Iodine in PDB 3apb: Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide

The structure of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide, PDB code: 3apb 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)	38.95 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.591, 75.869, 77.901, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide (pdb code 3apb). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 29 binding sites of Iodine where determined in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide, PDB code: 3apb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I155 b:31.6 occ:1.00 N B:ARG72 3.6 29.8 1.0 NH1 B:ARG99 3.6 23.4 1.0 N A:TRP86 3.7 27.7 1.0 NH2 B:ARG99 3.9 23.4 1.0 CD1 A:TRP86 4.0 24.0 1.0 CA B:LYS71 4.1 29.0 1.0 O B:HOH186 4.1 28.9 1.0 CA A:LYS85 4.2 29.8 1.0 O A:GLU84 4.2 30.8 1.0 CZ B:ARG99 4.2 24.4 1.0 O A:HOH208 4.3 33.1 1.0 CG B:LYS71 4.3 32.7 1.0 C B:LYS71 4.3 29.5 1.0 CG A:LYS85 4.3 34.3 1.0 CB A:TRP86 4.4 26.2 1.0 C A:LYS85 4.5 28.8 1.0 CA B:ARG72 4.5 31.2 1.0 CG A:TRP86 4.6 24.9 1.0 CA A:TRP86 4.7 26.9 1.0 O B:PHE70 4.7 27.3 1.0 CB B:LYS71 4.8 29.4 1.0 CB A:LYS85 4.8 30.6 1.0 O A:HOH188 4.9 28.2 1.0

Iodine binding site 2 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I156 b:36.0 occ:1.00 NE2 A:GLN47 3.4 26.6 1.0 CA A:PHE46 3.8 21.2 1.0 CG A:ARG45 3.8 29.3 1.0 O A:HOH232 3.9 37.8 1.0 C A:PHE46 4.0 21.3 1.0 CA A:GLY142 4.1 24.2 1.0 N A:PHE46 4.1 21.3 1.0 N A:GLN47 4.2 20.9 1.0 O A:ARG45 4.2 20.9 1.0 C A:ARG45 4.2 21.4 1.0 CG A:GLN47 4.3 22.9 1.0 O A:TYR141 4.3 22.5 1.0 CD A:GLN47 4.3 26.2 1.0 ND2 A:ASN67 4.4 21.6 1.0 CB A:GLN47 4.4 21.5 1.0 CB A:ARG45 4.5 23.9 1.0 N A:GLY142 4.5 23.7 1.0 O A:PHE46 4.6 21.4 1.0 C A:TYR141 4.6 22.6 1.0 NE A:ARG45 4.7 41.9 1.0 CD A:ARG45 4.8 36.3 1.0 CA A:GLN47 4.9 21.2 1.0

Iodine binding site 3 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I157 b:44.1 occ:1.00 CA A:PRO15 3.9 28.6 1.0 N A:VAL16 4.0 29.3 1.0 CB A:PRO15 4.1 28.4 1.0 CE1 A:PHE19 4.2 26.9 1.0 CD1 A:PHE19 4.4 26.8 1.0 CG2 A:ILE12 4.5 28.8 1.0 C A:PRO15 4.5 29.3 1.0 O A:HOH244 4.5 43.8 1.0

Iodine binding site 4 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I158 b:47.5 occ:1.00 NH1 A:ARG45 2.9 46.4 1.0 CD A:ARG45 3.7 36.3 1.0 CZ A:ARG45 3.9 45.1 1.0 O A:ASP44 4.0 21.7 1.0 CB A:ASP44 4.2 23.1 1.0 NE A:ARG45 4.2 41.9 1.0 CB A:LYS71 4.3 28.8 1.0 CB A:ARG69 4.3 21.7 1.0 CD A:ARG69 4.5 22.6 1.0 C A:ASP44 4.5 22.2 1.0 NH1 B:ARG45 4.6 37.6 1.0 CG A:ARG69 4.6 20.7 1.0 CB A:ARG45 4.8 23.9 1.0 CG A:ARG45 4.8 29.3 1.0 O B:HOH199 4.8 31.2 1.0 N A:LYS71 4.9 27.5 1.0 O B:HOH206 4.9 33.8 1.0 CA A:ASP44 5.0 23.0 1.0

Iodine binding site 5 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I159 b:58.8 occ:1.00 O A:HOH228 3.2 36.5 1.0 NE2 A:HIS38 3.6 23.2 1.0 OD1 A:ASN145 3.6 29.4 1.0 CE1 A:HIS38 4.0 24.1 1.0 CB A:ASN145 4.5 22.4 1.0 CG A:ASN145 4.5 23.9 1.0 CB A:PRO40 4.5 29.5 1.0 CD2 A:HIS38 4.8 22.9 1.0

Iodine binding site 6 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I160 b:63.1 occ:1.00 N A:GLY142 3.6 23.7 1.0 CD A:PRO18 3.6 29.6 1.0 CG A:PRO18 3.7 30.0 1.0 CB A:PRO18 3.7 29.0 1.0 N A:PRO18 4.2 29.2 1.0 CA A:TYR141 4.2 21.9 1.0 CB A:TYR141 4.2 22.1 1.0 CA A:PRO18 4.3 28.6 1.0 CA A:GLY142 4.4 24.2 1.0 C A:TYR141 4.4 22.6 1.0 CD1 A:TYR141 4.7 26.1 1.0 O A:GLY142 4.7 25.2 1.0 CG2 A:ILE17 4.8 27.7 1.0 C A:GLY142 4.9 25.2 1.0 C A:ILE17 4.9 29.1 1.0 CG A:TYR141 5.0 23.3 1.0

Iodine binding site 7 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I161 b:67.6 occ:1.00 OD2 A:ASP112 3.6 42.8 1.0 N A:ASP112 3.8 34.0 1.0 CB A:ASP112 3.9 34.2 1.0 CB A:LEU110 4.0 33.5 1.0 CG A:ASP112 4.0 37.6 1.0 CE A:LYS113 4.1 36.9 1.0 N A:LYS111 4.2 34.8 1.0 O A:HOH254 4.4 36.3 1.0 CA A:ASP112 4.4 33.7 1.0 CG A:LYS113 4.5 31.6 1.0 CD1 A:LEU110 4.6 35.9 1.0 CD A:LYS113 4.6 34.1 1.0 CB A:LYS111 4.6 35.8 1.0 CA A:LYS111 4.8 34.9 1.0 N A:LYS113 4.8 31.1 1.0 C A:LYS111 4.8 34.2 1.0 C A:LEU110 4.9 33.7 1.0 NZ A:LYS113 4.9 40.0 1.0 CG A:LEU110 4.9 34.2 1.0 OD1 A:ASP112 5.0 40.6 1.0 C A:ASP112 5.0 32.3 1.0

Iodine binding site 8 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I162 b:68.8 occ:1.00 O A:HOH196 3.6 30.0 1.0 NH1 A:ARG129 3.7 27.1 1.0 CD A:ARG129 3.8 29.4 1.0 CA A:GLY87 3.9 27.7 1.0 O A:HOH246 4.0 43.9 1.0 CB A:THR80 4.0 23.4 1.0 CD1 A:ILE82 4.1 32.6 1.0 CG2 A:THR80 4.2 23.1 1.0 O A:THR80 4.3 22.2 1.0 N A:GLY87 4.4 27.1 1.0 CG1 A:ILE82 4.6 29.8 1.0 CB A:ARG129 4.7 30.2 1.0 CZ A:ARG129 4.7 27.8 1.0 NE A:ARG129 4.7 27.2 1.0 C A:THR80 4.7 22.8 1.0 O A:HOH255 4.8 49.7 1.0 CG A:ARG129 4.8 29.7 1.0 OG1 A:THR80 4.9 22.8 1.0 CA A:THR80 4.9 22.3 1.0

Iodine binding site 9 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I163 b:73.5 occ:1.00 O A:HOH212 2.7 34.2 1.0 N A:ARG99 3.4 25.6 1.0 O A:HOH217 3.5 34.9 1.0 NZ A:LYS98 3.8 37.6 1.0 O A:HOH245 3.9 43.8 1.0 CA A:LYS98 3.9 25.6 1.0 NH1 A:ARG99 3.9 30.6 1.0 CE A:LYS98 3.9 36.5 1.0 CG A:ARG99 4.0 27.4 1.0 CB A:ARG99 4.1 26.8 1.0 C A:LYS98 4.2 25.4 1.0 CB A:LYS98 4.3 25.8 1.0 CD A:ARG99 4.3 28.6 1.0 O A:PHE70 4.3 26.2 1.0 CA A:ARG99 4.4 26.3 1.0 CG A:LYS98 4.5 28.6 1.0 CD2 A:PHE70 4.6 28.3 1.0 CZ A:ARG99 4.7 28.6 1.0 NE A:ARG99 4.8 27.6 1.0 CD A:LYS98 4.9 34.3 1.0 CB A:PHE70 4.9 25.2 1.0 O A:PHE97 5.0 24.9 1.0

Iodine binding site 10 out of 29 in the Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of the Galectin-8 N-Terminal Carbohydrate Recognition Domain in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I164 b:78.2 occ:1.00 N A:TYR93 3.4 26.8 1.0 N A:ASP94 3.7 28.8 1.0 CA A:TYR93 4.2 27.3 1.0 CB A:ASP94 4.2 30.9 1.0 CG2 A:THR92 4.2 26.3 1.0 CA A:THR92 4.2 26.0 1.0 CB A:TYR93 4.2 27.8 1.0 C A:THR92 4.3 26.4 1.0 C A:TYR93 4.4 27.9 1.0 CA A:ASP94 4.6 30.2 1.0 O A:HOH215 4.7 34.5 1.0 CD2 A:TYR93 4.8 26.9 1.0 CB A:THR92 4.8 25.8 1.0

H.Ideo, T.Matsuzaka, T.Nonaka, A.Seko, K.Yamashita. Galectin-8-N-Domain Recognition Mechanism For Sialylated and Sulfated Glycans To Be Published.