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

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

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

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

Fluorine

(F)

4 atoms

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

Chlorine 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 Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of EPHA2 with Peptide 135E2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl1 b:20.0 occ:1.00 CL E:DUG1 0.0 20.0 1.0 C03 E:DUG1 1.8 20.0 1.0 C02 E:DUG1 2.8 20.0 1.0 C05 E:DUG1 2.8 20.0 1.0 F E:DUG1 3.0 20.0 1.0 CE A:MET73 3.2 43.8 1.0 O G:ASP616 3.4 43.8 1.0 CD A:PRO109 3.5 48.1 1.0 C G:ASP616 3.7 43.5 1.0 CB G:ASP616 3.8 46.2 1.0 CA G:ASP616 3.9 44.8 1.0 CG A:PRO109 4.0 50.1 1.0 C12 E:DUG1 4.1 20.0 1.0 C06 E:DUG1 4.1 20.0 1.0 CG2 G:VAL618 4.2 45.9 1.0 CD1 A:PHE108 4.3 40.7 1.0 SD A:MET73 4.4 45.7 1.0 C11 E:DUG1 4.6 20.0 1.0 N G:SER617 4.6 42.4 1.0 CG G:ASP616 4.8 47.6 1.0 N A:PRO109 4.9 49.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of EPHA2 with Peptide 135E2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl1 b:20.0 occ:1.00 CL F:DUG1 0.0 20.0 1.0 C03 F:DUG1 1.8 20.0 1.0 O B:SER107 2.5 52.5 1.0 C02 F:DUG1 2.8 20.0 1.0 C05 F:DUG1 2.8 20.0 1.0 F F:DUG1 3.0 20.0 1.0 C B:SER107 3.4 52.5 1.0 CD1 B:PHE108 3.6 58.8 1.0 CE1 B:PHE108 3.6 54.9 1.0 NH2 B:ARG103 3.7 43.1 1.0 CB B:SER107 3.8 49.6 1.0 NH1 B:ARG103 3.8 44.6 1.0 C12 F:DUG1 4.1 20.0 1.0 C06 F:DUG1 4.1 20.0 1.0 CZ B:ARG103 4.1 42.8 1.0 CA B:SER107 4.1 52.4 1.0 OG B:SER153 4.2 51.5 1.0 N B:PHE108 4.3 63.6 1.0 CG B:PHE108 4.4 60.8 1.0 CZ B:PHE108 4.6 53.1 1.0 CA B:PHE108 4.6 66.9 1.0 C11 F:DUG1 4.6 20.0 1.0 OD1 H:ASP616 5.0 75.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of EPHA2 with Peptide 135E2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl1 b:20.0 occ:1.00 CL G:DUG1 0.0 20.0 1.0 C03 G:DUG1 1.8 20.0 1.0 C02 G:DUG1 2.8 20.0 1.0 C05 G:DUG1 2.8 20.0 1.0 F G:DUG1 3.0 20.0 1.0 OD1 E:ASP616 3.2 47.9 1.0 CG E:ASP616 3.4 47.3 1.0 CB E:ASP616 3.5 46.0 1.0 CA E:ASP616 3.9 45.1 1.0 C12 G:DUG1 4.0 20.0 1.0 C06 G:DUG1 4.0 20.0 1.0 OD2 E:ASP616 4.1 48.1 1.0 NH1 A:ARG159 4.1 52.5 1.0 O C:SER107 4.3 51.3 1.0 C11 G:DUG1 4.6 20.0 1.0 N E:ASP616 4.7 45.0 1.0 NE A:ARG159 4.8 50.9 1.0 CZ A:ARG159 4.9 52.1 1.0 C E:ASP616 5.0 43.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of EPHA2 with Peptide 135E2 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl1 b:20.0 occ:1.00 CL H:DUG1 0.0 20.0 1.0 C03 H:DUG1 1.8 20.0 1.0 C02 H:DUG1 2.8 20.0 1.0 C05 H:DUG1 2.8 20.0 1.0 F H:DUG1 3.0 20.0 1.0 OD1 F:ASP616 3.6 59.7 1.0 O D:SER107 3.7 58.0 1.0 C12 H:DUG1 4.1 20.0 1.0 CG F:ASP616 4.1 57.9 1.0 C06 H:DUG1 4.1 20.0 1.0 CB F:ASP616 4.4 55.5 1.0 C D:SER107 4.5 58.3 1.0 CD1 D:PHE108 4.6 54.4 1.0 CA F:ASP616 4.6 56.1 1.0 C11 H:DUG1 4.6 20.0 1.0 NH2 D:ARG103 4.7 49.4 1.0 OD2 F:ASP616 4.8 58.0 1.0 CE1 D:PHE108 4.9 53.4 1.0 CA D:PHE108 5.0 59.1 1.0

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