Calcium in PDB 7sj2: N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium

The structure of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium, PDB code: 7sj2 was solved by A.Gorelik, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.42 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.542, 87.142, 108.369, 90, 111.86, 90
R / Rfree (%)	16 / 20.2

The structure of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium (pdb code 7sj2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium, PDB code: 7sj2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:44.3 occ:1.00 OD1 A:ASP338 2.2 51.5 1.0 OD1 A:ASP340 2.3 50.0 1.0 O A:VAL344 2.3 55.1 1.0 O A:HOH730 2.4 48.4 1.0 OE1 A:GLU349 2.5 46.3 1.0 OG A:SER342 2.5 48.4 1.0 OE2 A:GLU349 2.8 45.3 1.0 CG A:ASP340 3.0 43.3 1.0 CD A:GLU349 3.0 54.6 1.0 OD2 A:ASP340 3.0 55.0 1.0 H A:SER342 3.4 60.0 1.0 CG A:ASP338 3.5 55.3 1.0 C A:VAL344 3.5 44.8 1.0 HA A:LEU345 3.6 67.5 1.0 H A:SER346 3.6 64.5 1.0 CB A:SER342 3.7 46.2 1.0 H A:VAL344 3.7 58.6 1.0 HA A:ASP338 3.7 55.5 1.0 HB3 A:SER342 3.7 55.5 1.0 H A:ASP340 3.9 43.7 1.0 O A:HOH723 4.1 55.3 1.0 N A:SER342 4.1 49.9 1.0 OD2 A:ASP338 4.2 48.9 1.0 HD23 A:LEU345 4.3 50.0 1.0 N A:SER346 4.3 53.7 1.0 N A:VAL344 4.3 48.7 1.0 CA A:LEU345 4.3 56.1 1.0 HB2 A:SER342 4.4 55.5 1.0 N A:LEU345 4.4 50.3 1.0 CA A:SER342 4.4 55.1 1.0 CB A:ASP340 4.4 42.2 1.0 CA A:ASP338 4.4 46.2 1.0 CB A:ASP338 4.4 45.5 1.0 CG A:GLU349 4.5 44.1 1.0 CA A:VAL344 4.5 49.1 1.0 HB3 A:SER346 4.5 52.8 1.0 H A:GLY343 4.6 63.9 1.0 HB2 A:ASP338 4.6 54.7 1.0 HB A:VAL344 4.6 67.3 1.0 N A:ASP340 4.6 36.4 1.0 H A:HIS341 4.7 60.1 1.0 OE1 A:GLU396 4.7 68.0 1.0 C A:ASP338 4.8 46.9 1.0 HB3 A:ASP340 4.8 50.8 1.0 C A:SER342 4.8 56.2 1.0 C A:LEU345 4.8 47.9 1.0 N A:GLY343 4.8 53.1 1.0 H A:THR339 4.8 47.9 1.0 HG3 A:GLU349 4.8 53.1 1.0 HB2 A:GLU349 4.9 46.6 1.0 N A:HIS341 4.9 50.0 1.0 OG A:SER346 4.9 52.8 1.0 CA A:ASP340 4.9 48.0 1.0 HG2 A:GLU349 4.9 53.1 1.0 N A:THR339 5.0 39.9 1.0 HD22 A:LEU345 5.0 50.0 1.0 HB2 A:ASP340 5.0 50.8 1.0

Calcium binding site 2 out of 2 in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, in Complex with Uridine Diphosphate N-Acetylglucosamine (Udp-Glcnac) and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:33.3 occ:1.00 OD1 B:ASP338 2.2 31.1 1.0 OD1 B:ASP340 2.2 37.4 1.0 O B:HOH735 2.3 34.6 1.0 O B:VAL344 2.4 38.3 1.0 OE1 B:GLU349 2.4 31.3 1.0 OG B:SER342 2.6 39.0 1.0 OE2 B:GLU349 2.8 32.7 1.0 CD B:GLU349 3.0 38.2 1.0 HG B:SER342 3.0 46.9 1.0 CG B:ASP340 3.1 31.0 1.0 OD2 B:ASP340 3.2 36.2 1.0 H B:SER342 3.3 41.1 1.0 CG B:ASP338 3.5 36.8 1.0 HB3 B:SER342 3.6 38.8 1.0 C B:VAL344 3.6 33.1 1.0 HA B:LEU345 3.6 41.0 1.0 CB B:SER342 3.6 32.8 1.0 H B:VAL344 3.7 43.9 1.0 H B:SER346 3.7 39.3 1.0 HA B:ASP338 3.7 39.8 1.0 H B:ASP340 3.8 35.3 1.0 N B:SER342 4.1 34.2 1.0 O B:HOH710 4.2 38.1 1.0 HD23 B:LEU345 4.3 37.9 1.0 OD2 B:ASP338 4.3 34.7 1.0 N B:VAL344 4.3 36.5 1.0 CA B:LEU345 4.3 34.0 1.0 CA B:ASP338 4.4 33.1 1.0 N B:SER346 4.4 32.7 1.0 HB2 B:SER342 4.4 38.8 1.0 H B:GLY343 4.4 48.4 1.0 CB B:ASP338 4.4 30.8 1.0 N B:LEU345 4.4 41.8 1.0 CA B:SER342 4.4 33.0 1.0 CB B:ASP340 4.4 30.4 1.0 CG B:GLU349 4.5 30.1 1.0 N B:ASP340 4.5 29.6 1.0 HB3 B:SER346 4.5 38.0 1.0 CA B:VAL344 4.6 41.5 1.0 HB2 B:ASP338 4.6 36.5 1.0 C B:ASP338 4.6 32.3 1.0 H B:HIS341 4.6 36.3 1.0 OE1 B:GLU396 4.6 48.5 1.0 N B:GLY343 4.7 40.2 1.0 H B:THR339 4.8 34.6 1.0 HB3 B:ASP340 4.8 36.0 1.0 C B:LEU345 4.8 38.2 1.0 N B:HIS341 4.8 30.6 1.0 HG3 B:GLU349 4.8 35.6 1.0 HB B:VAL344 4.8 47.9 1.0 HB2 B:GLU349 4.8 36.4 1.0 CA B:ASP340 4.9 35.8 1.0 N B:THR339 4.9 29.2 1.0 C B:SER342 4.9 35.1 1.0 O B:HOH738 4.9 38.3 1.0 C B:ASP340 4.9 36.8 1.0 HG2 B:GLU349 5.0 35.6 1.0 HD22 B:LEU345 5.0 37.9 1.0 O B:ASP338 5.0 32.1 1.0

A.Gorelik, K.Illes, K.H.Bui, B.Nagar. Structures of the Mannose-6-Phosphate Pathway Enzyme, Glcnac-1-Phosphotransferase. Proc.Natl.Acad.Sci.Usa V. 119 18119 2022.
ISSN: ESSN 1091-6490
PubMed: 35939698
DOI: 10.1073/PNAS.2203518119