Bromine in PDB 8znl: Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity

The structure of Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity, PDB code: 8znl was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.46 / 1.77
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.872, 58.956, 63.299, 92.52, 90.02, 94.8
R / Rfree (%)	20.1 / 27.5

The binding sites of Bromine atom in the Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity (pdb code 8znl). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity, PDB code: 8znl:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity within 5.0Å range: probe atom residue distance (Å) B Occ A:Br101 b:69.2 occ:1.00 O B:HOH237 3.1 21.7 1.0 NE A:ARG6 3.4 25.0 1.0 N B:ARG126 3.5 10.6 1.0 CD B:ARG126 3.7 20.1 1.0 CD B:LYS125 3.8 17.5 1.0 CG B:ARG126 3.9 18.2 1.0 NH2 A:ARG6 4.0 29.1 1.0 CA B:LYS125 4.0 10.5 1.0 CB B:ARG126 4.1 14.1 1.0 CZ A:ARG6 4.2 28.1 1.0 C B:LYS125 4.3 10.2 1.0 CD A:ARG6 4.3 17.5 1.0 CA B:ARG126 4.4 12.7 1.0 O B:TYR124 4.6 13.3 1.0 CB B:LYS125 4.7 11.6 1.0 CE B:LYS125 4.7 21.0 1.0 O B:ARG126 4.8 14.1 1.0 CG B:LYS125 4.8 15.7 1.0 CG A:ARG6 4.9 16.8 1.0 NE B:ARG126 4.9 19.0 1.0

Bromine binding site 2 out of 4 in the Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity within 5.0Å range: probe atom residue distance (Å) B Occ D:Br201 b:33.3 occ:1.00 O D:HOH314 3.0 23.0 1.0 NE C:ARG6 3.5 31.0 1.0 N D:ARG126 3.6 10.8 1.0 CD D:LYS125 3.9 19.3 1.0 CD D:ARG126 3.9 19.0 1.0 CD C:ARG6 4.0 24.5 1.0 CB D:ARG126 4.0 15.5 1.0 CG D:ARG126 4.1 19.3 1.0 CA D:LYS125 4.1 12.4 1.0 C D:LYS125 4.3 11.0 1.0 CA D:ARG126 4.4 14.2 1.0 CZ C:ARG6 4.5 36.2 1.0 NH2 C:ARG6 4.6 35.9 1.0 CG C:ARG6 4.7 20.4 1.0 CB D:LYS125 4.8 14.7 1.0 CE D:LYS125 4.8 22.6 1.0 O D:TYR124 4.8 11.9 1.0 O D:ARG126 4.8 15.8 1.0 NE D:ARG126 4.9 20.7 1.0 CG D:LYS125 5.0 17.8 1.0

Bromine binding site 3 out of 4 in the Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity within 5.0Å range: probe atom residue distance (Å) B Occ E:Br101 b:33.9 occ:1.00 O F:HOH238 3.1 28.7 1.0 NE E:ARG6 3.3 37.2 1.0 N F:ARG126 3.5 10.4 1.0 CD F:ARG126 3.7 15.3 1.0 CD F:LYS125 3.8 17.3 1.0 CG F:ARG126 3.9 13.6 1.0 NH2 E:ARG6 3.9 41.5 1.0 CB F:ARG126 4.0 13.9 1.0 CZ E:ARG6 4.1 41.0 1.0 CA F:LYS125 4.1 10.4 1.0 CD E:ARG6 4.2 30.8 1.0 C F:LYS125 4.3 11.0 1.0 CA F:ARG126 4.3 11.4 1.0 CE F:LYS125 4.6 18.5 1.0 NE F:ARG126 4.6 16.8 1.0 CB F:LYS125 4.7 13.5 1.0 O F:ARG126 4.8 12.7 1.0 O F:TYR124 4.8 12.3 1.0 CG F:LYS125 4.9 14.2 1.0 CG E:ARG6 5.0 25.1 1.0

Bromine binding site 4 out of 4 in the Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Pd-L1 De Novo Designed Binder with Picomolar Binding Affinity within 5.0Å range: probe atom residue distance (Å) B Occ H:Br201 b:74.3 occ:1.00 O H:HOH305 3.2 32.2 1.0 N H:ARG126 3.4 8.8 1.0 CD H:LYS125 3.7 18.1 1.0 CG H:ARG126 3.7 18.0 1.0 CD H:ARG126 3.8 22.4 1.0 CB H:ARG126 3.8 12.0 1.0 NH1 G:ARG6 3.9 50.7 1.0 CA H:LYS125 4.0 9.0 1.0 CD G:ARG6 4.1 35.5 1.0 C H:LYS125 4.1 10.2 1.0 CA H:ARG126 4.2 9.2 1.0 O H:HOH321 4.4 36.0 1.0 CB H:LYS125 4.5 11.0 1.0 O H:HOH338 4.5 28.6 1.0 CE H:LYS125 4.7 21.1 1.0 O H:TYR124 4.7 11.3 1.0 O H:ARG126 4.7 13.9 1.0 CG H:LYS125 4.8 14.7 1.0 CG G:ARG6 4.8 28.3 1.0 CZ G:ARG6 4.9 47.2 1.0 NE H:ARG126 5.0 25.5 1.0 NE G:ARG6 5.0 41.7 1.0 C H:ARG126 5.0 12.0 1.0

L.Zhao, L.Zhao. N/A N/A.