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

Protein crystallography data

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

Other elements in 5jds:

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

Sodium Binding Sites:

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 5jds

Go back to Sodium Binding Sites List in 5jds
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 5jds

Go back to Sodium Binding Sites List in 5jds
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

Reference:

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
Page generated: Mon Oct 7 21:52:18 2024

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