Sodium 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:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Pd-L1 Complexed with A Nanobody at 1.7 Angstron Resolution, PDB code: 5jds:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na201 b:52.3 occ:1.00 CL B:CL204 2.4 60.3 1.0 O B:HOH367 3.0 25.7 1.0 N B:ASN74 3.6 31.5 1.0 CB B:ASN73 3.9 27.9 1.0 CB B:ASN74 3.9 36.9 1.0 ND2 B:ASN74 4.3 42.4 1.0 CG B:ASN74 4.3 38.9 1.0 CA B:ASN74 4.4 33.0 1.0 CA B:ASN73 4.4 27.2 1.0 C B:ASN73 4.5 28.4 1.0 CG B:ASN73 4.8 27.6 1.0 ND2 B:ASN73 4.9 28.8 1.0

Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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 A:Na202 b:35.5 occ:1.00 N A:LEU48 3.7 34.9 1.0 CB A:SER93 3.9 20.3 1.0 CB A:LEU48 4.1 32.5 1.0 CA A:GLN47 4.3 38.9 1.0 OG A:SER93 4.3 22.4 1.0 O A:HOH332 4.3 27.8 1.0 OE1 A:GLN47 4.5 59.9 1.0 C A:GLN47 4.5 35.8 1.0 CA A:LEU48 4.6 33.8 1.0 O A:LYS46 4.6 36.2 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