Magnesium in PDB 9jma: Crystal Structure of Glycosyltransferase Avpgt

All present enzymatic activity of Crystal Structure of Glycosyltransferase Avpgt:
2.4.1.293;

The structure of Crystal Structure of Glycosyltransferase Avpgt, PDB code: 9jma was solved by J.H.Li, Z.Q.Wang, Z.Y.Zhang, W.Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.09 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.362, 95.144, 70.484, 90, 97.16, 90
R / Rfree (%)	19.5 / 24.5

The binding sites of Magnesium atom in the Crystal Structure of Glycosyltransferase Avpgt (pdb code 9jma). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Glycosyltransferase Avpgt, PDB code: 9jma:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Glycosyltransferase Avpgt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glycosyltransferase Avpgt within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:11.2 occ:1.00 O2A A:UDP401 2.3 22.6 1.0 O A:HOH629 2.3 20.4 1.0 O3B A:UDP401 2.3 24.4 1.0 OD2 A:ASP91 2.4 23.5 1.0 O A:HOH540 2.5 17.2 1.0 OD1 A:ASP91 2.6 19.4 1.0 CG A:ASP91 2.8 21.7 1.0 O A:HOH635 3.1 32.0 1.0 PA A:UDP401 3.5 23.3 1.0 PB A:UDP401 3.6 44.2 1.0 O3A A:UDP401 3.7 20.7 1.0 NH1 A:ARG12 4.2 23.9 1.0 OD1 A:ASP92 4.3 17.2 1.0 CB A:ASP91 4.3 19.8 1.0 O A:HOH653 4.4 31.5 1.0 O2B A:UDP401 4.4 46.7 1.0 O1A A:UDP401 4.4 31.5 1.0 O5' A:UDP401 4.6 26.2 1.0 C5' A:UDP401 4.6 17.2 1.0 OD2 A:ASP92 4.6 24.2 1.0 OD2 A:ASP89 4.7 23.0 1.0 O1B A:UDP401 4.8 39.8 1.0 CB A:ASP89 4.8 18.2 1.0 O A:HIS205 4.8 25.1 1.0 CG A:ASP92 4.8 25.9 1.0 NH2 A:ARG206 5.0 37.1 1.0 NH2 A:ARG12 5.0 24.3 1.0 CZ A:ARG12 5.0 20.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Glycosyltransferase Avpgt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Glycosyltransferase Avpgt within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:11.6 occ:1.00 OD2 B:ASP91 2.2 26.9 1.0 O1A B:UDP401 2.3 19.7 1.0 O B:HOH533 2.3 23.5 1.0 O B:HOH574 2.4 23.2 1.0 O1B B:UDP401 2.4 22.6 1.0 OD1 B:ASP91 2.7 28.1 1.0 O B:HOH608 2.7 24.4 1.0 CG B:ASP91 2.8 20.1 1.0 PA B:UDP401 3.5 18.6 1.0 PB B:UDP401 3.6 46.3 1.0 O3A B:UDP401 3.7 29.9 1.0 NH1 B:ARG12 4.1 12.7 1.0 O3B B:UDP401 4.2 41.8 1.0 CB B:ASP91 4.3 13.0 1.0 OD1 B:ASP92 4.4 28.0 1.0 OD2 B:ASP89 4.4 30.7 1.0 O2A B:UDP401 4.5 21.7 1.0 OD2 B:ASP92 4.5 24.7 1.0 O5' B:UDP401 4.6 21.4 1.0 C5' B:UDP401 4.7 24.7 1.0 O B:HIS205 4.7 28.3 1.0 CB B:ASP89 4.7 16.9 1.0 CG B:ASP92 4.8 25.0 1.0 O2B B:UDP401 4.9 38.9 1.0 NH2 B:ARG12 4.9 20.8 1.0 CZ B:ARG12 5.0 23.2 1.0

Z.Wang, J.Li, X.Wang, B.Jin, L.Zhou, Z.Zhao, M.Gu, X.Song, J.Wang, Z.Deng, S.Wu, Z.Zhang, W.Chen. Efficient Synthesis of Glycodiversified Nucleoside Analogues By A Thermophilic Promiscuous Glycosyltransferase Acs Catalysis V. 15 1217 2025.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C06506