Sodium in PDB 5c7g: Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule

The structure of Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule, PDB code: 5c7g was solved by C.Didierjean, C.Jelsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.28 / 1.45
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.280, 62.280, 85.960, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 17.3

The binding sites of Sodium atom in the Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule (pdb code 5c7g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule, PDB code: 5c7g:

Sodium binding site 1 out of 1 in the Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule


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 the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:17.4 occ:1.00 O A:HOH331 2.1 17.6 1.0 O A:HOH432 2.1 18.9 1.0 O A:HOH365 2.1 19.2 1.0 HO6 A:BCN201 2.1 21.4 1.0 O A:HOH396 2.1 18.5 1.0 O6 A:BCN201 2.1 17.8 1.0 O A:HOH496 2.1 19.6 1.0 H62 A:BCN201 3.1 20.6 1.0 C6 A:BCN201 3.2 17.2 1.0 HH A:TYR81 3.7 20.9 1.0 HE1 A:TYR81 3.8 20.1 1.0 H51 A:BCN201 3.8 23.0 1.0 H61 A:BCN201 3.9 20.6 1.0 C5 A:BCN201 4.1 19.2 1.0 O A:HOH470 4.2 22.6 1.0 O4 A:BCN201 4.2 19.8 1.0 OD2 A:ASP48 4.3 20.0 1.0 O A:HOH306 4.3 27.6 1.0 H42 A:BCN201 4.3 26.3 1.0 O A:HOH440 4.3 17.3 1.0 HA3 A:GLY142 4.4 20.9 1.0 O A:THR141 4.5 18.3 1.0 OH A:TYR81 4.5 17.4 1.0 CE1 A:TYR81 4.6 16.8 1.0 HE2 A:LYS79 4.7 26.1 1.0 N1 A:BCN201 4.7 16.7 1.0 HO4 A:BCN201 4.8 23.7 1.0 C4 A:BCN201 4.8 21.9 1.0 H52 A:BCN201 4.9 23.0 1.0

M.Richard, N.Pelligrini Moise, C.Jelsch, B.Maigret, C.Didierjean, X.Manival, C.Charron. Design, Synthesis and Biological Evaluation of New Peptidomimetic Compounds Targeting Nrp-1 Receptor to Be Published To Be Published.