Magnesium in PDB 2q3f: X-Ray Crystal Structure of Putative Human Ras-Related Gtp Binding D in Complex with Gmppnp

The structure of X-Ray Crystal Structure of Putative Human Ras-Related Gtp Binding D in Complex with Gmppnp, PDB code: 2q3f was solved by A.M.Mulichak, W.M.Rabeh, W.Tempel, L.Nedyalkova, R.Landry, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, L.J.Keefe, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.730, 67.130, 66.360, 90.00, 110.92, 90.00
R / Rfree (%)	22.1 / 26.8

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Putative Human Ras-Related Gtp Binding D in Complex with Gmppnp (pdb code 2q3f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Putative Human Ras-Related Gtp Binding D in Complex with Gmppnp, PDB code: 2q3f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Crystal Structure of Putative Human Ras-Related Gtp Binding D in Complex with Gmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Putative Human Ras-Related Gtp Binding D in Complex with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:28.3 occ:1.00 O2B A:GNP401 2.1 25.8 1.0 OG A:SER57 2.1 23.6 1.0 OG1 A:THR78 2.1 30.6 1.0 O1G A:GNP401 2.2 26.3 1.0 O A:HOH408 2.2 23.7 1.0 O A:HOH406 2.3 21.1 1.0 CB A:SER57 3.1 26.2 1.0 CB A:THR78 3.2 31.1 1.0 PB A:GNP401 3.3 24.7 1.0 PG A:GNP401 3.3 28.2 1.0 N3B A:GNP401 3.4 24.8 1.0 N A:THR78 3.8 31.4 1.0 N A:SER57 3.8 25.9 1.0 O3G A:GNP401 3.9 27.3 1.0 CA A:SER57 4.1 25.5 1.0 CA A:THR78 4.1 32.0 1.0 OD2 A:ASP98 4.1 33.0 1.0 O2A A:GNP401 4.2 29.9 1.0 O1B A:GNP401 4.3 23.9 1.0 CG2 A:THR78 4.3 31.7 1.0 OD1 A:ASP98 4.3 26.4 1.0 O3A A:GNP401 4.4 25.4 1.0 O1A A:GNP401 4.5 28.7 1.0 PA A:GNP401 4.5 26.5 1.0 O2G A:GNP401 4.5 31.5 1.0 O A:GLU76 4.5 33.1 1.0 CG A:ASP98 4.6 29.8 1.0 O A:HOH414 4.7 46.6 1.0 O A:PHE99 4.8 28.9 1.0 C A:SER77 4.8 34.1 1.0 CB A:LYS56 4.9 25.6 1.0 C A:LYS56 5.0 26.4 1.0 CE A:LYS56 5.0 23.7 1.0

Magnesium binding site 2 out of 2 in the X-Ray Crystal Structure of Putative Human Ras-Related Gtp Binding D in Complex with Gmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Putative Human Ras-Related Gtp Binding D in Complex with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:26.7 occ:1.00 O1G B:GNP402 2.0 29.3 1.0 O2B B:GNP402 2.0 26.0 1.0 O B:HOH415 2.1 28.2 1.0 O B:HOH425 2.1 29.6 1.0 OG1 B:THR78 2.2 26.9 1.0 OG B:SER57 2.2 24.8 1.0 PG B:GNP402 3.2 30.2 1.0 CB B:THR78 3.2 31.1 1.0 PB B:GNP402 3.2 25.9 1.0 CB B:SER57 3.2 25.7 1.0 N3B B:GNP402 3.4 27.0 1.0 N B:THR78 3.7 35.7 1.0 N B:SER57 3.8 26.5 1.0 O3G B:GNP402 3.9 27.8 1.0 CA B:THR78 4.1 32.9 1.0 CA B:SER57 4.1 25.9 1.0 OD2 B:ASP98 4.2 35.8 1.0 O2A B:GNP402 4.2 30.5 1.0 O1B B:GNP402 4.2 26.8 1.0 O2G B:GNP402 4.3 32.5 1.0 O3A B:GNP402 4.3 29.1 1.0 CG2 B:THR78 4.3 29.2 1.0 OD1 B:ASP98 4.3 29.8 1.0 O1A B:GNP402 4.4 31.5 1.0 O B:GLU76 4.4 34.6 1.0 PA B:GNP402 4.5 30.2 1.0 O B:HOH445 4.5 62.9 1.0 CG B:ASP98 4.7 32.9 1.0 O B:PHE99 4.7 24.9 1.0 C B:SER77 4.7 36.6 1.0 CB B:LYS56 4.8 22.6 1.0 CE B:LYS56 4.9 21.0 1.0 NZ B:LYS56 5.0 19.4 1.0 C B:LYS56 5.0 25.4 1.0

A.M.Mulichak, W.M.Rabeh, W.Tempel, L.Nedyalkova, R.Landry, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, L.J.Keefe, A.Bochkarev, H.Park. Crystal Structure of Human Ras-Related Gtp-Binding D. To Be Published.