Chlorine in PDB 5kc9: Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)

The structure of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1), PDB code: 5kc9 was solved by J.Elegheert, J.E.Clay, C.Siebold, A.R.Aricescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.22 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.420, 128.420, 153.230, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 22.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) (pdb code 5kc9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 14 binding sites of Chlorine where determined in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1), PDB code: 5kc9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl515 b:93.2 occ:1.00 OH A:TYR220 3.4 61.5 1.0 CG1 A:VAL204 3.8 51.8 1.0 OE1 A:GLN195 3.8 60.2 1.0 CE1 A:PHE168 3.9 43.1 1.0 NH1 B:ARG187 4.4 0.9 1.0 CD1 A:PHE168 4.6 41.2 1.0 CD2 A:LEU208 4.6 54.7 1.0 CZ A:TYR220 4.6 61.2 1.0 O A:LYS196 4.6 44.2 1.0 NH2 B:ARG187 4.7 0.2 1.0 CZ A:PHE168 4.8 44.2 1.0 CD A:GLN195 4.9 57.5 1.0 CZ B:ARG187 4.9 0.3 1.0 CD1 A:LEU208 4.9 57.1 1.0 CB A:GLN195 4.9 50.7 1.0

Chlorine binding site 2 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl516 b:96.4 occ:1.00 O A:HOH608 3.5 58.1 1.0 CB A:ASP170 3.7 48.1 1.0 O A:ASP198 3.8 55.4 1.0 O A:VAL197 4.1 42.6 1.0 CA A:LYS199 4.2 63.1 1.0 CD1 A:ILE201 4.3 62.8 1.0 O A:LYS199 4.4 55.7 1.0 C A:ASP198 4.4 56.7 1.0 CA A:ASP170 4.5 47.2 1.0 CG1 A:VAL197 4.6 52.1 1.0 N A:LYS199 4.7 58.2 1.0 CA A:GLY235 4.7 45.0 1.0 C A:LYS199 4.7 56.3 1.0 N A:SER171 4.8 51.3 1.0 CG A:ASP170 4.8 50.6 1.0 CG1 A:ILE201 4.9 61.5 1.0 C A:VAL197 4.9 45.5 1.0 OD2 A:ASP170 4.9 50.9 1.0 OG A:SER171 5.0 62.2 1.0

Chlorine binding site 3 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl517 b:90.7 occ:1.00 O A:HOH606 3.6 46.5 1.0 O A:ASP222 3.9 46.1 1.0 O A:LYS164 4.0 55.3 1.0 CD A:ARG226 4.0 79.5 1.0 CG A:ARG226 4.2 67.5 1.0 O A:THR223 4.3 49.6 1.0 CB A:ARG226 4.3 55.7 1.0 NH2 A:ARG225 4.4 50.9 1.0 CA A:THR223 4.5 49.2 1.0 N A:ARG226 4.6 43.9 1.0 C A:THR223 4.7 47.3 1.0 CB A:LYS164 4.8 67.8 1.0 C A:LYS164 4.8 56.0 1.0 C A:ASP222 4.9 47.7 1.0 NE A:ARG225 4.9 50.7 1.0 CB A:ARG225 4.9 51.7 1.0 NE A:ARG226 4.9 87.6 1.0 CZ A:ARG225 5.0 50.0 1.0

Chlorine binding site 4 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl518 b:0.4 occ:1.00 O A:LEU316 3.4 58.5 1.0 O A:LEU313 3.7 80.7 1.0 CD1 A:LEU321 3.8 53.0 1.0 O1 A:EDO511 3.9 0.3 1.0 C1 A:EDO511 4.2 98.5 1.0 C A:LEU316 4.3 57.9 1.0 CG A:LEU321 4.4 50.2 1.0 C A:GLN317 4.7 51.3 1.0 CD2 A:LEU321 4.7 49.9 1.0 N A:ILE318 4.7 48.6 1.0 C A:LEU313 4.8 80.1 1.0 CG1 A:ILE318 4.9 46.3 1.0 O A:GLN317 4.9 50.1 1.0 CE2 A:PHE285 4.9 49.2 1.0 CA A:ILE318 4.9 46.9 1.0

Chlorine binding site 5 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl519 b:0.1 occ:1.00 O A:SER417 4.1 53.5 1.0 CZ2 A:TRP415 4.1 52.4 1.0 O A:HOH602 4.1 61.4 1.0 CA A:GLY420 4.1 60.9 1.0 N A:GLY420 4.1 62.8 1.0 O A:ASP416 4.2 53.5 1.0 C A:SER417 4.3 53.7 1.0 O A:GLU418 4.6 65.1 1.0 CH2 A:TRP415 4.6 52.6 1.0 CA A:SER417 4.7 53.0 1.0 C A:LYS419 4.8 65.4 1.0 C A:GLU418 4.8 63.7 1.0 CE2 A:TRP415 4.8 52.1 1.0 NH2 A:ARG148 4.9 55.0 1.0 N A:GLU418 4.9 55.7 1.0

