Chlorine in PDB 5jds: Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution

The structure of Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution, PDB code: 5jds was solved by A.Zhou, H.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.60 / 1.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	83.130, 83.130, 73.230, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 20.4

The structure of Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution (pdb code 5jds). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution, PDB code: 5jds:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution


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 Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:42.2 occ:1.00 N B:ASP62 3.1 27.0 1.0 OH B:TYR59 3.6 27.1 1.0 CG B:ASP62 3.7 33.7 1.0 CA B:ALA61 3.7 21.9 1.0 O B:HOH355 3.8 29.0 1.0 OD1 B:ASP62 3.8 34.1 1.0 CB B:ASP62 3.9 31.3 1.0 C B:ALA61 3.9 24.2 1.0 OD2 B:ASP62 4.0 36.4 1.0 CA B:ASP62 4.1 29.4 1.0 CB B:ALA61 4.2 21.8 1.0 CZ B:TYR59 4.5 25.5 1.0 CE2 B:TYR59 4.6 23.9 1.0 NZ B:LYS65 4.7 39.0 1.0 O B:LEU60 4.9 21.6 1.0 N B:ALA61 5.0 20.9 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution


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 Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:32.7 occ:1.00 NE B:ARG47 3.0 16.1 1.0 NH1 B:ARG47 3.4 19.3 1.0 CZ B:ARG47 3.7 17.6 1.0 C B:VAL48 3.7 17.5 1.0 CD2 B:TYR59 3.7 22.4 1.0 O B:ARG47 3.8 18.9 1.0 CE2 B:TYR59 3.8 23.9 1.0 N B:ALA61 3.8 20.9 1.0 CB B:ALA61 3.8 21.8 1.0 C B:ARG47 3.9 17.5 1.0 N B:ALA49 3.9 16.5 1.0 CB B:ARG47 3.9 16.0 1.0 CG B:ARG47 4.0 15.6 1.0 O B:VAL48 4.0 17.6 1.0 O B:HOH343 4.0 37.4 1.0 CA B:ALA61 4.0 21.9 1.0 CA B:VAL48 4.0 17.5 1.0 CD B:ARG47 4.1 15.6 1.0 N B:VAL48 4.1 16.8 1.0 CA B:ALA49 4.4 16.4 1.0 C B:LEU60 4.5 21.0 1.0 CA B:ARG47 4.6 16.4 1.0 CG2 B:THR110 4.7 21.9 1.0 C B:ALA49 4.7 15.4 1.0 O B:TYR59 4.9 17.3 1.0 O B:ALA49 5.0 14.4 1.0 NH2 B:ARG47 5.0 16.3 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution


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 Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl204 b:60.3 occ:1.00 NA B:NA201 2.4 52.3 1.0 N B:ASN74 3.5 31.5 1.0 CA B:ASN73 3.9 27.2 1.0 CG B:ASN74 4.0 38.9 1.0 CB B:ASN73 4.1 27.9 1.0 ND2 B:ASN74 4.1 42.4 1.0 C B:ASN73 4.2 28.4 1.0 CB B:ASN74 4.2 36.9 1.0 OD1 B:ASN74 4.3 40.7 1.0 CA B:ASN74 4.4 33.0 1.0 O B:HOH367 5.0 25.7 1.0 O B:GLN72 5.0 24.1 1.0

F.Zhang, H.Wei, X.Wang, Y.Bai, P.Wang, J.Wu, X.Jiang, Y.Wang, H.Cai, T.Xu, A.Zhou. Structural Basis of A Novel Pd-L1 Nanobody For Immune Checkpoint Blockade. Cell Discov V. 3 17004 2017.
ISSN: ESSN 2056-5968
PubMed: 28280600
DOI: 10.1038/CELLDISC.2017.4