Sodium in PDB 5eel: GRB7 SH2 with Bicyclic Peptide Inhibitor

The structure of GRB7 SH2 with Bicyclic Peptide Inhibitor, PDB code: 5eel was solved by G.M.Watson, M.J.Gunzburg, M.C.J.Wilce, J.A.Wilce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.72 / 2.47
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.228, 95.228, 241.566, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.2

The binding sites of Sodium atom in the GRB7 SH2 with Bicyclic Peptide Inhibitor (pdb code 5eel). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the GRB7 SH2 with Bicyclic Peptide Inhibitor, PDB code: 5eel:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the GRB7 SH2 with Bicyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of GRB7 SH2 with Bicyclic Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:74.8 occ:1.00 O2 A:FMT602 1.9 47.8 1.0 C A:FMT602 3.2 44.4 1.0 N A:MET495 3.4 35.7 1.0 O A:THR500 3.5 42.7 1.0 CE2 A:PHE502 3.6 37.3 1.0 CB A:THR500 3.7 36.0 1.0 CB A:MET495 3.7 27.3 1.0 OD2 A:ASP496 3.9 44.5 1.0 CE A:MET495 4.0 32.1 1.0 O1 A:FMT602 4.0 51.9 1.0 CG A:ASP496 4.0 39.2 1.0 OD1 A:ASP496 4.0 35.9 1.0 CG A:MET495 4.0 31.3 1.0 CA A:MET495 4.1 27.9 1.0 CD2 A:PHE502 4.1 35.5 1.0 C A:THR500 4.2 40.3 1.0 CG2 A:THR500 4.2 34.7 1.0 N A:ASP496 4.3 34.7 1.0 CA A:SER494 4.3 32.8 1.0 CE1 A:HIS512 4.3 40.1 1.0 C A:SER494 4.3 33.0 1.0 OG A:SER494 4.3 35.5 1.0 OG1 A:THR500 4.4 36.1 1.0 CA A:THR500 4.5 42.1 1.0 C A:MET495 4.5 34.4 1.0 CZ A:PHE502 4.7 36.6 1.0 CB A:ASP496 4.8 33.0 1.0 CB A:SER494 4.8 33.4 1.0 NE2 A:HIS512 4.9 42.8 1.0 SD A:MET495 4.9 41.4 1.0 N A:THR500 4.9 44.3 1.0

Sodium binding site 2 out of 6 in the GRB7 SH2 with Bicyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of GRB7 SH2 with Bicyclic Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:80.6 occ:1.00 O2 B:FMT601 1.9 48.7 1.0 C B:FMT601 3.2 45.4 1.0 N B:MET495 3.3 26.8 1.0 O B:THR500 3.5 27.0 1.0 CE2 B:PHE502 3.5 26.9 1.0 CB B:THR500 3.7 29.7 1.0 CB B:MET495 3.8 32.8 1.0 O1 B:FMT601 3.9 41.3 1.0 OD1 B:ASP496 4.0 27.2 1.0 CA B:MET495 4.0 27.2 1.0 CE B:MET495 4.0 28.2 1.0 N B:ASP496 4.1 22.9 1.0 CD2 B:PHE502 4.1 24.7 1.0 CG B:ASP496 4.1 35.5 1.0 CG B:MET495 4.1 27.3 1.0 CG2 B:THR500 4.2 22.5 1.0 CA B:SER494 4.3 21.9 1.0 C B:THR500 4.3 27.6 1.0 C B:SER494 4.3 25.4 1.0 OD2 B:ASP496 4.3 35.1 1.0 OG B:SER494 4.3 29.1 1.0 CE1 B:HIS512 4.3 26.4 1.0 C B:MET495 4.4 26.5 1.0 OG1 B:THR500 4.5 33.2 1.0 CA B:THR500 4.6 27.1 1.0 CZ B:PHE502 4.6 18.8 1.0 CB B:ASP496 4.8 32.0 1.0 CB B:SER494 4.8 24.4 1.0 NE2 B:HIS512 4.9 30.6 1.0 CD1 B:LEU508 4.9 27.0 1.0 SD B:MET495 5.0 65.1 1.0

