Chlorine in PDB 3ap9: Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III

The structure of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III, PDB code: 3ap9 was solved by T.Matsuzaka, H.Ideo, K.Yamashita, T.Nonaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.98 / 1.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.419, 49.952, 70.207, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.8

The binding sites of Chlorine atom in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III (pdb code 3ap9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III, PDB code: 3ap9:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III


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 Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl161 b:13.4 occ:1.00 O A:HOH363 3.0 19.2 1.0 NH1 A:ARG59 3.1 14.9 1.0 NE1 A:TRP86 3.2 8.9 1.0 O A:HOH200 3.3 34.8 1.0 NH2 A:ARG59 3.3 13.7 1.0 CZ A:ARG59 3.7 14.6 1.0 C1 A:NAG157 3.7 9.0 1.0 C5 A:NAG157 3.9 8.2 1.0 C3 A:NAG157 3.9 10.3 1.0 CE2 A:TRP86 4.1 8.8 1.0 CZ2 A:TRP86 4.2 9.2 1.0 O5 A:NAG157 4.3 7.6 1.0 C2 A:NAG157 4.3 9.7 1.0 CD1 A:TRP86 4.3 9.3 1.0 C4 A:NAG157 4.3 8.5 1.0 N2 A:NAG157 4.4 11.2 1.0 O4 A:NAG157 4.5 8.1 1.0 O5 A:FUC156 4.5 14.1 1.0 C3 A:GAL158 4.5 8.6 1.0 O3 A:GAL158 4.7 8.4 1.0 O A:HOH209 4.7 36.2 1.0 C6 A:FUC156 4.8 18.9 1.0 C6 A:NAG157 4.9 6.9 1.0 NE A:ARG59 5.0 14.1 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III


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 Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl162 b:17.7 occ:1.00 O A:HOH450 3.0 11.8 0.5 NZ A:LYS113 3.0 17.7 1.0 N A:ASP112 3.1 10.7 1.0 CB A:ASP112 3.6 11.5 1.0 N A:LYS111 3.6 11.0 1.0 CB A:LEU110 3.7 9.6 1.0 O A:HOH450 3.7 12.6 0.3 CA A:ASP112 3.8 10.9 1.0 N A:LYS113 4.0 8.5 1.0 CG A:LYS113 4.0 9.5 1.0 C A:LYS111 4.1 11.0 1.0 CA A:LYS111 4.1 11.6 1.0 CG A:ASP112 4.2 14.1 1.0 CE A:LYS113 4.2 13.8 1.0 CB A:LYS111 4.2 12.2 1.0 C A:LEU110 4.2 10.5 1.0 C A:ASP112 4.3 9.6 1.0 OD2 A:ASP112 4.4 19.6 1.0 CD A:LYS113 4.4 11.9 1.0 O A:HOH220 4.5 6.8 0.7 CD1 A:LEU110 4.6 11.5 1.0 CA A:LEU110 4.6 9.7 1.0 CG A:LEU110 4.7 9.6 1.0 O A:HOH220 4.8 11.3 0.3 OD1 A:ASP112 4.9 17.0 1.0 CB A:LYS113 4.9 8.5 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III


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 Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Lacto-N-Fucopentaose III within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl163 b:18.1 occ:1.00 O6 A:GAL155 3.1 13.2 1.0 N A:GLY142 3.2 7.3 1.0 O A:HOH194 3.3 33.7 1.0 O A:HOH446 3.4 29.9 1.0 O A:HOH250 3.5 13.2 0.3 CB A:PRO18 3.7 10.2 1.0 CA A:TYR141 3.9 6.6 1.0 C6 A:GAL155 3.9 11.9 1.0 CB A:TYR141 4.0 7.1 1.0 CD A:PRO18 4.0 10.6 1.0 C A:TYR141 4.0 6.9 1.0 CG A:PRO18 4.1 11.3 1.0 CA A:GLY142 4.1 8.1 1.0 CA A:PRO18 4.1 9.9 1.0 N A:PRO18 4.2 10.3 1.0 CD1 A:TYR141 4.4 8.0 1.0 CG2 A:ILE17 4.4 11.0 1.0 O A:HOH236 4.6 9.7 0.5 O A:GLY142 4.6 8.8 1.0 CG A:TYR141 4.7 7.3 1.0 C A:GLY142 4.8 8.4 1.0 C A:ILE17 4.9 10.5 1.0

H.Ideo, T.Matsuzaka, T.Nonaka, A.Seko, K.Yamashita. Galectin-8-N-Domain Recognition Mechanism For Sialylated and Sulfated Glycans J.Biol.Chem. V. 286 11346 2011.
ISSN: ISSN 0021-9258
PubMed: 21288902
DOI: 10.1074/JBC.M110.195925