Sodium in PDB 7p3i: Crystal Structure of Human CD40/TNFRSF5 in Complex with the Anti-CD40 Darpin Protein

The structure of Crystal Structure of Human CD40/TNFRSF5 in Complex with the Anti-CD40 Darpin Protein, PDB code: 7p3i was solved by F.Malvezzi, S.Mangold, T.Hospodarsch, C.Reichen, C.Iss, A.Lammens, S.Krapp, C.Domke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.61 / 2.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	193.67, 59.564, 81.842, 90, 106.99, 90
R / Rfree (%)	22 / 25.3

The binding sites of Sodium atom in the Crystal Structure of Human CD40/TNFRSF5 in Complex with the Anti-CD40 Darpin Protein (pdb code 7p3i). 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 Human CD40/TNFRSF5 in Complex with the Anti-CD40 Darpin Protein, PDB code: 7p3i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human CD40/TNFRSF5 in Complex with the Anti-CD40 Darpin Protein


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 Human CD40/TNFRSF5 in Complex with the Anti-CD40 Darpin Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:58.2 occ:1.00 O A:HOH332 2.3 56.0 1.0 OG A:SER152 2.5 50.9 1.0 O A:PHE129 2.5 54.9 1.0 O A:VAL154 2.5 57.6 1.0 O A:CYS125 2.7 53.5 1.0 O A:SER126 3.0 54.3 1.0 CB A:SER152 3.6 51.7 1.0 C A:CYS125 3.6 53.2 1.0 C A:VAL154 3.6 57.8 1.0 C A:PHE129 3.7 53.4 1.0 C A:SER126 3.7 56.4 1.0 CB A:CYS125 4.0 54.8 1.0 N A:SER156 4.1 55.1 1.0 CG2 A:VAL154 4.3 56.4 1.0 N A:PRO127 4.3 55.4 1.0 N A:SER126 4.4 53.3 1.0 CA A:CYS125 4.4 54.9 1.0 CA A:PRO127 4.4 53.8 1.0 CA A:GLY130 4.4 57.8 1.0 N A:VAL154 4.4 58.8 1.0 CA A:SER155 4.5 59.6 1.0 N A:SER155 4.5 61.4 1.0 N A:GLY130 4.5 56.1 1.0 CA A:SER126 4.5 53.2 1.0 CA A:VAL154 4.5 58.5 1.0 O A:SER156 4.5 56.6 1.0 N A:PHE129 4.6 54.4 1.0 CA A:PHE129 4.7 52.8 1.0 O A:GLU159 4.7 58.1 1.0 CA A:SER152 4.7 51.3 1.0 O A:SER152 4.8 51.3 1.0 C A:SER155 4.8 58.2 1.0 C A:SER152 4.8 52.1 1.0 CB A:SER156 4.9 56.5 1.0 CA A:SER156 5.0 56.0 1.0 CB A:VAL154 5.0 58.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human CD40/TNFRSF5 in Complex with the Anti-CD40 Darpin Protein


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 Human CD40/TNFRSF5 in Complex with the Anti-CD40 Darpin Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:51.2 occ:1.00 O C:HOH318 2.3 50.2 1.0 OG C:SER152 2.4 53.4 1.0 O C:VAL154 2.5 56.0 1.0 O C:PHE129 2.5 41.0 1.0 O C:CYS125 2.7 46.0 1.0 O C:SER126 2.9 47.8 1.0 CB C:SER152 3.5 49.6 1.0 C C:CYS125 3.6 44.6 1.0 C C:VAL154 3.6 52.3 1.0 C C:SER126 3.7 47.0 1.0 C C:PHE129 3.7 40.9 1.0 CB C:CYS125 4.0 42.4 1.0 N C:SER156 4.2 49.0 1.0 N C:PRO127 4.3 45.3 1.0 N C:SER126 4.4 46.2 1.0 CA C:PRO127 4.4 45.1 1.0 CA C:CYS125 4.4 41.3 1.0 CG2 C:VAL154 4.5 54.9 1.0 N C:SER155 4.5 55.5 1.0 CA C:SER126 4.5 46.5 1.0 CA C:SER155 4.5 49.8 1.0 N C:VAL154 4.5 52.4 1.0 CA C:GLY130 4.5 42.8 1.0 N C:PHE129 4.5 42.4 1.0 O C:HOH301 4.5 57.2 1.0 O C:SER156 4.5 47.3 1.0 N C:GLY130 4.5 41.8 1.0 CA C:VAL154 4.6 53.6 1.0 CA C:PHE129 4.7 40.2 1.0 O C:GLU159 4.7 49.1 1.0 CA C:SER152 4.7 51.4 1.0 C C:SER155 4.8 50.3 1.0 O C:SER152 4.8 49.0 1.0 C C:SER152 4.8 51.3 1.0 CB C:SER156 4.9 51.3 1.0 CA C:SER156 5.0 49.6 1.0

N.Rigamonti, N.Veitonmaki, C.Domke, S.Barsin, S.Jetzer, O.Abdelmotaleb, R.Bessey, T.Lekishvili, F.Malvezzi, M.Gachechiladze, M.Behe, V.Levitsky, P.A.Trail. A Multispecific Anti-CD40 Darpin Construct Induces Tumor-Selective CD40 Activation and Tumor Regression. Cancer Immunol Res V. 10 626 2022.
ISSN: ISSN 2326-6074
PubMed: 35319751
DOI: 10.1158/2326-6066.CIR-21-0553