Calcium in PDB 7s6n: N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish

The structure of N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish, PDB code: 7s6n 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)	48.42 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.182, 86.605, 106.985, 90, 112.17, 90
R / Rfree (%)	18.4 / 23.1

The binding sites of Calcium atom in the N-Acetylglucosamine-1-Phosphotransferase (Gnpt) Alpha and Beta Subunits (Gnptab) Catalytic Domain, From Zebrafish (pdb code 7s6n). 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, PDB code: 7s6n:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:40.4 occ:1.00 O A:VAL344 2.2 48.0 1.0 OD1 A:ASP340 2.3 44.3 1.0 OE1 A:GLU349 2.3 37.2 1.0 HG A:SER342 2.3 49.6 1.0 OD1 A:ASP338 2.4 38.4 1.0 OD2 A:ASP340 2.7 47.6 1.0 O A:HOH701 2.7 48.6 1.0 OG A:SER342 2.8 41.3 1.0 CG A:ASP340 2.8 38.8 1.0 OE2 A:GLU349 2.9 31.8 1.0 CD A:GLU349 2.9 39.8 1.0 HA A:LEU345 3.1 42.9 1.0 H A:SER346 3.1 45.6 1.0 C A:VAL344 3.3 49.8 1.0 CG A:ASP338 3.6 50.7 1.0 HA A:ASP338 3.6 42.5 1.0 H A:SER342 3.7 47.6 1.0 H A:VAL344 3.8 56.1 1.0 N A:SER346 3.8 38.0 1.0 CA A:LEU345 3.8 35.7 1.0 HD23 A:LEU345 3.9 51.1 1.0 H A:ASP340 3.9 64.7 1.0 HB3 A:SER346 4.0 41.1 1.0 N A:LEU345 4.0 45.7 1.0 CB A:SER342 4.1 41.2 1.0 C A:LEU345 4.2 43.5 1.0 HB3 A:SER342 4.3 49.5 1.0 CB A:ASP340 4.3 29.0 1.0 O A:HOH714 4.3 39.7 1.0 N A:VAL344 4.3 46.7 1.0 CA A:ASP338 4.4 35.4 1.0 H A:GLY343 4.4 55.3 1.0 OD2 A:ASP338 4.4 36.2 1.0 CG A:GLU349 4.4 34.2 1.0 CA A:VAL344 4.5 48.4 1.0 N A:SER342 4.5 39.6 1.0 CB A:ASP338 4.5 51.6 1.0 HB3 A:ASP340 4.5 34.9 1.0 HB2 A:GLU349 4.7 37.6 1.0 HB2 A:ASP338 4.7 62.0 1.0 N A:ASP340 4.7 53.8 1.0 HB2 A:SER342 4.7 49.5 1.0 HG3 A:GLU349 4.7 41.1 1.0 CB A:SER346 4.7 34.2 1.0 CD2 A:LEU345 4.8 42.5 1.0 HB A:VAL344 4.8 59.5 1.0 C A:ASP338 4.8 27.4 1.0 HD22 A:LEU345 4.8 51.1 1.0 CA A:SER342 4.8 37.3 1.0 OE1 A:GLU396 4.8 53.3 1.0 H A:HIS341 4.8 41.2 1.0 N A:GLY343 4.8 46.0 1.0 HB2 A:ASP340 4.9 34.9 1.0 H A:LEU345 4.9 54.9 1.0 CA A:SER346 4.9 32.9 1.0 H A:THR339 5.0 39.1 1.0 CA A:ASP340 5.0 37.2 1.0 HG2 A:GLU349 5.0 41.1 1.0 OG A:SER346 5.0 40.1 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:32.6 occ:1.00 OD1 B:ASP340 2.3 46.4 1.0 OE1 B:GLU349 2.3 25.9 1.0 OD1 B:ASP338 2.4 33.9 1.0 O B:VAL344 2.5 44.8 1.0 O B:HOH709 2.6 39.4 1.0 OE2 B:GLU349 2.6 38.2 1.0 OG B:SER342 2.6 31.4 1.0 CD B:GLU349 2.8 30.2 1.0 CG B:ASP340 2.9 39.4 1.0 OD2 B:ASP340 2.9 39.8 1.0 H B:SER346 3.3 39.1 1.0 HA B:LEU345 3.4 41.8 1.0 HA B:ASP338 3.6 33.0 1.0 H B:SER342 3.6 56.6 1.0 C B:VAL344 3.6 35.9 1.0 CG B:ASP338 3.6 41.0 1.0 H B:ASP340 3.8 32.8 1.0 H B:VAL344 3.9 43.3 1.0 CB B:SER342 3.9 45.6 1.0 HB3 B:SER346 3.9 48.6 1.0 N B:SER346 3.9 32.5 1.0 HB3 B:SER342 4.0 54.8 1.0 HD23 B:LEU345 4.1 42.9 1.0 CA B:LEU345 4.1 34.8 1.0 CG B:GLU349 4.2 26.1 1.0 CB B:ASP340 4.3 20.1 1.0 H B:GLY343 4.3 49.8 1.0 N B:LEU345 4.3 26.3 1.0 O B:HOH763 4.3 39.2 1.0 N B:SER342 4.3 47.1 1.0 CA B:ASP338 4.3 27.4 1.0 HG3 B:GLU349 4.4 31.4 1.0 C B:LEU345 4.5 34.2 1.0 N B:VAL344 4.5 36.0 1.0 CB B:ASP338 4.5 34.3 1.0 OD2 B:ASP338 4.5 30.3 1.0 HB2 B:SER342 4.5 54.8 1.0 HB3 B:ASP340 4.6 24.2 1.0 N B:ASP340 4.6 27.2 1.0 H B:HIS341 4.6 34.2 1.0 CA B:SER342 4.7 36.7 1.0 HB2 B:ASP338 4.7 41.2 1.0 CA B:VAL344 4.7 35.9 1.0 H B:THR339 4.7 42.0 1.0 CB B:SER346 4.7 40.5 1.0 C B:ASP338 4.7 25.2 1.0 HB2 B:GLU349 4.7 27.5 1.0 HG2 B:GLU349 4.7 31.4 1.0 O B:HOH737 4.8 42.6 1.0 N B:GLY343 4.8 41.4 1.0 CA B:ASP340 4.9 21.5 1.0 N B:THR339 4.9 34.9 1.0 N B:HIS341 4.9 28.4 1.0 HB2 B:ASP340 4.9 24.2 1.0 CA B:SER346 4.9 30.3 1.0 HD22 B:LEU345 4.9 42.9 1.0 CD2 B:LEU345 4.9 35.7 1.0 OE1 B:GLU396 5.0 48.2 1.0 O B:HOH721 5.0 37.3 1.0 CB B:GLU349 5.0 22.8 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