Atomistry » Calcium » PDB 7s6e-7skl » 7sj2
Atomistry »
  Calcium »
    PDB 7s6e-7skl »
      7sj2 »

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

Protein crystallography data

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

Other elements in 7sj2:

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

Calcium Binding Sites:

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 7sj2

Go back to Calcium Binding Sites List in 7sj2
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 7sj2

Go back to Calcium Binding Sites List in 7sj2
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

Reference:

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
Page generated: Fri Jul 19 04:04:06 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy