Iodine in PDB 7jhi: Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative

All present enzymatic activity of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative:
2.4.1.149;

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative, PDB code: 7jhi was solved by Y.Hao, X.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.33 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.431, 81.385, 157.138, 90.00, 98.63, 90.00
R / Rfree (%)	20.2 / 24.8

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	5 atoms

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 - 41;

Binding sites:

The binding sites of Iodine atom in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative (pdb code 7jhi). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 41 binding sites of Iodine where determined in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative, PDB code: 7jhi:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:70.8 occ:0.41 O A:HOH549 3.3 36.5 1.0 OE1 A:GLN69 3.6 49.4 1.0 NH1 A:ARG124 3.7 49.5 1.0 CD2 A:LEU66 4.2 29.0 1.0 CB A:LYS65 4.3 29.4 1.0 C A:LYS65 4.7 29.2 1.0 N A:LEU66 4.8 29.3 1.0 CB A:HIS92 4.8 34.3 1.0 CD A:GLN69 4.8 38.5 1.0 O A:LYS65 4.8 31.4 1.0 CG A:LEU66 4.9 33.0 1.0 CZ A:ARG124 4.9 46.9 1.0 ND1 A:HIS92 5.0 33.6 1.0

Iodine binding site 2 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:42.0 occ:0.66 NH1 A:ARG115 3.5 22.5 1.0 N A:ARG115 3.7 30.8 1.0 CG A:ARG115 3.8 21.8 1.0 CB A:ARG115 4.0 22.0 1.0 N A:ASP114 4.0 34.3 1.0 CD A:ARG115 4.0 22.3 1.0 CB A:PRO113 4.3 27.4 1.0 CB A:ASP114 4.4 33.0 1.0 CA A:ARG115 4.5 27.1 1.0 CA A:ASP114 4.5 33.1 1.0 CZ A:ARG115 4.5 28.8 1.0 C A:ASP114 4.6 38.2 1.0 C A:PRO113 4.7 32.4 1.0 NE A:ARG115 4.7 24.2 1.0 CA A:PRO113 4.9 25.0 1.0

Iodine binding site 3 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:62.9 occ:0.79 CD A:ARG229 3.6 20.8 1.0 CD1 A:LEU130 3.7 28.9 1.0 CA A:TRP230 4.0 21.8 1.0 N A:TRP230 4.2 18.9 1.0 CG A:ARG229 4.2 28.4 1.0 CB A:TRP230 4.3 18.7 1.0 CG A:LEU130 4.4 31.4 1.0 CD1 A:TRP230 4.4 19.5 1.0 C A:ARG229 4.4 17.9 1.0 O A:ARG229 4.4 26.6 1.0 NH1 A:ARG229 4.4 29.9 1.0 OG1 A:THR233 4.6 34.0 1.0 NE1 A:TRP211 4.6 23.9 1.0 O A:HOH597 4.7 36.8 1.0 CB A:ARG229 4.7 26.0 1.0 CB A:THR233 4.8 31.9 1.0 CG A:TRP230 4.8 21.5 1.0 NE A:ARG229 4.8 28.7 1.0

Iodine binding site 4 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I407 b:46.6 occ:0.62 O A:HOH561 3.3 21.4 1.0 OG1 A:THR185 3.7 27.9 1.0 N A:THR185 3.8 26.1 1.0 OG1 A:THR152 4.0 24.9 1.0 O A:HOH539 4.3 32.8 1.0 CA A:GLN184 4.3 25.9 1.0 CG2 A:THR152 4.3 12.0 1.0 O A:THR185 4.4 24.5 1.0 CE A:MET210 4.4 32.2 1.0 CD2 A:LEU198 4.5 38.8 1.0 C A:GLN184 4.6 24.2 1.0 CG A:GLN184 4.6 27.7 1.0 CA A:THR185 4.6 28.5 1.0 C A:THR185 4.6 27.0 1.0 CB A:SER195 4.6 32.2 1.0 CB A:GLN184 4.7 26.6 1.0 CB A:THR152 4.7 23.0 1.0 O A:GLY183 4.8 21.8 1.0 CB A:THR185 4.8 27.2 1.0 CA A:SER195 4.8 32.0 1.0 SD A:MET210 4.8 37.2 1.0

Iodine binding site 5 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:49.2 occ:0.46 NZ A:LYS141 3.3 36.7 1.0 CD1 A:PHE143 4.0 22.3 1.0 CB A:PHE143 4.0 18.4 1.0 CA A:PHE143 4.1 21.3 1.0 CE A:LYS141 4.2 39.1 1.0 CD A:LYS141 4.3 21.0 1.0 N A:PHE143 4.3 23.2 1.0 CG A:PHE143 4.5 20.8 1.0 O A:PRO142 4.6 27.7 1.0 C A:PRO142 4.6 25.9 1.0 CG A:LYS141 4.6 32.1 1.0 O A:LYS141 4.8 34.0 1.0 CB A:GLU239 4.9 24.0 1.0 O A:ASN173 4.9 53.5 1.0 OE1 A:GLU239 5.0 42.5 1.0

