Magnesium in PDB 9jn3: Crystal Structure of Avpgt in Complex with Ara-A

All present enzymatic activity of Crystal Structure of Avpgt in Complex with Ara-A:
2.4.1.293;

The structure of Crystal Structure of Avpgt in Complex with Ara-A, PDB code: 9jn3 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)	24.81 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.302, 95.114, 70.988, 90, 101.12, 90
R / Rfree (%)	18.1 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Avpgt in Complex with Ara-A (pdb code 9jn3). 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 Avpgt in Complex with Ara-A, PDB code: 9jn3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Avpgt in Complex with Ara-A


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 Avpgt in Complex with Ara-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:33.5 occ:1.00 O1B A:UPG401 2.2 49.2 1.0 O A:HOH503 2.2 54.1 1.0 O A:HOH505 2.2 40.5 1.0 OD2 A:ASP91 2.3 46.3 1.0 O2A A:UPG401 2.4 41.3 1.0 OD1 A:ASP91 2.7 44.4 1.0 CG A:ASP91 2.8 48.8 1.0 PB A:UPG401 3.5 50.7 1.0 PA A:UPG401 3.6 43.9 1.0 O A:HIS205 3.7 54.6 1.0 O3A A:UPG401 3.7 54.8 1.0 OD2 A:ASP89 4.1 41.6 1.0 OD2 A:ASP92 4.3 37.8 1.0 CB A:ASP91 4.4 44.4 1.0 OD1 A:ASP92 4.4 43.9 1.0 O2B A:UPG401 4.5 64.8 1.0 NH1 A:ARG206 4.5 63.7 1.0 NH1 A:ARG12 4.5 41.6 1.0 O3B A:UPG401 4.6 58.2 1.0 O1A A:UPG401 4.7 55.4 1.0 C5C A:UPG401 4.7 41.9 1.0 O5C A:UPG401 4.7 50.3 1.0 CG A:ASP92 4.7 39.9 1.0 CB A:ASP89 4.8 33.1 1.0 C A:HIS205 4.9 52.7 1.0 CG A:ASP89 4.9 40.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Avpgt in Complex with Ara-A


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 Avpgt in Complex with Ara-A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:25.2 occ:1.00 O1B B:UPG401 2.1 39.8 1.0 OD2 B:ASP91 2.2 35.0 1.0 O B:HOH517 2.4 34.4 1.0 O B:HOH506 2.4 42.0 1.0 O2A B:UPG401 2.4 31.2 1.0 OD1 B:ASP91 2.7 36.0 1.0 CG B:ASP91 2.8 37.1 1.0 PB B:UPG401 3.5 38.2 1.0 PA B:UPG401 3.6 38.4 1.0 O3A B:UPG401 3.7 39.6 1.0 O B:HIS205 4.0 52.4 1.0 O3B B:UPG401 4.0 49.7 1.0 CB B:ASP91 4.2 33.3 1.0 OD2 B:ASP92 4.3 34.2 1.0 NH1 B:ARG12 4.3 34.0 1.0 OD1 B:ASP92 4.4 42.0 1.0 OD2 B:ASP89 4.5 31.6 1.0 O1A B:UPG401 4.5 36.2 1.0 O2B B:UPG401 4.6 52.1 1.0 CG B:ASP92 4.7 37.4 1.0 C5C B:UPG401 4.7 32.5 1.0 NH2 B:ARG12 4.7 34.4 1.0 O5C B:UPG401 4.7 32.8 1.0 CB B:ASP89 4.8 33.4 1.0 O5' B:UPG401 4.8 47.2 1.0 CZ B:ARG12 4.9 32.5 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