Chlorine in PDB 5o0o: Deglycosylated Nogo Receptor with Native Disulfide Structure 5

The structure of Deglycosylated Nogo Receptor with Native Disulfide Structure 5, PDB code: 5o0o was solved by M.F.Pronker, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.39 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	168.490, 168.490, 256.180, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 94;

Binding sites:

The binding sites of Chlorine atom in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5 (pdb code 5o0o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 94 binding sites of Chlorine where determined in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5, PDB code: 5o0o:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:52.2 occ:1.00 NE2 A:GLN162 3.3 34.4 1.0 NH2 A:ARG139 3.5 67.5 1.0 O A:HOH716 3.5 51.6 1.0 CE1 A:HIS186 3.5 53.1 1.0 NH1 A:ARG139 3.7 51.5 1.0 CG A:GLN162 4.1 30.9 1.0 CZ A:ARG139 4.1 61.3 1.0 CD A:GLN162 4.2 30.5 1.0 NE2 A:HIS186 4.4 55.4 1.0 OD2 A:ASP163 4.5 50.8 1.0 O A:HOH727 4.5 57.9 1.0 ND1 A:HIS186 4.5 48.2 1.0 O A:HOH667 4.5 49.0 1.0

Chlorine binding site 2 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:45.5 occ:1.00 CB A:ASN258 3.2 45.5 1.0 O A:HOH719 3.3 44.9 1.0 CD A:ARG256 3.3 39.9 1.0 NH1 A:ARG256 3.4 47.0 1.0 N A:ASN258 3.4 24.8 1.0 CB A:PHE234 3.5 26.7 1.0 CB A:SER283 3.6 34.9 1.0 OG A:SER283 3.6 31.1 1.0 CB A:ARG256 3.8 30.6 1.0 CA A:ASN258 3.9 36.6 1.0 CG A:PHE234 3.9 33.3 1.0 N A:LEU257 4.0 27.6 1.0 CD2 A:PHE234 4.1 35.1 1.0 CG A:ARG256 4.1 36.1 1.0 NE A:ARG256 4.2 43.0 1.0 CA A:ARG256 4.2 29.8 1.0 CZ A:ARG256 4.2 48.9 1.0 C A:ARG256 4.3 25.6 1.0 CG A:ASN258 4.4 60.2 1.0 C A:LEU257 4.6 27.3 1.0 C A:ASN258 4.6 38.0 1.0 CD1 A:PHE234 4.7 31.6 1.0 ND2 A:ASN258 4.7 63.1 1.0 O A:ASN258 4.7 40.2 1.0 O A:HOH680 4.7 31.7 1.0 CA A:LEU257 4.9 27.6 1.0 CA A:PHE234 4.9 28.7 1.0 CE2 A:PHE234 5.0 33.2 1.0

Chlorine binding site 3 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl409 b:50.0 occ:1.00 NH1 A:ARG267 3.2 28.1 1.0 N A:ALA312 3.3 84.1 1.0 CB A:ALA312 3.4 92.8 1.0 NH2 A:ARG267 3.6 26.7 1.0 CD2 A:LEU332 3.6 39.4 1.0 CA A:ALA312 3.8 94.6 1.0 CZ A:ARG267 3.9 29.4 1.0 C A:VAL311 4.3 67.0 1.0 CA A:VAL311 4.3 55.2 1.0 O A:ALA310 4.4 47.3 1.0 CD A:PRO333 4.6 32.2 1.0 CG1 A:VAL311 4.8 54.7 1.0 CG A:LEU332 4.9 34.8 1.0

Chlorine binding site 4 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl410 b:48.3 occ:1.00 NH1 A:ARG68 3.0 55.6 1.0 NE2 A:GLN49 3.4 50.2 1.0 CD A:ARG68 3.4 49.1 1.0 CZ A:ARG68 4.0 50.7 1.0 CB A:ARG68 4.1 41.0 1.0 CG A:ARG68 4.1 43.7 1.0 NE A:ARG68 4.1 51.7 1.0 O A:HOH585 4.2 42.2 1.0 OE1 A:GLN49 4.3 46.7 1.0 CD A:GLN49 4.3 51.7 1.0 O A:HOH733 4.7 44.6 1.0

Chlorine binding site 5 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl411 b:67.1 occ:1.00 OG1 A:THR84 3.0 54.0 1.0 NH1 A:ARG61 3.0 54.1 1.0 CD A:ARG61 3.5 47.8 1.0 CD1 A:ILE85 3.8 30.4 1.0 O A:HOH586 4.0 35.0 1.0 CG A:LYS38 4.0 44.7 1.0 CG1 A:ILE85 4.1 29.7 1.0 CZ A:ARG61 4.1 61.3 1.0 CB A:THR84 4.1 44.1 1.0 CG A:ARG61 4.2 45.6 1.0 NE A:ARG61 4.3 57.2 1.0 CD A:LYS38 4.5 45.6 1.0 CE A:LYS38 4.5 48.6 1.0 CB A:LYS38 4.7 40.3 1.0 CG2 A:THR84 4.7 38.4 1.0