Chlorine binding site 6 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl510 b:87.8 occ:1.00 CB B:ASN100 4.2 55.4 1.0 CG B:ASN100 4.2 58.0 1.0 O B:HOH630 4.3 73.7 1.0 CA B:ALA97 4.5 43.5 1.0 CG A:ASN100 4.5 52.3 1.0 CB A:ASN100 4.5 49.7 1.0 OD1 B:ASN100 4.5 58.4 1.0 ND2 B:ASN100 4.5 58.9 1.0 O B:CYS96 4.6 45.5 1.0 OD1 A:ASN100 4.7 53.1 1.0 ND2 A:ASN100 4.8 53.8 1.0 CA A:ALA97 4.8 47.5 1.0 O B:HOH607 4.8 59.4 1.0 N B:ALA97 5.0 43.4 1.0

Chlorine binding site 7 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl511 b:86.8 occ:1.00 N B:SER180 3.3 49.2 1.0 OG B:SER180 3.3 61.4 1.0 O B:GLY177 3.5 47.6 1.0 ND2 B:ASN150 3.5 52.4 1.0 CB B:SER180 3.7 57.1 1.0 CB B:GLN179 3.8 59.2 1.0 N B:GLN179 3.9 50.3 1.0 CA B:SER180 4.1 52.8 1.0 CA B:GLN179 4.1 52.0 1.0 C B:GLN179 4.2 48.8 1.0 C B:GLY177 4.2 47.0 1.0 OE1 B:GLN179 4.4 84.2 1.0 O B:ARG176 4.5 48.2 1.0 CD B:GLN179 4.5 82.2 1.0 C B:LEU178 4.6 51.4 1.0 CG B:GLN179 4.7 70.1 1.0 CA B:GLY177 4.8 47.8 1.0 CG B:ASN150 4.8 51.3 1.0 N B:LEU178 4.9 46.4 1.0 O B:HOH625 4.9 50.9 1.0

Chlorine binding site 8 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl512 b:0.7 occ:1.00 O B:ALA69 3.5 50.9 1.0 O A:PRO132 3.9 55.2 1.0 OE1 B:GLU68 3.9 73.3 1.0 O B:ASN70 4.0 53.3 1.0 O B:HOH652 4.2 64.2 1.0 O A:HOH626 4.4 52.5 1.0 C B:ASN70 4.5 52.6 1.0 ND2 B:ASN71 4.5 52.0 1.0 O A:HOH629 4.6 47.6 1.0 CB B:ASN71 4.6 51.8 1.0 C B:ALA69 4.7 51.9 1.0 CB B:ASN70 4.7 57.0 1.0 CB B:GLU68 4.7 59.7 1.0 C A:PRO132 4.8 54.4 1.0 CG B:ASN71 4.9 50.8 1.0 CD B:GLU68 4.9 74.0 1.0 N B:ASN71 5.0 52.0 1.0

Chlorine binding site 9 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl513 b:0.1 occ:1.00 OH B:TYR220 3.4 72.2 1.0 NE2 B:GLN195 3.9 62.1 1.0 O B:HOH647 3.9 81.4 1.0 CG1 B:VAL204 3.9 95.6 1.0 CD1 B:LEU208 4.1 0.9 1.0 CD2 B:LEU208 4.3 0.8 1.0 CZ B:TYR220 4.4 73.0 1.0 CE1 B:PHE168 4.5 50.4 1.0 CG B:LEU208 4.5 0.4 1.0 O B:VAL204 4.9 0.2 1.0 O B:LYS196 4.9 58.2 1.0 CE1 B:PHE205 5.0 0.3 1.0

Chlorine binding site 10 out of 14 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-1 (GLUD1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl507 b:90.4 occ:1.00 N C:TYR62 3.3 63.4 1.0 O C:TYR62 3.4 63.2 1.0 CD2 C:TYR62 3.8 69.3 1.0 CE2 C:TYR62 3.9 69.4 1.0 CA C:THR61 3.9 71.1 1.0 CG C:TYR62 3.9 67.0 1.0 CZ C:TYR62 4.0 67.7 1.0 C C:THR61 4.1 66.8 1.0 CD1 C:TYR62 4.1 69.1 1.0 CB C:THR61 4.1 70.9 1.0 CE1 C:TYR62 4.1 69.2 1.0 CA C:TYR62 4.2 61.1 1.0 C C:TYR62 4.2 61.0 1.0 CB C:TYR62 4.7 62.2 1.0 CG2 C:THR61 4.7 71.0 1.0 OH C:TYR62 4.7 63.7 1.0 O C:ILE60 5.0 76.5 1.0

J.Elegheert, W.Kakegawa, J.E.Clay, N.F.Shanks, E.Behiels, K.Matsuda, K.Kohda, E.Miura, M.Rossmann, N.Mitakidis, J.Motohashi, V.T.Chang, C.Siebold, I.H.Greger, T.Nakagawa, M.Yuzaki, A.R.Aricescu. Structural Basis For Integration of Glud Receptors Within Synaptic Organizer Complexes. Science V. 353 295 2016.
ISSN: ESSN 1095-9203
PubMed: 27418511
DOI: 10.1126/SCIENCE.AAE0104