Sodium binding site 3 out of 6 in the GRB7 SH2 with Bicyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of GRB7 SH2 with Bicyclic Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na603 b:83.7 occ:1.00 O2 C:FMT602 1.9 77.5 1.0 C C:FMT602 3.2 78.4 1.0 N C:MET495 3.5 54.7 1.0 CB C:THR500 3.6 56.5 1.0 OD1 C:ASP496 3.7 60.2 1.0 CE2 C:PHE502 3.7 57.6 1.0 CB C:MET495 3.8 57.8 1.0 CG C:ASP496 3.8 66.0 1.0 CE C:MET495 3.8 54.3 1.0 O1 C:FMT602 4.0 77.7 1.0 O C:THR500 4.0 57.0 1.0 N C:ASP496 4.0 59.8 1.0 OG1 C:THR500 4.0 59.1 1.0 CA C:MET495 4.0 55.9 1.0 CE1 C:HIS512 4.1 46.0 1.0 OD2 C:ASP496 4.1 70.3 1.0 CG C:MET495 4.2 52.9 1.0 C C:MET495 4.4 58.9 1.0 CB C:ASP496 4.4 63.4 1.0 CG2 C:THR500 4.4 55.5 1.0 OG C:SER494 4.5 62.6 1.0 NE2 C:HIS512 4.5 51.5 1.0 C C:SER494 4.5 56.5 1.0 CD2 C:PHE502 4.5 55.8 1.0 C C:THR500 4.5 59.9 1.0 CA C:THR500 4.6 57.3 1.0 CA C:SER494 4.6 54.4 1.0 CZ C:PHE502 4.6 56.4 1.0 CA C:ASP496 4.9 63.2 1.0 SD C:MET495 4.9 64.0 1.0 N C:THR500 4.9 60.0 1.0

Sodium binding site 4 out of 6 in the GRB7 SH2 with Bicyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of GRB7 SH2 with Bicyclic Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Na603 b:59.1 occ:1.00 O2 D:FMT602 1.9 58.3 1.0 C D:FMT602 3.2 55.6 1.0 N D:MET495 3.2 41.1 1.0 O D:THR500 3.4 48.0 1.0 CE2 D:PHE502 3.6 33.8 1.0 CB D:THR500 3.6 37.0 1.0 CB D:MET495 3.8 38.0 1.0 CA D:SER494 3.9 35.2 1.0 CE D:MET495 3.9 37.9 1.0 O1 D:FMT602 4.0 60.4 1.0 CD2 D:PHE502 4.0 32.2 1.0 CG D:MET495 4.0 42.1 1.0 CA D:MET495 4.0 37.7 1.0 C D:SER494 4.0 38.9 1.0 C D:THR500 4.0 46.4 1.0 OD1 D:ASP496 4.1 47.9 1.0 OG D:SER494 4.1 44.4 1.0 CG2 D:THR500 4.3 32.5 1.0 N D:ASP496 4.3 42.8 1.0 CG D:ASP496 4.4 44.8 1.0 OG1 D:THR500 4.4 34.0 1.0 CA D:THR500 4.4 40.1 1.0 OD2 D:ASP496 4.6 42.1 1.0 C D:MET495 4.6 40.9 1.0 CB D:SER494 4.6 37.9 1.0 CE1 D:HIS512 4.6 31.8 1.0 CD1 D:LEU508 4.7 40.5 1.0 CZ D:PHE502 4.8 33.8 1.0 O D:PHE493 4.8 37.4 1.0 SD D:MET495 4.9 48.6 1.0 N D:THR500 4.9 40.0 1.0 N D:ARG501 4.9 42.2 1.0 N D:SER494 5.0 37.8 1.0

