Manganese in PDB 8tjc: Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A

All present enzymatic activity of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A:
2.4.1.149;

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A, PDB code: 8tjc was solved by A.Sudom, X.Min, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.01 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.41, 93.876, 205.066, 90, 90, 90
R / Rfree (%)	22.7 / 27.5

The binding sites of Manganese atom in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A (pdb code 8tjc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A, PDB code: 8tjc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn500 b:66.0 occ:1.00 O A:HOH622 2.3 57.4 1.0 O A:HOH638 2.4 57.0 1.0 NE2 A:HIS376 2.4 53.9 1.0 O A:HOH646 2.7 64.5 1.0 O A:HOH648 2.9 56.3 1.0 CD2 A:HIS376 3.0 47.8 1.0 OD2 A:ASP247 3.2 55.9 1.0 OD1 A:ASP247 3.5 48.6 1.0 CE1 A:HIS376 3.6 51.8 1.0 CG A:ASP247 3.8 53.9 1.0 OD2 A:ASP245 3.8 59.8 1.0 CG A:HIS376 4.3 54.9 1.0 ND1 A:HIS376 4.5 55.2 1.0 O A:HOH624 4.7 52.7 1.0 CG A:ASP245 4.8 48.5 1.0 CB A:SER377 5.0 51.4 1.0

Manganese binding site 2 out of 4 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:105.7 occ:1.00 NE2 B:HIS376 2.6 79.7 1.0 CD2 B:HIS376 2.9 74.5 1.0 O B:HOH529 3.1 71.1 1.0 OD2 B:ASP247 3.1 56.9 1.0 OD1 B:ASP247 3.2 63.8 1.0 CG B:ASP247 3.5 65.4 1.0 OD2 B:ASP245 3.6 67.6 1.0 CE1 B:HIS376 3.8 78.4 1.0 CG B:HIS376 4.3 76.8 1.0 CG B:ASP245 4.5 60.4 1.0 O B:HOH515 4.6 61.8 1.0 CB B:ASP245 4.6 59.5 1.0 ND1 B:HIS376 4.7 80.2 1.0

Manganese binding site 3 out of 4 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:95.9 occ:1.00 NE2 C:HIS376 2.4 68.0 1.0 O C:HOH521 2.6 81.5 1.0 O C:HOH516 2.9 80.4 1.0 OD2 C:ASP247 3.0 64.3 1.0 CD2 C:HIS376 3.3 61.9 1.0 CE1 C:HIS376 3.4 63.3 1.0 OD1 C:ASP247 3.5 54.5 1.0 CG C:ASP247 3.6 60.0 1.0 OD2 C:ASP245 4.1 67.1 1.0 O C:HOH518 4.3 59.5 1.0 CG C:HIS376 4.5 66.2 1.0 ND1 C:HIS376 4.5 67.7 1.0 NZ C:LYS288 4.8 74.1 1.0 CB C:SER377 4.9 52.8 1.0

Manganese binding site 4 out of 4 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:106.2 occ:1.00 CE1 D:HIS376 2.4 72.9 1.0 OD1 D:ASP247 3.1 62.2 1.0 ND1 D:HIS376 3.2 73.5 1.0 OD2 D:ASP247 3.3 70.3 1.0 NE2 D:HIS376 3.4 70.3 1.0 OD2 D:ASP245 3.6 65.4 1.0 CG D:ASP247 3.6 69.8 1.0 O D:HOH515 4.4 70.4 1.0 CG D:HIS376 4.5 79.6 1.0 CD2 D:HIS376 4.6 77.5 1.0 CG D:ASP245 4.6 62.9 1.0 O D:HOH507 4.6 59.1 1.0 CB D:ASP245 4.9 56.0 1.0 CB D:SER377 5.0 69.6 1.0

J.J.Jackson, A.C.Siegmund, W.J.Bai, A.B.Reed, A.B.Birkholz, I.D.G.Campuzano, A.Crequer-Grandhomme, R.Hu, R.V.Modak, A.Sudom, N.Javier, C.Sanders, M.C.Lo, F.Xie, V.J.Cee, P.Manzanillo, J.G.Allen. Imidazolone As An Amide Bioisostere in the Development of Beta-1,3- N -Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37988652
DOI: 10.1021/ACS.JMEDCHEM.3C01517