Manganese in PDB 5vcm: Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese

All present enzymatic activity of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese:
2.4.1.143;

The structure of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese, PDB code: 5vcm was solved by J.H.Sanders, R.Kadirvelraj, Z.A.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.04 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.130, 139.330, 63.210, 90.00, 111.08, 90.00
R / Rfree (%)	18.6 / 22

The binding sites of Manganese atom in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese (pdb code 5vcm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese, PDB code: 5vcm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:21.8 occ:0.80 OD2 A:ASP261 2.0 23.9 1.0 O2A A:UDP502 2.0 28.0 0.8 O3B A:UDP502 2.1 25.1 0.8 O A:HOH666 2.2 28.1 1.0 NE2 A:HIS374 2.2 27.5 1.0 O A:HOH640 2.3 27.1 1.0 CG A:ASP261 3.0 19.8 1.0 CE1 A:HIS374 3.1 35.2 1.0 PB A:UDP502 3.2 28.2 0.8 CD2 A:HIS374 3.3 26.4 1.0 PA A:UDP502 3.3 28.1 0.8 OD1 A:ASP261 3.3 20.9 1.0 O3A A:UDP502 3.7 24.4 0.8 O1B A:UDP502 3.7 31.9 0.8 NH2 A:ARG127 4.1 22.4 1.0 NH1 A:ARG127 4.1 31.6 1.0 ND1 A:HIS374 4.3 33.5 1.0 O A:GLY376 4.3 35.4 1.0 O1A A:UDP502 4.3 29.9 0.8 CG A:HIS374 4.4 30.4 1.0 CB A:ASP261 4.4 21.5 1.0 O5' A:UDP502 4.4 27.9 0.8 C5' A:UDP502 4.5 23.1 0.8 O2B A:UDP502 4.6 36.5 0.8 CA A:GLY376 4.6 33.0 1.0 CZ A:ARG127 4.6 25.6 1.0 O A:HOH721 4.7 25.3 1.0 C A:GLY376 4.7 34.7 1.0 OE1 A:GLU259 4.8 25.3 1.0

Manganese binding site 2 out of 2 in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Udp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:25.1 occ:0.60 O B:HOH641 2.0 34.5 1.0 OD2 B:ASP261 2.1 30.4 1.0 O B:HOH783 2.1 37.4 1.0 O B:HOH713 2.1 36.5 1.0 NE2 B:HIS374 2.2 28.9 1.0 O B:HOH636 2.3 31.0 1.0 CE1 B:HIS374 2.9 30.2 1.0 CG B:ASP261 3.0 26.4 1.0 OD1 B:ASP261 3.2 26.0 1.0 CD2 B:HIS374 3.3 28.4 1.0 ND1 B:HIS374 4.1 30.9 1.0 NH2 B:ARG127 4.1 38.1 1.0 NH1 B:ARG127 4.1 35.8 1.0 CG B:HIS374 4.4 28.0 1.0 CB B:ASP261 4.4 22.9 1.0 O B:GLY376 4.4 41.6 1.0 OE2 B:GLU316 4.5 66.1 1.0 CZ B:ARG127 4.6 39.9 1.0 OE1 B:GLU259 4.7 42.2 1.0 O B:HOH754 4.7 33.4 1.0 CA B:GLY376 4.7 36.9 1.0 C B:GLY376 4.8 40.6 1.0

R.Kadirvelraj, J.Y.Yang, J.H.Sanders, L.Liu, A.Ramiah, P.K.Prabhakar, G.J.Boons, Z.A.Wood, K.W.Moremen. Humann-Acetylglucosaminyltransferase II Substrate Recognition Uses A Modular Architecture That Includes A Convergent Exosite. Proc. Natl. Acad. Sci. V. 115 4637 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29666272
DOI: 10.1073/PNAS.1716988115