Sodium binding site 5 out of 6 in the GRB7 SH2 with Bicyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of GRB7 SH2 with Bicyclic Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ E:Na603 b:55.5 occ:1.00 O2 E:FMT602 1.9 53.1 1.0 C E:FMT602 3.2 49.0 1.0 N E:MET495 3.2 36.6 1.0 O E:THR500 3.5 25.7 1.0 CB E:THR500 3.6 31.7 1.0 CE2 E:PHE502 3.6 26.6 1.0 CB E:MET495 3.7 23.3 1.0 OD1 E:ASP496 3.7 36.1 1.0 CE E:MET495 3.8 19.9 1.0 CG E:ASP496 3.9 36.8 1.0 CA E:MET495 3.9 32.2 1.0 O1 E:FMT602 4.0 46.8 1.0 OD2 E:ASP496 4.0 37.2 1.0 N E:ASP496 4.1 32.2 1.0 CG E:MET495 4.1 24.6 1.0 OG E:SER494 4.1 35.5 1.0 CA E:SER494 4.2 28.9 1.0 C E:THR500 4.2 36.7 1.0 CD2 E:PHE502 4.2 27.9 1.0 C E:SER494 4.2 35.7 1.0 CG2 E:THR500 4.2 33.2 1.0 OG1 E:THR500 4.3 36.0 1.0 C E:MET495 4.3 34.7 1.0 CA E:THR500 4.4 33.9 1.0 CB E:ASP496 4.6 34.5 1.0 CE1 E:HIS512 4.7 32.4 1.0 CZ E:PHE502 4.7 24.3 1.0 CB E:SER494 4.7 30.9 1.0 N E:THR500 4.8 36.2 1.0 SD E:MET495 4.9 32.0 1.0 CA E:ASP496 5.0 34.3 1.0

Sodium binding site 6 out of 6 in the GRB7 SH2 with Bicyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of GRB7 SH2 with Bicyclic Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ F:Na603 b:55.4 occ:1.00 O2 F:FMT602 1.9 45.4 1.0 C F:FMT602 3.2 46.1 1.0 N F:MET495 3.3 27.4 1.0 CE2 F:PHE502 3.3 27.2 1.0 O F:THR500 3.4 26.9 1.0 CB F:THR500 3.7 28.8 1.0 CB F:MET495 3.7 20.4 1.0 OD1 F:ASP496 4.0 35.0 1.0 CA F:MET495 4.0 22.8 1.0 CD2 F:PHE502 4.0 25.1 1.0 CE F:MET495 4.0 27.9 1.0 O1 F:FMT602 4.0 45.0 1.0 CG2 F:THR500 4.1 22.5 1.0 CG F:MET495 4.1 22.4 1.0 CA F:SER494 4.2 26.1 1.0 C F:SER494 4.2 26.8 1.0 OG F:SER494 4.2 25.4 1.0 C F:THR500 4.2 29.3 1.0 CE1 F:HIS512 4.2 29.3 1.0 CG F:ASP496 4.2 35.8 1.0 N F:ASP496 4.3 29.7 1.0 CZ F:PHE502 4.4 25.6 1.0 OD2 F:ASP496 4.4 34.2 1.0 OG1 F:THR500 4.5 36.8 1.0 CA F:THR500 4.5 27.2 1.0 C F:MET495 4.5 25.2 1.0 CB F:SER494 4.7 25.0 1.0 NE2 F:HIS512 4.8 24.4 1.0 CD1 F:LEU508 5.0 23.9 1.0 SD F:MET495 5.0 52.9 1.0 N F:THR500 5.0 27.4 1.0

M.J.Gunzburg, K.Kulkarni, G.M.Watson, N.D.Ambaye, M.P.Del Borgo, R.Brandt, S.C.Pero, P.Perlmutter, M.C.Wilce, J.A.Wilce. Unexpected Involvement of Staple Leads to Redesign of Selective Bicyclic Peptide Inhibitor of GRB7. Sci Rep V. 6 27060 2016.
ISSN: ESSN 2045-2322
PubMed: 27257138
DOI: 10.1038/SREP27060