 4.0 48.1 1.0
OD2 G:ASP616 4.1 48.6 1.0
C06 E:DUG1 4.2 20.0 1.0
CA G:ASP616 4.2 44.8 1.0
CG A:PRO109 4.6 50.1 1.0
CA A:PHE108 4.8 46.5 1.0
C A:SER107 4.8 46.3 1.0
CD1 A:PHE108 4.9 40.7 1.0

Fluorine binding site 2 out of 4 in 6b9l

Go back to Fluorine Binding Sites List in 6b9l
Fluorine binding site 2 out of 4 in the Crystal Structure of EPHA2 with Peptide 135E2


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 EPHA2 with Peptide 135E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1

b:20.0
occ:1.00
 F F:DUG1 0.0 20.0 1.0
C02 F:DUG1 1.4 20.0 1.0
C12 F:DUG1 2.4 20.0 1.0
C03 F:DUG1 2.4 20.0 1.0
CL F:DUG1 3.0 20.0 1.0
CG H:ASP616 3.3 72.0 1.0
OD1 H:ASP616 3.3 75.8 1.0
CB H:ASP616 3.4 66.5 1.0
C11 F:DUG1 3.7 20.0 1.0
C05 F:DUG1 3.7 20.0 1.0
O B:SER107 3.8 52.5 1.0
OD2 H:ASP616 3.9 70.9 1.0
CA H:ASP616 4.1 65.1 1.0
C06 F:DUG1 4.2 20.0 1.0
CD B:PRO109 4.3 76.0 1.0
CD1 B:PHE108 4.7 58.8 1.0
CA B:PHE108 4.9 66.9 1.0
C B:SER107 5.0 52.5 1.0
C H:ASP616 5.0 62.2 1.0

Fluorine binding site 3 out of 4 in 6b9l

Go back to Fluorine Binding Sites List in 6b9l
Fluorine binding site 3 out of 4 in the Crystal Structure of EPHA2 with Peptide 135E2


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 EPHA2 with Peptide 135E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1

b:20.0
occ:1.00
 F G:DUG1 0.0 20.0 1.0
C02 G:DUG1 1.4 20.0 1.0
C12 G:DUG1 2.4 20.0 1.0
C03 G:DUG1 2.4 20.0 1.0
CL G:DUG1 3.0 20.0 1.0
O C:SER107 3.5 51.3 1.0
CD C:PRO109 3.6 57.9 1.0
C11 G:DUG1 3.6 20.0 1.0
C05 G:DUG1 3.6 20.0 1.0
CA C:PHE108 3.8 53.2 1.0
CD1 C:PHE108 4.0 48.7 1.0
C06 G:DUG1 4.1 20.0 1.0
CB C:PHE108 4.1 51.2 1.0
CB E:ASP616 4.2 46.0 1.0
C C:SER107 4.4 51.0 1.0
N C:PRO109 4.5 57.3 1.0
N C:PHE108 4.6 52.8 1.0
CG C:PHE108 4.6 49.2 1.0
O E:ASP616 4.6 43.8 1.0
CA E:ASP616 4.7 45.1 1.0
C C:PHE108 4.7 55.3 1.0
CE C:MET73 4.7 47.4 1.0
CG C:PRO109 4.8 60.9 1.0
C E:ASP616 4.9 43.9 1.0
CG E:ASP616 4.9 47.3 1.0
CG2 E:VAL618 5.0 45.7 1.0

Fluorine binding site 4 out of 4 in 6b9l

Go back to Fluorine Binding Sites List in 6b9l
Fluorine binding site 4 out of 4 in the Crystal Structure of EPHA2 with Peptide 135E2


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 EPHA2 with Peptide 135E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F1

b:20.0
occ:1.00
 F H:DUG1 0.0 20.0 1.0
C02 H:DUG1 1.4 20.0 1.0
C12 H:DUG1 2.4 20.0 1.0
C03 H:DUG1 2.4 20.0 1.0
CL H:DUG1 3.0 20.0 1.0
CD D:PRO109 3.1 58.6 1.0
C11 H:DUG1 3.7 20.0 1.0
C05 H:DUG1 3.7 20.0 1.0
CE D:MET73 3.8 48.0 1.0
CG D:PRO109 4.0 59.6 1.0
CD1 D:PHE108 4.0 54.4 1.0
CB F:ASP616 4.0 55.5 1.0
O F:ASP616 4.0 52.1 1.0
CA D:PHE108 4.0 59.1 1.0
C06 H:DUG1 4.2 20.0 1.0
CA F:ASP616 4.3 56.1 1.0
N D:PRO109 4.3 60.5 1.0
CB D:PHE108 4.4 57.4 1.0
O D:SER107 4.4 58.0 1.0
C F:ASP616 4.5 54.0 1.0
CG F:ASP616 4.7 57.9 1.0
CG D:PHE108 4.7 56.0 1.0
SD D:MET73 4.7 52.9 1.0
C D:PHE108 4.7 60.9 1.0
OD1 F:ASP616 4.9 59.7 1.0
CE1 D:PHE108 5.0 53.4 1.0
N D:PHE108 5.0 60.3 1.0

Reference:

L.Gambini, A.F.Salem, P.Udompholkul, X.F.Tan, C.Baggio, N.Shah, A.Aronson, J.Song, M.Pellecchia. Structure-Based Design of Novel EPHA2 Agonistic Agents with Nanomolar Affinity in Vitro and in Cell. Acs Chem. Biol. V. 13 2633 2018.
ISSN: ESSN 1554-8937
PubMed: 30110533
DOI: 10.1021/ACSCHEMBIO.8B00556
Page generated: Thu Aug 1 18:01:09 2024

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