Magnesium in PDB 5ekp: Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt)

The structure of Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt), PDB code: 5ekp was solved by C.Ardiccioni, O.B.Clarke, D.Tomasek, S.Banerjee, K.R.Rajashankar, Q.Liu, L.Shapiro, F.Mancia, New York Consortium On Membrane Protein Structure(Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 3.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.331, 137.518, 101.448, 90.00, 98.50, 90.00
R / Rfree (%)	24.8 / 29.1

The binding sites of Magnesium atom in the Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt) (pdb code 5ekp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt), PDB code: 5ekp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:0.6 occ:1.00 CD C:GLN98 1.9 1.0 1.0 NE2 C:GLN98 1.9 0.0 1.0 OD2 C:ASP96 2.0 0.4 1.0 O1B C:UDP401 2.1 0.6 1.0 OE1 C:GLN98 2.2 0.8 1.0 OD1 C:ASP96 2.2 0.6 1.0 CG C:ASP96 2.4 0.5 1.0 O1A C:UDP401 2.6 0.5 1.0 CG C:GLN98 2.9 0.9 1.0 PB C:UDP401 3.5 0.3 1.0 PA C:UDP401 3.6 0.9 1.0 O5' C:UDP401 3.6 0.2 1.0 CB C:ASP96 3.8 0.5 1.0 OD2 C:ASP94 3.9 0.8 1.0 CB C:GLN98 3.9 0.4 1.0 O3A C:UDP401 4.0 0.3 1.0 CB C:ASP94 4.3 0.8 1.0 O3B C:UDP401 4.3 0.6 1.0 CG C:ASP94 4.4 0.4 1.0 O2B C:UDP401 4.5 0.1 1.0 C5' C:UDP401 4.5 0.7 1.0 CA C:ASP96 4.8 0.0 1.0 N C:GLN98 4.9 0.9 1.0 N C:ASP96 4.9 0.7 1.0 O2A C:UDP401 4.9 0.3 1.0 C C:ASP96 5.0 0.4 1.0 CA C:GLN98 5.0 0.0 1.0

Magnesium binding site 2 out of 4 in the Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:0.0 occ:1.00 OD2 A:ASP96 2.0 0.6 1.0 OD1 A:ASP96 2.2 0.6 1.0 CG A:ASP96 2.4 0.3 1.0 O1A A:UDP401 2.4 0.3 1.0 O1B A:UDP401 2.5 0.8 1.0 O5' A:UDP401 2.9 0.4 1.0 PA A:UDP401 3.1 0.6 1.0 C5' A:UDP401 3.5 0.3 1.0 PB A:UDP401 3.6 0.7 1.0 O3A A:UDP401 3.7 0.1 1.0 CB A:ASP96 3.9 0.5 1.0 OD2 A:ASP94 4.1 0.8 1.0 OE1 A:GLN98 4.2 1.0 1.0 O A:ASP96 4.3 0.4 1.0 CB A:ASP94 4.3 0.9 1.0 C3' A:UDP401 4.3 0.6 1.0 C4' A:UDP401 4.4 0.2 1.0 O3B A:UDP401 4.4 0.6 1.0 O2A A:UDP401 4.5 0.9 1.0 CG A:ASP94 4.5 0.9 1.0 CD A:GLN98 4.5 0.5 1.0 NE2 A:GLN98 4.6 0.6 1.0 O2B A:UDP401 4.7 0.6 1.0 O3' A:UDP401 4.8 0.5 1.0 CA A:ASP96 4.8 0.1 1.0 N A:ASP96 4.9 0.4 1.0

Magnesium binding site 3 out of 4 in the Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:0.6 occ:1.00 O1A B:UDP401 1.9 0.4 1.0 OE1 B:GLN98 2.0 0.2 1.0 OD2 B:ASP96 2.1 0.6 1.0 O1B B:UDP401 2.3 0.1 1.0 O5' B:UDP401 2.8 0.3 1.0 PA B:UDP401 2.8 0.9 1.0 CG B:ASP96 2.9 0.0 1.0 CB B:ASP96 3.1 0.2 1.0 CD B:GLN98 3.2 0.6 1.0 PB B:UDP401 3.5 0.5 1.0 O3A B:UDP401 3.6 0.9 1.0 NE2 B:GLN98 3.8 0.7 1.0 O2A B:UDP401 4.1 0.6 1.0 C5' B:UDP401 4.1 0.5 1.0 OD1 B:ASP96 4.1 0.9 1.0 CG B:GLN98 4.4 0.7 1.0 CA B:ASP96 4.4 0.4 1.0 O2B B:UDP401 4.5 0.7 1.0 O3B B:UDP401 4.5 0.1 1.0 N B:ASP96 4.6 0.7 1.0 C4' B:UDP401 4.7 0.9 1.0 C3' B:UDP401 4.7 0.1 1.0 O3' B:UDP401 4.8 0.6 1.0 OD2 B:ASP94 4.8 0.7 1.0 CB B:ASP94 5.0 0.5 1.0

Magnesium binding site 4 out of 4 in the Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb (Wt) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:0.6 occ:1.00 OD2 D:ASP96 2.1 0.1 1.0 OD1 D:ASP96 2.1 0.3 1.0 CG D:ASP96 2.3 0.4 1.0 O1A D:UDP401 2.4 0.6 1.0 O1B D:UDP401 2.5 0.3 1.0 PA D:UDP401 3.4 0.5 1.0 O5' D:UDP401 3.4 0.5 1.0 CB D:ASP96 3.7 0.6 1.0 PB D:UDP401 3.8 0.5 1.0 OE1 D:GLN98 3.9 0.5 1.0 O3A D:UDP401 4.1 0.6 1.0 CB D:GLN98 4.2 0.8 1.0 OD2 D:ASP94 4.3 0.2 1.0 CB D:ASP94 4.5 0.1 1.0 O2A D:UDP401 4.6 0.2 1.0 C5' D:UDP401 4.6 0.8 1.0 O3B D:UDP401 4.7 0.7 1.0 CG D:ASP94 4.7 0.2 1.0 O2B D:UDP401 4.8 0.8 1.0 CD D:GLN98 4.8 0.8 1.0 CG D:GLN98 4.8 1.0 1.0 CA D:ASP96 4.8 0.1 1.0 N D:ASP96 4.8 0.9 1.0

C.Ardiccioni, O.B.Clarke, D.Tomasek, H.A.Issa, D.C.Von Alpen, H.L.Pond, S.Banerjee, K.R.Rajashankar, Q.Liu, Z.Guan, C.Li, B.Kloss, R.Bruni, E.Kloppmann, B.Rost, M.C.Manzini, L.Shapiro, F.Mancia. Structure of the Polyisoprenyl-Phosphate Glycosyltransferase Gtrb and Insights Into the Mechanism of Catalysis. Nat Commun V. 7 10175 2016.
ISSN: ESSN 2041-1723
PubMed: 26729507
DOI: 10.1038/NCOMMS10175