Magnesium 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:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg604 b:19.2 occ:1.00 OD1 A:ASN471 2.0 22.7 1.0 O A:HOH861 2.1 15.6 1.0 O2B A:UD1606 2.1 11.1 1.0 O2A A:UD1606 2.1 15.9 1.0 O A:HOH738 2.1 14.2 1.0 OD2 A:ASP219 2.2 19.0 1.0 CG A:ASN471 2.9 21.7 1.0 HD21 A:ASN471 3.1 23.7 1.0 CG A:ASP219 3.1 15.4 1.0 PA A:UD1606 3.3 19.4 1.0 PB A:UD1606 3.4 18.1 1.0 ND2 A:ASN471 3.4 19.7 1.0 OD1 A:ASP219 3.4 16.2 1.0 O3A A:UD1606 3.6 22.8 1.0 HA A:ASN471 3.6 37.5 1.0 O1' A:UD1606 3.8 19.3 1.0 O1A A:UD1606 4.0 18.1 1.0 O A:HOH797 4.0 14.5 1.0 O A:HOH879 4.1 17.1 1.0 H A:ASP472 4.1 35.3 1.0 O A:HOH704 4.2 46.4 1.0 CB A:ASN471 4.2 24.9 1.0 HD22 A:ASN471 4.2 23.7 1.0 H5'1 A:UD1606 4.3 20.1 1.0 OD1 A:ASN217 4.3 12.6 1.0 CA A:ASN471 4.4 31.2 1.0 HN2' A:UD1606 4.4 18.0 1.0 O A:HOH792 4.4 26.1 1.0 O A:HOH711 4.4 17.0 1.0 CB A:ASP219 4.5 15.8 1.0 O5B A:UD1606 4.6 24.6 1.0 O1B A:UD1606 4.6 18.2 1.0 HB3 A:ASP219 4.6 19.0 1.0 HB3 A:ASN217 4.6 16.3 1.0 H3B A:UD1606 4.6 16.3 1.0 HB2 A:ASP219 4.7 19.0 1.0 HB3 A:ASN471 4.7 29.9 1.0 HG A:CYS469 4.7 24.0 1.0 SG A:CYS469 4.8 19.9 1.0 HB2 A:ASN471 4.8 29.9 1.0 N A:ASP472 4.8 29.4 1.0 C5B A:UD1606 4.9 16.6 1.0 H1' A:UD1606 5.0 22.5 1.0 C1' A:UD1606 5.0 18.6 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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 A:Mg605 b:19.5 occ:1.00 O A:HOH879 2.1 17.1 1.0 O A:HOH780 2.1 18.3 1.0 O A:HOH711 2.1 17.0 1.0 O A:HOH891 2.1 18.3 1.0 O A:HOH726 2.1 22.5 1.0 O A:HOH797 2.2 14.5 1.0 HB2 A:ASP472 3.6 29.4 1.0 HB3 A:ASP472 3.8 29.4 1.0 O A:SER132 3.8 26.8 1.0 O A:GLU135 3.8 23.0 1.0 O A:HOH861 3.9 15.6 1.0 O1A A:UD1606 4.1 18.1 1.0 HB3 A:ASP219 4.1 19.0 1.0 OD2 A:ASP219 4.1 19.0 1.0 CB A:ASP472 4.2 24.5 1.0 OD1 A:ASP218 4.2 15.3 1.0 O A:HOH883 4.3 21.0 1.0 O A:ARG133 4.3 29.1 1.0 O2A A:UD1606 4.3 15.9 1.0 OD2 A:ASP218 4.3 20.2 1.0 OE2 A:GLU139 4.3 25.5 1.0 O A:HOH763 4.3 21.2 1.0 H A:ASP472 4.5 35.3 1.0 H A:GLU135 4.5 30.8 1.0 H2B A:UD1606 4.5 22.8 1.0 H3B A:UD1606 4.7 16.3 1.0 C A:ARG133 4.7 26.9 1.0 OD2 A:ASP472 4.7 29.6 1.0 HD22 A:ASN137 4.7 30.9 1.0 PA A:UD1606 4.7 19.4 1.0 CG A:ASP218 4.7 23.1 1.0 N A:GLU135 4.8 25.6 1.0 C A:GLU135 4.8 26.3 1.0 CG A:ASP219 4.9 15.4 1.0 CB A:ASP219 4.9 15.8 1.0 CG A:ASP472 4.9 33.6 1.0 CD A:GLU139 5.0 30.5 1.0 HA A:ARG133 5.0 31.9 1.0 HD21 A:ASN137 5.0 30.9 1.0 C A:SER132 5.0 27.7 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg604 b:43.6 occ:1.00 O2A B:UD1606 2.0 44.7 1.0 OD1 B:ASN471 2.1 46.4 1.0 OD2 B:ASP219 2.1 45.3 1.0 O B:HOH717 2.2 39.5 1.0 O B:HOH801 2.2 35.8 1.0 O2B B:UD1606 2.3 40.5 1.0 CG B:ASN471 3.1 54.8 1.0 CG B:ASP219 3.1 42.3 1.0 HD21 B:ASN471 3.2 56.5 1.0 PA B:UD1606 3.3 46.0 1.0 OD1 B:ASP219 3.4 40.9 1.0 PB B:UD1606 3.5 58.1 1.0 ND2 B:ASN471 3.5 47.0 1.0 O3A B:UD1606 3.6 48.0 1.0 HA B:ASN471 3.8 50.6 1.0 O1A B:UD1606 4.0 45.4 1.0 O B:HOH751 4.0 34.9 1.0 O1' B:UD1606 4.0 48.7 1.0 O B:HOH701 4.0 43.6 1.0 H5'1 B:UD1606 4.1 44.9 1.0 H B:ASP472 4.2 50.9 1.0 O B:HOH864 4.3 40.1 1.0 HN2' B:UD1606 4.3 51.4 1.0 OD1 B:ASN217 4.3 39.2 1.0 O B:HOH736 4.3 57.5 1.0 CB B:ASN471 4.4 48.9 1.0 HD22 B:ASN471 4.4 56.5 1.0 H3B B:UD1606 4.4 48.7 1.0 CB B:ASP219 4.5 36.8 1.0 HB3 B:ASN217 4.5 42.3 1.0 O5B B:UD1606 4.5 41.5 1.0 CA B:ASN471 4.5 42.1 1.0 HB3 B:ASP219 4.6 44.3 1.0 H8'3 B:UD1606 4.7 55.4 1.0 O1B B:UD1606 4.7 64.3 1.0 HB2 B:ASP219 4.7 44.3 1.0 C5B B:UD1606 4.8 37.3 1.0 H1' B:UD1606 4.9 55.7 1.0 HB3 B:ASN471 4.9 58.8 1.0 HB2 B:ASN471 4.9 58.8 1.0 N B:ASP472 5.0 42.9 1.0 N2' B:UD1606 5.0 42.8 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg605 b:49.3 occ:1.00 O B:HOH770 2.0 52.1 1.0 O B:HOH705 2.1 57.8 1.0 O B:HOH712 2.2 41.6 1.0 O B:HOH751 2.2 34.9 1.0 O B:HOH864 2.3 40.1 1.0 O B:HOH701 2.3 43.6 1.0 O B:GLU135 2.8 84.9 1.0 O B:SER132 3.7 72.0 1.0 O B:ARG133 3.9 71.6 1.0 O1A B:UD1606 3.9 45.4 1.0 C B:GLU135 4.0 96.6 1.0 HB3 B:ASP472 4.0 68.3 1.0 H B:GLU135 4.1 94.1 1.0 O B:HOH769 4.2 42.9 1.0 O B:HOH801 4.2 35.8 1.0 HB2 B:ASP472 4.3 68.3 1.0 OD2 B:ASP218 4.3 46.0 1.0 N B:GLU135 4.3 78.4 1.0 OD1 B:ASP218 4.3 35.4 1.0 C B:ARG133 4.4 98.0 1.0 HB3 B:ASP219 4.5 44.3 1.0 O B:HOH709 4.5 40.8 1.0 HA B:ASP136 4.5 88.9 1.0 OD2 B:ASP219 4.6 45.3 1.0 OE2 B:GLU139 4.6 58.9 1.0 HB3 B:GLU135 4.6 112.2 1.0 O2A B:UD1606 4.6 44.7 1.0 CB B:ASP472 4.6 56.9 1.0 HA B:ARG133 4.7 119.6 1.0 H2B B:UD1606 4.7 47.6 1.0 C B:PHE134 4.7 75.4 1.0 CA B:GLU135 4.7 98.3 1.0 CG B:ASP218 4.8 43.9 1.0 HA B:PHE134 4.8 71.4 1.0 C B:SER132 4.8 89.8 1.0 PA B:UD1606 4.8 46.0 1.0 OE1 B:GLU139 4.8 46.8 1.0 N B:PHE134 4.8 76.3 1.0 OD2 B:ASP472 4.9 89.7 1.0 HD22 B:ASN137 5.0 98.4 1.0 CD B:GLU139 5.0 49.8 1.0 H3B B:UD1606 5.0 48.7 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