Magnesium in PDB 4xj4: Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Atp Bound Form

The structure of Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Atp Bound Form, PDB code: 4xj4 was solved by K.Kato, R.Ishii, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.04 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.090, 51.300, 71.540, 90.00, 93.85, 90.00
R / Rfree (%)	17.2 / 20

The binding sites of Magnesium atom in the Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Atp Bound Form (pdb code 4xj4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Atp Bound Form, PDB code: 4xj4:

Magnesium binding site 1 out of 1 in the Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Atp Bound Form


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 Vibrio Cholerae Dncv 3'-Deoxy Atp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1008 b:23.5 occ:1.00 O A:HOH1187 2.1 18.9 1.0 O1B A:3AT1006 2.1 26.7 1.0 O1G A:3AT1006 2.2 23.4 1.0 OD2 A:ASP133 2.2 25.1 1.0 OD1 A:ASP131 2.3 32.0 1.0 O1A A:3AT1006 2.3 32.2 1.0 CG A:ASP133 3.2 30.7 1.0 PB A:3AT1006 3.3 24.8 1.0 PG A:3AT1006 3.4 20.5 1.0 CG A:ASP131 3.4 36.9 1.0 PA A:3AT1006 3.5 33.0 1.0 OD1 A:ASP133 3.6 29.5 1.0 O A:HOH1379 3.6 38.0 1.0 O3B A:3AT1006 3.7 22.2 1.0 O A:HOH1205 3.7 25.9 1.0 O3A A:3AT1006 3.8 29.4 1.0 OD2 A:ASP131 3.8 40.4 1.0 OG A:SER114 4.0 24.1 1.0 O2G A:3AT1006 4.1 20.6 1.0 O A:ASP131 4.2 24.2 1.0 O A:HOH1196 4.2 21.4 1.0 C5' A:3AT1006 4.2 39.4 1.0 O5' A:3AT1006 4.3 32.1 1.0 N A:SER114 4.3 24.8 1.0 O A:HOH1212 4.5 26.5 1.0 O3G A:3AT1006 4.6 22.3 1.0 CB A:ASP133 4.6 23.5 1.0 C A:ASP131 4.6 27.3 1.0 O2B A:3AT1006 4.7 24.6 1.0 CB A:ASP131 4.7 30.0 1.0 O2A A:3AT1006 4.8 36.0 1.0 CA A:GLY113 4.8 26.4 1.0 CB A:SER114 4.9 26.0 1.0 N A:ASP133 5.0 20.8 1.0

K.Kato, R.Ishii, S.Hirano, R.Ishitani, O.Nureki. Structural Basis For the Catalytic Mechanism of Dncv, Bacterial Homolog of Cyclic Gmp-Amp Synthase Structure V. 23 843 2015.
ISSN: ISSN 0969-2126
PubMed: 25865248
DOI: 10.1016/J.STR.2015.01.023