Chlorine binding site 6 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl412 b:50.1 occ:1.00 N A:ARG279 3.0 28.9 1.0 O H:HOH564 3.1 34.0 1.0 O2 A:GOL405 3.4 69.8 1.0 CB A:ARG279 3.5 48.8 1.0 CZ A:ARG279 3.5 83.3 1.0 NH2 A:ARG279 3.6 81.4 1.0 NH1 D:ARG279 3.6 73.2 1.0 NE A:ARG279 3.6 82.1 1.0 CA A:PHE278 3.8 25.0 1.0 CA A:ARG279 3.8 39.5 1.0 CG A:ARG279 3.8 64.5 1.0 C A:PHE278 3.9 27.2 1.0 CD1 A:PHE278 3.9 27.5 1.0 NH1 A:ARG279 4.1 85.2 1.0 O A:LYS277 4.1 27.1 1.0 CE H:LYS277 4.2 38.3 1.0 CD A:ARG279 4.3 78.1 1.0 NZ H:LYS277 4.4 41.7 1.0 CZ D:ARG279 4.5 77.6 1.0 CE1 A:PHE278 4.6 25.9 1.0 N A:GLY280 4.6 30.6 1.0 C1 A:GOL405 4.6 55.4 1.0 C2 A:GOL405 4.6 64.7 1.0 C A:ARG279 4.7 38.3 1.0 N A:PHE278 4.7 22.0 1.0 CG A:PHE278 4.7 30.4 1.0 C A:LYS277 4.8 23.8 1.0 O A:HOH522 4.8 31.2 1.0 CB A:PHE278 4.8 26.6 1.0 NE D:ARG279 4.9 76.0 1.0

Chlorine binding site 7 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl413 b:52.5 occ:1.00 N A:ASP297 3.2 36.5 1.0 NE A:ARG296 3.3 52.0 1.0 CD A:ARG296 3.8 50.5 1.0 CA A:ARG296 3.8 48.9 1.0 CD A:ARG300 4.0 62.4 1.0 CB A:ASP297 4.0 42.9 1.0 C A:ARG296 4.0 44.4 1.0 CB A:ARG300 4.0 38.2 1.0 CB A:ARG296 4.0 44.9 1.0 CA A:ASP297 4.1 39.6 1.0 O A:ASP297 4.2 42.2 1.0 CZ A:ARG296 4.4 52.0 1.0 CG A:ARG300 4.5 45.6 1.0 CG A:ARG296 4.5 49.1 1.0 NH2 A:ARG296 4.6 51.5 1.0 C A:ASP297 4.6 39.0 1.0

Chlorine binding site 8 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl414 b:57.3 occ:1.00 O A:HOH682 2.9 27.7 1.0 NE2 D:HIS65 3.1 24.8 1.0 N A:ASP326 3.2 31.2 1.0 CB A:THR325 3.4 43.5 1.0 CA A:THR325 3.6 38.7 1.0 CE1 D:HIS65 3.8 30.4 1.0 C A:THR325 3.9 34.6 1.0 OD1 A:ASP326 3.9 43.6 1.0 CB A:ASP326 4.0 34.8 1.0 CA A:ASP326 4.2 32.9 1.0 CG2 A:THR325 4.2 46.4 1.0 CG A:ASP326 4.2 36.6 1.0 CD2 D:HIS65 4.3 24.2 1.0 CG D:PRO44 4.3 28.8 1.0 OG1 A:THR325 4.5 41.3 1.0 NE2 D:GLN45 4.6 55.6 1.0 CB D:PRO44 4.6 31.4 1.0 N A:GLU327 4.9 30.3 1.0 N A:THR325 4.9 42.3 1.0

Chlorine binding site 9 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl415 b:68.5 occ:1.00 ND1 A:HIS196 3.1 45.2 1.0 O A:HOH538 3.2 35.7 1.0 CB A:ARG199 3.4 30.6 1.0 CA A:ARG199 3.8 27.0 1.0 CD A:ARG199 3.8 47.8 1.0 CE1 A:HIS196 3.9 46.3 1.0 CG A:ARG199 4.0 40.0 1.0 OD2 A:ASP224 4.1 38.9 1.0 O A:GLU195 4.2 32.1 1.0 CG A:HIS196 4.2 40.7 1.0 NE A:ARG199 4.3 50.2 1.0 CA A:HIS196 4.3 28.8 1.0 NH1 A:ARG199 4.4 48.3 1.0 N A:ARG199 4.4 26.2 1.0 CG A:ASP224 4.5 38.3 1.0 CB A:HIS196 4.5 34.6 1.0 CZ A:ARG199 4.6 51.0 1.0 CD A:ARG223 4.6 60.0 1.0 O A:HOH611 4.6 28.0 1.0 OD1 A:ASP224 4.6 33.5 1.0 CB A:ARG223 4.7 28.4 1.0 CG A:ARG223 4.9 41.8 1.0 O A:HIS220 5.0 26.5 1.0

Chlorine binding site 10 out of 94 in the Deglycosylated Nogo Receptor with Native Disulfide Structure 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Deglycosylated Nogo Receptor with Native Disulfide Structure 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl416 b:89.4 occ:1.00 NE A:ARG300 3.8 77.5 1.0 CG A:ARG300 3.8 45.6 1.0 CE A:LYS299 3.8 49.4 1.0 CZ A:ARG300 3.9 86.1 1.0 NH2 A:ARG300 4.0 89.9 1.0 O A:HOH692 4.0 52.0 1.0 CB A:LYS299 4.2 41.5 1.0 CD A:ARG300 4.4 62.4 1.0 NH1 A:ARG300 4.5 88.2 1.0 NZ A:LYS299 4.5 51.3 1.0 OD2 A:ASP297 4.8 56.3 1.0 C A:LYS299 4.9 39.0 1.0 CD A:LYS299 4.9 44.2 1.0 O A:LYS299 4.9 44.0 1.0 O A:HOH542 5.0 50.1 1.0

M.F.Pronker, R.P.Tas, H.C.Vlieg, B.J.C.Janssen. Nogo Receptor Crystal Structures with A Native Disulfide Pattern Suggest A Novel Mode of Self-Interaction. Acta Crystallogr D Struct V. 73 860 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 29095159
DOI: 10.1107/S2059798317013791