Chlorine in PDB 5nmt: Dimer Structure of Sortilin Ectodomain Crystal Form 1, 2.3A

The structure of Dimer Structure of Sortilin Ectodomain Crystal Form 1, 2.3A, PDB code: 5nmt was solved by N.O.L.Leloup, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.64 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.020, 131.130, 154.630, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.4

The binding sites of Chlorine atom in the Dimer Structure of Sortilin Ectodomain Crystal Form 1, 2.3A (pdb code 5nmt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Dimer Structure of Sortilin Ectodomain Crystal Form 1, 2.3A, PDB code: 5nmt:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Dimer Structure of Sortilin Ectodomain Crystal Form 1, 2.3A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dimer Structure of Sortilin Ectodomain Crystal Form 1, 2.3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl808 b:76.8 occ:1.00 OD1 A:ASN512 3.3 40.1 1.0 N A:ASN512 3.6 40.8 1.0 CA A:ILE511 3.7 39.6 1.0 O A:PRO510 4.0 36.4 1.0 CB A:ILE511 4.1 41.4 1.0 C A:ILE511 4.1 42.2 1.0 CG2 A:ILE511 4.2 39.6 1.0 NH2 A:ARG509 4.3 47.4 1.0 CG A:ASN512 4.4 42.4 1.0 CG2 A:VAL513 4.4 36.8 1.0 CZ A:ARG509 4.4 49.2 1.0 NE A:ARG509 4.4 44.7 1.0 OE1 A:GLU505 4.5 45.1 1.0 N A:VAL513 4.6 42.5 1.0 CB A:VAL513 4.6 39.9 1.0 CA A:ASN512 4.7 41.6 1.0 N A:ILE511 4.7 37.9 1.0 C A:PRO510 4.8 39.3 1.0 C A:ASN512 4.9 43.2 1.0

Chlorine binding site 2 out of 2 in the Dimer Structure of Sortilin Ectodomain Crystal Form 1, 2.3A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dimer Structure of Sortilin Ectodomain Crystal Form 1, 2.3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl809 b:79.0 occ:1.00 O A:HOH983 2.7 63.7 1.0 O A:HOH903 3.3 64.6 1.0 OE1 A:GLN300 3.4 65.5 1.0 NE2 A:GLN300 3.9 58.8 1.0 CD A:GLN300 4.0 61.2 1.0 CB A:LEU280 4.0 54.9 1.0 C A:PHE279 4.0 50.5 1.0 O A:PHE279 4.0 49.6 1.0 N A:LEU280 4.1 51.1 1.0 CD A:PRO230 4.3 66.0 1.0 O A:ARG278 4.4 60.2 1.0 CA A:LEU280 4.4 51.6 1.0 CD2 A:LEU275 4.4 62.8 1.0 C A:ARG278 4.4 56.7 1.0 N A:PHE279 4.4 52.8 1.0 CG A:LEU275 4.6 59.9 1.0 CE2 A:PHE235 4.6 57.4 1.0 CZ A:PHE235 4.6 59.0 1.0 CA A:PHE279 4.7 49.9 1.0 CG A:PRO230 4.7 66.0 1.0 O A:GLY277 4.9 57.2 1.0 CD1 A:LEU280 5.0 55.9 1.0

N.Leloup, P.Lossl, D.H.Meijer, M.Brennich, A.J.R.Heck, D.M.E.Thies-Weesie, B.J.C.Janssen. Low pH-Induced Conformational Change and Dimerization of Sortilin Triggers Endocytosed Ligand Release. Nat Commun V. 8 1708 2017.
ISSN: ESSN 2041-1723
PubMed: 29167428
DOI: 10.1038/S41467-017-01485-5