Sodium in PDB 5l74: Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom

The structure of Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom, PDB code: 5l74 was solved by Y.Kong, B.J.C.Janssen, T.Malinauskas, V.R.Vangoor, C.H.Coles, R.Kaufmann, T.Ni, R.J.C.Gilbert, S.Padilla-Parra, R.J.Pasterkamp, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.09 / 1.36
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.710, 44.560, 33.010, 90.00, 104.70, 90.00
R / Rfree (%)	17.5 / 20.3

The structure of Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom (pdb code 5l74). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom, PDB code: 5l74:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:34.8 occ:1.00 O A:HOH1044 2.4 23.3 1.0 O A:HOH1089 2.6 38.1 1.0 ND2 A:ASN679 2.7 11.7 1.0 O A:LYS676 2.7 16.1 1.0 NE1 A:TRP785 3.7 13.4 1.0 C A:LYS676 3.7 13.6 1.0 NE1 A:TRP674 3.8 14.4 1.0 CG A:ASN679 3.8 15.5 1.0 CZ2 A:TRP785 3.8 15.4 1.0 CA A:LYS676 3.9 13.9 1.0 CB A:ASN679 4.0 14.5 1.0 CA A:ASN679 4.0 13.9 1.0 CE2 A:TRP785 4.1 15.1 1.0 CZ2 A:TRP674 4.3 16.7 1.0 O A:HOH1021 4.3 15.0 1.0 CD2 A:PHE789 4.3 11.3 1.0 CB A:PHE789 4.4 10.5 1.0 CE2 A:TRP674 4.4 13.8 1.0 CB A:LYS676 4.5 21.4 1.0 N A:ASN679 4.5 14.8 1.0 O A:HOH1062 4.6 21.2 1.0 CG A:PRO728 4.6 18.6 1.0 CG A:PHE789 4.6 11.1 1.0 O A:CYS675 4.7 15.0 1.0 CD1 A:TRP674 4.9 13.3 1.0 N A:TYR677 4.9 14.8 1.0 CD1 A:TRP785 4.9 12.9 1.0 OD1 A:ASN679 4.9 18.2 1.0

Sodium binding site 2 out of 2 in the Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Plexin A2 Extracellular Segment Domains 4-5 (PSI2-IPT2), Resolution 1.36 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na905 b:17.9 occ:1.00 OD1 A:ASN793 2.8 9.9 1.0 N A:GLN795 2.8 9.6 1.0 O A:LEU704 3.0 15.2 1.0 N A:PRO794 3.2 10.8 1.0 CD A:PRO794 3.2 10.7 1.0 C A:ASN793 3.3 8.8 1.0 CB A:GLN795 3.4 14.0 1.0 CA A:ASN793 3.5 8.4 1.0 CA A:GLN795 3.6 10.1 1.0 C A:LEU704 3.6 9.9 1.0 CG A:ASN793 3.8 8.2 1.0 CG A:PRO794 3.8 12.9 1.0 C A:PRO794 3.8 12.2 1.0 O A:ASN793 3.9 10.0 1.0 CB A:LEU704 3.9 10.3 1.0 CG A:LEU797 3.9 14.0 1.0 CG A:GLN795 3.9 23.7 1.0 CA A:PRO794 4.0 10.4 1.0 CD1 A:LEU797 4.1 11.8 1.0 N A:ASP796 4.1 9.8 1.0 C A:GLN795 4.1 10.2 1.0 CB A:ASN793 4.2 9.3 1.0 CA A:LEU704 4.3 8.6 1.0 N A:VAL705 4.4 10.6 1.0 C A:VAL705 4.6 11.8 1.0 CA A:VAL705 4.6 11.8 1.0 CB A:PRO794 4.6 12.2 1.0 O A:HOH1029 4.6 19.5 1.0 N A:LEU704 4.7 9.3 1.0 N A:ASN793 4.7 8.9 1.0 O A:VAL705 4.7 11.9 1.0 N A:LEU797 4.7 9.2 1.0 CD2 A:LEU797 4.7 14.6 1.0 O A:ASP792 4.9 8.3 1.0 CB A:LEU797 4.9 12.1 1.0 O A:PRO794 5.0 13.4 1.0 ND2 A:ASN793 5.0 11.3 1.0 N A:PRO706 5.0 13.3 1.0

Y.Kong, B.J.Janssen, T.Malinauskas, V.R.Vangoor, C.H.Coles, R.Kaufmann, T.Ni, R.J.Gilbert, S.Padilla-Parra, R.J.Pasterkamp, E.Y.Jones. Structural Basis For Plexin Activation and Regulation. Neuron V. 91 548 2016.
ISSN: ISSN 1097-4199
PubMed: 27397516
DOI: 10.1016/J.NEURON.2016.06.018