Magnesium in PDB 8xlz: Beta-1,4-Galacosyltransferase

The structure of Beta-1,4-Galacosyltransferase, PDB code: 8xlz was solved by G.Luo, Z.Huang, J.Chen, X.Hou, Y.Zhu, D.Ni, W.Xu, W.Zhang, Y.Rao, W.Mu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.81 / 1.84
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.747, 53.21, 77.55, 90, 116.42, 90
R / Rfree (%)	20.7 / 24.2

The binding sites of Magnesium atom in the Beta-1,4-Galacosyltransferase (pdb code 8xlz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Beta-1,4-Galacosyltransferase, PDB code: 8xlz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Beta-1,4-Galacosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-1,4-Galacosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:34.4 occ:1.00 O2B A:UDP301 2.1 34.2 1.0 OD2 A:ASP95 2.1 31.7 1.0 OE1 A:GLN213 2.2 31.6 1.0 O2A A:UDP301 2.2 35.9 1.0 O A:HOH469 2.2 29.8 1.0 O A:HOH414 2.2 27.5 1.0 CG A:ASP95 3.1 35.2 1.0 CD A:GLN213 3.2 29.5 1.0 PB A:UDP301 3.3 42.2 1.0 OD1 A:ASP95 3.4 32.9 1.0 PA A:UDP301 3.4 38.4 1.0 O3A A:UDP301 3.6 36.6 1.0 CG A:GLN213 3.9 30.5 1.0 O A:HOH478 4.0 45.3 1.0 O1B A:UDP301 4.0 46.9 1.0 NE2 A:GLN213 4.1 29.6 1.0 O A:HOH413 4.2 28.9 1.0 C5' A:UDP301 4.2 28.9 1.0 CB A:GLN213 4.3 31.5 1.0 O5' A:UDP301 4.3 31.9 1.0 CB A:ASP95 4.4 33.4 1.0 O3B A:UDP301 4.5 39.7 1.0 OE2 A:GLU93 4.5 23.9 1.0 O1A A:UDP301 4.6 36.1 1.0

Magnesium binding site 2 out of 5 in the Beta-1,4-Galacosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-1,4-Galacosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:36.8 occ:1.00 O A:HOH458 2.2 28.6 1.0 O A:HOH457 2.2 30.9 1.0 O A:HOH453 2.2 28.8 1.0 O A:HOH479 2.2 37.9 1.0 O A:HOH413 2.2 28.9 1.0 O3B A:UDP301 2.2 39.7 1.0 O2B A:UDP301 3.3 34.2 1.0 PB A:UDP301 3.3 42.2 1.0 O A:HOH501 3.8 39.0 1.0 OG1 A:THR159 4.0 18.9 1.0 OE2 A:GLU93 4.0 23.9 1.0 O A:HOH420 4.0 36.4 1.0 O A:HOH459 4.3 47.3 1.0 O A:TRP157 4.3 22.4 1.0 O1B A:UDP301 4.3 46.9 1.0 OE1 A:GLU93 4.4 22.7 1.0 O3A A:UDP301 4.5 36.6 1.0 CB A:ASP156 4.5 30.5 1.0 CD A:GLU93 4.6 24.4 1.0 N A:THR159 4.7 20.2 1.0 C5' A:UDP301 4.9 28.9 1.0 O A:HOH414 4.9 27.5 1.0

Magnesium binding site 3 out of 5 in the Beta-1,4-Galacosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beta-1,4-Galacosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:41.4 occ:1.00 O A:HOH500 1.9 45.1 1.0 O A:HOH483 2.0 52.9 1.0 O A:HOH415 2.2 27.4 1.0 O A:HOH446 2.3 27.4 1.0 O A:HOH416 2.3 33.5 1.0 OD1 A:ASP156 4.0 32.8 1.0 O A:HOH510 4.2 34.4 1.0 OD1 B:ASN193 4.2 36.5 1.0 O A:MET155 4.3 27.9 1.0 OE1 A:GLU189 4.3 44.1 1.0 OD2 A:ASP188 4.4 29.4 1.0 CA A:ASP156 4.5 26.7 1.0 O B:HOH425 4.6 43.4 1.0 C A:MET155 4.7 30.1 1.0 O A:HOH449 4.9 38.7 1.0 N A:ASP156 4.9 27.1 1.0 O B:HOH484 5.0 45.4 1.0

Magnesium binding site 4 out of 5 in the Beta-1,4-Galacosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Beta-1,4-Galacosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:35.6 occ:1.00 O B:HOH401 2.2 43.8 1.0 O B:HOH415 2.2 29.2 1.0 O1A B:UDP301 2.2 33.6 1.0 O1B B:UDP301 2.2 41.6 1.0 OD2 B:ASP95 2.2 33.5 1.0 OE1 B:GLN213 2.2 37.1 1.0 CG B:ASP95 3.2 33.4 1.0 CD B:GLN213 3.3 38.4 1.0 PB B:UDP301 3.4 46.5 1.0 OD1 B:ASP95 3.5 33.1 1.0 PA B:UDP301 3.5 36.9 1.0 O3A B:UDP301 3.9 40.4 1.0 O2B B:UDP301 4.1 44.0 1.0 CG B:GLN213 4.2 37.6 1.0 C5' B:UDP301 4.2 30.0 1.0 NE2 B:GLN213 4.2 37.7 1.0 O5' B:UDP301 4.4 35.8 1.0 O B:HOH446 4.4 51.1 1.0 OE2 B:GLU93 4.5 22.0 1.0 CB B:ASP95 4.5 30.3 1.0 O3B B:UDP301 4.6 50.8 1.0 O B:HOH438 4.7 27.6 1.0 O2A B:UDP301 4.8 38.0 1.0 CB B:GLN213 4.8 35.7 1.0 NH1 B:ARG19 5.0 30.0 1.0

Magnesium binding site 5 out of 5 in the Beta-1,4-Galacosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Beta-1,4-Galacosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:54.2 occ:1.00 O B:HOH434 1.7 37.8 1.0 O B:HOH441 2.0 40.5 1.0 O B:HOH407 2.1 44.4 1.0 O B:HOH465 2.2 49.5 1.0 O B:HOH438 2.8 27.6 1.0 O3B B:UDP301 3.3 50.8 1.0 O1B B:UDP301 3.8 41.6 1.0 OG1 B:THR159 3.9 22.7 1.0 O B:TRP157 4.0 32.5 1.0 OE2 B:GLU93 4.0 22.0 1.0 PB B:UDP301 4.2 46.5 1.0 OE1 B:GLU93 4.3 21.6 1.0 CG B:ASP188 4.4 37.4 1.0 CB B:ASP188 4.4 34.3 1.0 OD1 B:ASP156 4.4 44.9 1.0 OD1 B:ASP188 4.5 39.5 1.0 CD B:GLU93 4.6 20.4 1.0 OD2 B:ASP188 4.7 45.8 1.0 O B:HOH483 4.7 47.5 1.0 N B:THR159 4.7 24.3 1.0 O B:HOH415 4.9 29.2 1.0 C5' B:UDP301 5.0 30.0 1.0

G.Luo, Z.Huang, Y.Zhu, J.Chen, X.Hou, D.Ni, W.Xu, W.Zhang, Y.Rao, W.Mu. Crystal Structure and Structure-Guided Tunnel Engineering in A Bacterial Beta-1,4-Galactosyltransferase. Int.J.Biol.Macromol. V. 279 35374 2024.
ISSN: ISSN 0141-8130
PubMed: 39265897
DOI: 10.1016/J.IJBIOMAC.2024.135374