Iodine binding site 6 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:47.5 occ:0.62 CD2 A:LEU390 3.7 36.7 1.0 O A:VAL370 3.7 30.3 1.0 ND2 A:ASN251 3.8 20.4 1.0 CG1 A:VAL370 3.8 25.7 1.0 CA A:VAL370 4.0 32.1 1.0 OD1 A:ASN251 4.1 17.0 1.0 C A:VAL370 4.3 31.0 1.0 CB A:VAL370 4.4 36.0 1.0 CB A:HIS253 4.4 24.5 1.0 CG A:ASN251 4.4 19.5 1.0 CG2 A:VAL370 4.6 26.9 1.0 CD1 A:LEU390 4.7 26.3 1.0 ND1 A:HIS253 4.8 41.9 1.0 CG A:LEU390 4.8 29.7 1.0 O A:LEU390 4.9 38.8 1.0

Iodine binding site 7 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:51.9 occ:0.51 CA A:TYR258 3.9 21.2 1.0 N A:TYR258 3.9 23.2 1.0 C A:ASN257 4.1 21.2 1.0 O A:ASN257 4.2 26.6 1.0 CB A:ASN257 4.3 23.4 1.0 OG A:SER261 4.3 25.1 1.0 CB A:TYR258 4.3 18.9 1.0 NE2 A:HIS254 4.3 43.8 1.0 O A:HOH554 4.5 30.9 1.0 CD2 A:HIS254 4.7 33.3 1.0 CB A:SER261 4.8 20.4 1.0 CD2 A:TYR258 4.8 18.9 1.0 CA A:ASN257 4.9 22.9 1.0 O A:HIS254 4.9 28.8 1.0

Iodine binding site 8 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I411 b:73.0 occ:0.65 CG A:ARG214 3.6 36.2 1.0 CD A:ARG214 3.6 42.6 1.0 CG A:PRO186 4.0 32.3 1.0 O A:HOH582 4.1 33.0 1.0 NE A:ARG214 4.1 36.6 1.0 CB A:GLU188 4.2 51.0 1.0 OE1 A:GLU188 4.3 58.1 1.0 C5 E:NAG2 4.3 39.0 1.0 OD2 A:ASP189 4.3 53.7 1.0 CG A:GLU188 4.5 32.0 1.0 CB A:PRO186 4.6 29.0 1.0 C1 E:NAG2 4.7 36.8 1.0 CD A:GLU188 4.7 43.6 1.0 O5 E:NAG2 4.8 42.4 1.0 C3 E:NAG2 4.9 47.0 1.0 CB A:ARG214 4.9 28.5 1.0 O6 E:NAG1 5.0 31.7 1.0

Iodine binding site 9 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I412 b:41.3 occ:0.44 CD2 A:TYR289 3.7 38.5 1.0 CB A:LEU287 3.9 34.5 1.0 CD1 A:LEU287 3.9 35.3 1.0 N A:TYR289 4.0 24.4 1.0 CE1 A:HIS282 4.1 42.2 1.0 N A:LYS288 4.1 29.0 1.0 ND1 A:HIS282 4.1 37.1 1.0 CG A:LEU287 4.2 37.9 1.0 CD2 A:LEU287 4.3 38.0 1.0 CB A:TYR289 4.3 27.8 1.0 NE2 A:HIS282 4.4 40.1 1.0 CG A:HIS282 4.4 40.3 1.0 CG A:TYR289 4.5 31.5 1.0 CE2 A:TYR289 4.5 45.4 1.0 CD2 A:HIS282 4.6 32.8 1.0 CB A:LYS288 4.7 31.2 1.0 CA A:TYR289 4.7 30.2 1.0 CA A:LEU287 4.7 34.5 1.0 CA A:LYS288 4.8 30.6 1.0 C A:LEU287 4.8 35.5 1.0 C A:LYS288 4.9 33.8 1.0 O C:HOH576 4.9 34.5 1.0

Iodine binding site 10 out of 41 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I413 b:23.9 occ:0.68 O A:HOH535 3.4 10.4 1.0 CA A:HIS154 3.8 14.0 1.0 CD A:ARG157 3.8 15.6 1.0 NE A:ARG157 3.8 24.4 1.0 CG A:ARG157 3.9 14.9 1.0 CB A:ALA156 3.9 15.4 1.0 O D:HOH583 4.0 16.4 1.0 N A:ARG157 4.0 14.6 1.0 N A:ALA156 4.2 14.8 1.0 CD2 A:HIS154 4.2 20.1 1.0 C A:HIS154 4.3 16.7 1.0 CB A:HIS154 4.3 14.5 1.0 O A:PRO153 4.3 17.6 1.0 CG A:HIS154 4.4 19.3 1.0 CA A:ALA156 4.5 13.3 1.0 N A:PHE155 4.5 14.1 1.0 CB A:ARG157 4.6 13.1 1.0 O A:HOH611 4.7 25.7 1.0 C A:ALA156 4.7 11.6 1.0 N A:HIS154 4.9 18.0 1.0 O A:HIS154 4.9 17.4 1.0 CA A:ARG157 4.9 14.8 1.0 C A:PRO153 5.0 18.5 1.0

Y.Hao, A.Crequer-Grandhomme, N.Javier, A.Singh, H.Chen, P.Manzanillo, M.C.Lo, X.Huang. Structures and Mechanism of Human Glycosyltransferase Beta 1,3-N-Acetylglucosaminyltransferase 2 (B3GNT2), An Important Player in Immune Homeostasis. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33158990
DOI: 10.1074/JBC.RA120.015306