Magnesium in PDB 2gf0: The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State

The structure of The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State, PDB code: 2gf0 was solved by A.P.Turnbull, E.Papagrigoriou, X.Yang, G.Schoch, J.Elkins, O.Gileadi, E.Salah, J.Bray, L.Wen-Hwa, O.Fedorov, F.E.Niesen, F.Von Delft, J.Weigelt, A.Edwards, C.Arrowsmith, M.Sundstrom, D.Doyle, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.09 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.053, 94.031, 61.214, 90.00, 89.98, 90.00
R / Rfree (%)	16 / 20.8

The binding sites of Magnesium atom in the The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State (pdb code 2gf0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State, PDB code: 2gf0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:16.8 occ:1.00 O A:HOH863 2.0 21.3 1.0 O3B A:GDP801 2.0 13.9 1.0 OG A:SER21 2.0 22.2 1.0 O A:HOH945 2.0 14.6 1.0 O A:HOH817 2.1 13.3 0.5 O A:HOH858 2.1 16.0 1.0 CB A:SER21 3.2 21.8 1.0 PB A:GDP801 3.3 15.0 1.0 O2B A:GDP801 3.5 13.6 1.0 O A:HOH817 3.9 13.3 0.5 N A:SER21 4.0 23.4 1.0 O1A A:GDP801 4.0 17.2 1.0 O A:HOH846 4.1 36.1 1.0 CA A:SER21 4.1 22.2 1.0 OD2 A:ASP61 4.1 23.8 1.0 NH1 A:ARG33 4.2 42.8 1.0 OD1 A:ASP61 4.3 27.0 1.0 NE A:ARG33 4.3 41.9 1.0 O3A A:GDP801 4.3 16.0 1.0 O1B A:GDP801 4.4 14.0 1.0 PA A:GDP801 4.6 14.9 1.0 CG A:ASP61 4.6 23.9 1.0 O A:HOH813 4.6 18.9 1.0 CZ A:ARG33 4.6 51.4 1.0 O A:THR62 4.6 22.1 1.0 O2A A:GDP801 4.7 13.2 1.0 NZ A:LYS20 5.0 22.9 1.0 CG2 A:THR39 5.0 24.4 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:19.3 occ:1.00 O3B B:GDP901 2.0 14.4 1.0 O B:HOH914 2.0 12.7 0.5 O B:HOH1041 2.0 15.6 1.0 O B:HOH1024 2.1 21.6 1.0 O B:HOH958 2.1 14.7 1.0 OG B:SER21 2.1 22.9 1.0 CB B:SER21 3.1 18.4 1.0 PB B:GDP901 3.2 16.8 1.0 O2B B:GDP901 3.4 15.7 1.0 O B:HOH951 4.0 28.8 1.0 O1A B:GDP901 4.0 14.2 1.0 N B:SER21 4.0 22.2 1.0 O B:HOH914 4.1 12.7 0.5 CA B:SER21 4.1 21.4 1.0 OD2 B:ASP61 4.2 23.4 1.0 OD1 B:ASP61 4.2 27.0 1.0 NE B:ARG33 4.3 37.3 1.0 NH2 B:ARG33 4.3 37.0 1.0 O1B B:GDP901 4.3 16.1 1.0 O3A B:GDP901 4.3 17.2 1.0 O B:HOH916 4.5 14.5 1.0 PA B:GDP901 4.6 15.4 1.0 O B:THR62 4.6 21.6 1.0 CG B:ASP61 4.6 25.6 1.0 CZ B:ARG33 4.7 48.1 1.0 O2A B:GDP901 4.7 12.3 1.0 O B:HOH989 4.8 26.4 1.0 CG2 B:THR39 4.9 19.6 1.0 NZ B:LYS20 4.9 22.2 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1003 b:19.0 occ:1.00 O3B C:GDP1001 2.0 13.8 1.0 O C:HOH1050 2.0 13.8 1.0 OG C:SER21 2.0 27.3 1.0 O C:HOH1014 2.1 19.3 1.0 O D:HOH1142 2.1 17.0 1.0 O D:HOH1144 2.1 16.2 1.0 CB C:SER21 3.1 17.6 1.0 PB C:GDP1001 3.2 16.0 1.0 O2B C:GDP1001 3.4 16.9 1.0 OE2 D:GLU141 3.7 33.1 1.0 N C:SER21 3.8 23.0 1.0 CA C:SER21 4.0 21.1 1.0 OD2 C:ASP61 4.1 27.5 1.0 OD1 C:ASP61 4.1 24.4 1.0 O1A C:GDP1001 4.1 19.8 1.0 O1B C:GDP1001 4.2 18.6 1.0 O C:HOH1022 4.2 19.1 1.0 O3A C:GDP1001 4.3 15.1 1.0 OE1 D:GLU141 4.4 36.0 1.0 O C:THR62 4.4 21.0 1.0 CD D:GLU141 4.4 35.4 1.0 CG C:ASP61 4.5 28.1 1.0 PA C:GDP1001 4.6 16.3 1.0 O C:HOH1016 4.7 26.1 1.0 O2A C:GDP1001 4.7 14.7 1.0 CB C:LYS20 4.8 23.1 1.0 CE C:LYS20 4.8 22.5 1.0 NZ C:LYS20 4.9 16.2 1.0 C C:LYS20 4.9 19.6 1.0 O C:HOH1132 5.0 29.1 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1103 b:17.6 occ:1.00 O D:HOH1113 2.0 14.2 1.0 O D:HOH1235 2.0 15.1 1.0 OG D:SER21 2.0 24.8 1.0 O D:HOH1236 2.0 19.6 1.0 O3B D:GDP1101 2.1 15.3 1.0 O D:HOH1111 2.2 15.4 1.0 CB D:SER21 3.1 19.6 1.0 PB D:GDP1101 3.3 15.4 1.0 O2B D:GDP1101 3.5 17.4 1.0 N D:SER21 3.9 21.6 1.0 CA D:SER21 4.0 20.2 1.0 OD1 D:ASP61 4.1 25.2 1.0 OD2 D:ASP61 4.1 24.3 1.0 O1A D:GDP1101 4.2 19.1 1.0 O D:HOH1131 4.2 18.6 1.0 O D:THR62 4.3 22.5 1.0 O1B D:GDP1101 4.3 16.0 1.0 CG D:ASP61 4.4 27.4 1.0 O3A D:GDP1101 4.5 15.4 1.0 O D:HOH1124 4.6 24.0 1.0 PA D:GDP1101 4.7 15.3 1.0 O D:HOH1226 4.8 47.4 1.0 CB D:LYS20 4.8 23.3 1.0 O2A D:GDP1101 4.8 16.1 1.0 CE D:LYS20 4.8 22.6 1.0 NZ D:LYS20 4.9 17.5 1.0 C D:LYS20 4.9 20.1 1.0

A.P.Turnbull, E.Papagrigoriou, X.Yang, G.Schoch, J.Elkins, O.Gileadi, E.Salah, J.Bray, L.Wen-Hwa, O.Fedorov, F.E.Niesen, F.Von Delft, J.Weigelt, A.Edwards, C.Arrowsmith, M.Sundstrom, D.Doyle. The Crystal Structure of the Human DIRAS1 Gtpase in the Inactive Gdp Bound State To Be Published.