Magnesium in PDB 4xj5: Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form

The structure of Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form, PDB code: 4xj5 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)	47.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.950, 50.060, 72.270, 90.00, 93.40, 90.00
R / Rfree (%)	17.5 / 19.3

The structure of Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form (pdb code 4xj5). 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 Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form, PDB code: 4xj5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp 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 Gtp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:21.7 occ:1.00 OD2 A:ASP131 2.0 31.1 1.0 O A:HOH1282 2.0 22.7 1.0 O2A A:GH31014 2.1 22.9 1.0 OD2 A:ASP133 2.2 22.6 1.0 O3G A:GH31014 2.2 20.8 1.0 O2B A:GH31014 2.2 22.4 1.0 CG A:ASP131 3.1 34.0 1.0 CG A:ASP133 3.2 24.1 1.0 PB A:GH31014 3.3 21.9 1.0 PA A:GH31014 3.3 22.0 1.0 PG A:GH31014 3.4 20.9 1.0 OD1 A:ASP133 3.6 25.6 1.0 O3A A:GH31014 3.6 21.1 1.0 O3B A:GH31014 3.6 20.2 1.0 CB A:ASP131 3.7 30.1 1.0 O A:HOH1284 3.7 42.3 1.0 MG A:MG1002 3.8 32.4 1.0 C5' A:GH31014 4.0 22.4 1.0 OG A:SER114 4.0 22.6 1.0 O2G A:GH31014 4.1 21.4 1.0 O A:HOH1303 4.1 34.9 1.0 OD1 A:ASP131 4.1 35.4 1.0 O5' A:GH31014 4.2 23.9 1.0 O A:HOH1203 4.2 22.1 1.0 O A:ASP131 4.3 26.6 1.0 N A:SER114 4.4 21.1 1.0 C A:ASP131 4.5 29.2 1.0 O1A A:GH31014 4.5 22.1 1.0 CB A:ASP133 4.5 24.1 1.0 O1G A:GH31014 4.5 22.0 1.0 O1B A:GH31014 4.6 22.4 1.0 CA A:ASP131 4.7 30.8 1.0 CA A:GLY113 4.8 22.9 1.0 CB A:SER114 4.9 22.1 1.0 N A:ASP133 4.9 27.0 1.0 O A:HOH1267 5.0 28.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form


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 Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:32.4 occ:1.00 OD2 A:ASP193 2.1 28.4 1.0 O A:HOH1303 2.2 34.9 1.0 OD1 A:ASP133 2.2 25.6 1.0 OD2 A:ASP131 2.3 31.1 1.0 OD1 A:ASP131 2.3 35.4 1.0 CG A:ASP131 2.6 34.0 1.0 CG A:ASP193 3.1 34.9 1.0 CG A:ASP133 3.2 24.1 1.0 CB A:ASP193 3.5 24.3 1.0 OD2 A:ASP133 3.6 22.6 1.0 O2A A:GH31014 3.6 22.9 1.0 C3' A:GH31013 3.7 29.1 1.0 MG A:MG1001 3.8 21.7 1.0 C4' A:GH31013 4.1 26.8 1.0 CB A:ASP131 4.1 30.1 1.0 NH2 A:ARG182 4.1 30.0 1.0 OD1 A:ASP193 4.1 40.2 1.0 O A:HOH1284 4.2 42.3 1.0 O2' A:GH31013 4.3 25.7 1.0 C5' A:GH31013 4.4 28.0 1.0 CB A:ASP133 4.4 24.1 1.0 NE2 A:HIS191 4.5 28.9 1.0 CD2 A:HIS191 4.6 30.9 1.0 C2' A:GH31013 4.6 30.7 1.0 CA A:ASP133 4.8 24.3 1.0 O A:ILE132 4.8 30.3 1.0 CA A:ASP193 4.8 27.8 1.0 PA A:GH31014 4.9 22.0 1.0 N A:ASP193 4.9 26.8 1.0 N A:ASP133 4.9 27.0 1.0 C A:ILE132 5.0 29.4 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