Magnesium in PDB 1svw: Crystal Structure of Ysxc Complexed with Gmppnp

The structure of Crystal Structure of Ysxc Complexed with Gmppnp, PDB code: 1svw was solved by S.N.Ruzheinikov, S.K.Das, S.E.Sedelnikova, P.J.Baker, P.J.Artymiuk, J.Garcia-Lara, S.J.Foster, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.586, 70.599, 72.583, 90.00, 102.26, 90.00
R / Rfree (%)	30.6 / 33.5

The binding sites of Magnesium atom in the Crystal Structure of Ysxc Complexed with Gmppnp (pdb code 1svw). 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 Ysxc Complexed with Gmppnp, PDB code: 1svw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ysxc Complexed with Gmppnp


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 Ysxc Complexed with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:20.5 occ:1.00 O A:VAL76 2.8 16.0 1.0 OG A:SER37 2.8 4.6 1.0 O2B A:GTP401 2.8 18.8 1.0 CE A:LYS36 2.9 3.3 1.0 O3G A:GTP401 2.9 18.8 1.0 OD2 A:ASP75 2.9 6.7 1.0 OD1 A:ASP75 3.2 6.7 1.0 CG A:ASP75 3.3 6.7 1.0 CB A:LYS36 3.4 3.3 1.0 N A:SER37 3.4 4.6 1.0 NZ A:LYS36 3.5 3.3 1.0 O1G A:GTP401 3.5 18.8 1.0 CB A:THR59 3.6 41.0 1.0 PG A:GTP401 3.7 18.8 1.0 OG1 A:THR59 3.8 41.0 1.0 CG2 A:THR59 3.8 41.0 1.0 PB A:GTP401 3.9 18.8 1.0 CB A:SER37 3.9 4.6 1.0 C A:VAL76 3.9 16.0 1.0 CA A:SER37 4.0 4.6 1.0 CD A:LYS36 4.0 3.3 1.0 C A:LYS36 4.1 3.3 1.0 O3B A:GTP401 4.1 18.8 1.0 CA A:LYS36 4.3 3.3 1.0 N A:VAL76 4.3 16.0 1.0 CG A:LYS36 4.3 3.3 1.0 O1B A:GTP401 4.4 18.8 1.0 CB A:ASP75 4.6 6.7 1.0 N A:LYS36 4.7 3.3 1.0 CA A:VAL76 4.7 16.0 1.0 N A:PRO77 4.8 5.3 1.0 O A:LYS36 5.0 3.3 1.0 CA A:PRO77 5.0 5.3 1.0 CA A:THR59 5.0 41.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ysxc Complexed with Gmppnp


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 Ysxc Complexed with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:38.5 occ:1.00 O2B B:GTP402 2.1 36.8 1.0 O3G B:GTP402 2.1 36.8 1.0 OG1 B:THR59 2.2 17.6 1.0 OG B:SER37 2.4 48.1 1.0 OD2 B:ASP75 3.3 38.8 1.0 PB B:GTP402 3.3 36.8 1.0 N B:SER37 3.3 48.1 1.0 CB B:THR59 3.3 17.6 1.0 PG B:GTP402 3.4 36.8 1.0 CB B:SER37 3.6 48.1 1.0 CB B:LYS36 3.6 13.8 1.0 O3B B:GTP402 3.6 36.8 1.0 CE B:LYS36 3.7 13.8 1.0 CA B:SER37 3.9 48.1 1.0 OD1 B:ASP75 3.9 38.8 1.0 CG B:ASP75 3.9 38.8 1.0 O B:VAL76 4.0 20.9 1.0 O1B B:GTP402 4.0 36.8 1.0 CG2 B:THR59 4.0 17.6 1.0 O1G B:GTP402 4.1 36.8 1.0 NZ B:LYS36 4.2 13.8 1.0 C B:LYS36 4.2 13.8 1.0 CA B:LYS36 4.3 13.8 1.0 N B:LYS36 4.4 13.8 1.0 O3A B:GTP402 4.5 36.8 1.0 O2G B:GTP402 4.5 36.8 1.0 N B:THR59 4.6 17.6 1.0 CA B:THR59 4.6 17.6 1.0 O2A B:GTP402 4.6 36.8 1.0 CD B:LYS36 4.7 13.8 1.0 CG B:LYS36 4.7 13.8 1.0 C B:VAL76 5.0 20.9 1.0 PA B:GTP402 5.0 36.8 1.0

S.N.Ruzheinikov, S.K.Das, S.E.Sedelnikova, P.J.Baker, P.J.Artymiuk, J.Garcia-Lara, S.J.Foster, D.W.Rice. Analysis of the Open and Closed Conformations of the Gtp-Binding Protein Ysxc From Bacillus Subtilis. J.Mol.Biol. V. 339 265 2004.
ISSN: ISSN 0022-2836
PubMed: 15136032
DOI: 10.1016/J.JMB.2004.03.043