Magnesium in PDB 2c2h: Crystal Structure of the Human RAC3 in Complex with Gdp

The structure of Crystal Structure of the Human RAC3 in Complex with Gdp, PDB code: 2c2h was solved by J.E.Debreczeni, X.Yang, Y.Zao, J.Elkins, C.Gileadi, N.Burgess, S.Colebrook, O.Gileadi, O.Fedorov, G.Bunkoczi, F.Von Delft, D.Doyle, M.Sundstrom, C.Arrowsmith, J.Weigelt, A.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.14 / 1.85
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	110.320, 110.320, 81.790, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.9

The structure of Crystal Structure of the Human RAC3 in Complex with Gdp also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Human RAC3 in Complex with Gdp (pdb code 2c2h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the Human RAC3 in Complex with Gdp, PDB code: 2c2h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Human RAC3 in Complex with Gdp


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 the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1190 b:17.6 occ:1.00 OG1 A:THR17 2.0 22.9 1.0 O1B A:GDP1178 2.0 19.1 1.0 O A:HOH2019 2.1 20.6 1.0 O A:HOH2081 2.1 21.1 1.0 O A:HOH2008 2.1 21.3 1.0 O A:HOH2082 2.2 20.1 1.0 CB A:THR17 3.1 21.6 1.0 PB A:GDP1178 3.3 19.2 1.0 O2B A:GDP1178 3.5 20.5 1.0 N A:THR17 3.9 21.2 1.0 OD2 A:ASP57 4.0 25.8 1.0 CA A:THR17 4.0 22.0 1.0 OD1 A:ASP57 4.1 26.2 1.0 O2A A:GDP1178 4.1 20.1 1.0 CG2 A:THR17 4.1 23.0 1.0 O3B A:GDP1178 4.2 19.1 1.0 O A:HOH2023 4.4 25.1 1.0 O3A A:GDP1178 4.4 19.2 1.0 CG A:ASP57 4.4 27.2 1.0 PA A:GDP1178 4.6 18.1 1.0 O1A A:GDP1178 4.7 17.2 1.0 O A:THR58 4.8 28.4 1.0 NZ A:LYS16 4.9 21.3 1.0 CB A:LYS16 4.9 21.5 1.0 C A:LYS16 5.0 21.3 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Human RAC3 in Complex with Gdp


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 the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1191 b:20.4 occ:1.00 O1B A:GDP1179 2.0 17.9 1.0 O1B A:GDP1180 2.0 19.0 1.0 O1A A:GDP1179 2.1 19.7 1.0 O1A A:GDP1180 2.1 20.1 1.0 O A:HOH2089 2.2 23.0 1.0 O A:HOH2086 2.2 24.5 1.0 PA A:GDP1179 3.2 23.1 1.0 PB A:GDP1180 3.2 21.0 1.0 PB A:GDP1179 3.3 18.5 1.0 PA A:GDP1180 3.3 19.7 1.0 O3A A:GDP1179 3.5 22.6 1.0 O3A A:GDP1180 3.6 22.2 1.0 O3B A:GDP1180 3.9 16.8 1.0 O3B A:GDP1179 4.0 22.3 1.0 O5' A:GDP1179 4.1 26.9 1.0 O2A A:GDP1180 4.2 21.6 1.0 O2A A:GDP1179 4.4 22.9 1.0 O A:HOH2091 4.4 18.6 1.0 O2B A:GDP1179 4.4 19.6 1.0 O5' A:GDP1180 4.4 21.7 1.0 CA A:CA1184 4.4 8.3 1.0 O2B A:GDP1180 4.5 20.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1192 b:23.9 occ:1.00 O A:HOH2087 2.0 17.7 1.0 O A:HOH2001 2.1 31.6 1.0 O A:HOH2085 2.1 20.6 1.0 O6 A:GDP1180 2.2 16.8 1.0 O A:HOH2102 2.2 25.5 1.0 O A:HOH2094 2.6 25.8 1.0 C6 A:GDP1180 3.3 15.9 1.0 N1 A:GDP1180 3.9 14.9 1.0 O2B A:GDP1179 4.0 19.6 1.0 O3B A:GDP1179 4.0 22.3 1.0 O A:HOH2048 4.2 20.9 1.0 CE1 A:HIS103 4.2 19.1 1.0 O1 A:SO41188 4.4 22.3 1.0 C5 A:GDP1180 4.5 13.7 1.0 PB A:GDP1179 4.6 18.5 1.0 NE2 A:HIS103 4.7 18.7 1.0 CA A:CA1184 4.8 8.3 1.0 ND1 A:HIS103 4.9 17.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1189 b:30.7 occ:1.00 O B:HOH2044 2.0 32.1 1.0 O B:HOH2013 2.0 30.4 1.0 O B:HOH2045 2.0 32.3 1.0 O2B B:GDP1178 2.0 25.4 1.0 OG1 B:THR17 2.1 24.3 1.0 O B:HOH2005 2.1 29.7 1.0 PB B:GDP1178 3.2 29.4 1.0 CB B:THR17 3.2 22.3 1.0 O3B B:GDP1178 3.3 27.7 1.0 N B:THR17 3.9 22.2 1.0 OD2 B:ASP57 4.0 27.9 1.0 OD1 B:ASP57 4.0 28.3 1.0 O2A B:GDP1178 4.1 33.0 1.0 O1B B:GDP1178 4.1 28.2 1.0 CA B:THR17 4.1 22.5 1.0 CG2 B:THR17 4.3 23.1 1.0 O B:HOH2004 4.3 37.5 1.0 CG B:ASP57 4.3 28.4 1.0 O3A B:GDP1178 4.4 29.3 1.0 O B:THR58 4.6 28.7 1.0 PA B:GDP1178 4.6 29.9 1.0 O1A B:GDP1178 4.7 30.5 1.0 CB B:LYS16 4.7 22.5 1.0 NZ B:LYS16 4.8 21.4 1.0 C B:LYS16 4.9 22.0 1.0 CE B:LYS16 4.9 21.8 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1190 b:26.1 occ:1.00 O B:HOH2048 1.8 32.9 1.0 O3B B:GDP1179 1.8 26.9 1.0 O B:HOH2046 2.0 26.7 1.0 O1A B:GDP1179 2.0 32.6 1.0 O3B B:GDP1180 2.1 26.3 1.0 O1A B:GDP1180 2.1 26.2 1.0 PA B:GDP1180 3.2 27.8 1.0 PB B:GDP1179 3.2 28.3 1.0 PA B:GDP1179 3.3 35.9 1.0 PB B:GDP1180 3.3 24.4 1.0 O3A B:GDP1180 3.5 26.9 1.0 O3A B:GDP1179 3.6 31.9 1.0 O2B B:GDP1180 3.8 22.1 1.0 O B:HOH2051 4.0 26.6 1.0 O2A B:GDP1180 4.0 26.6 1.0 O2B B:GDP1179 4.0 30.8 1.0 O5' B:GDP1179 4.1 38.4 1.0 O1B B:GDP1179 4.2 26.8 1.0 CA B:CA1185 4.4 14.9 1.0 O2A B:GDP1179 4.4 34.5 1.0 O1B B:GDP1180 4.5 25.0 1.0 O5' B:GDP1180 4.6 29.8 1.0 C5' B:GDP1180 4.9 27.8 1.0

J.E.Debreczeni, X.Yang, Y.Zao, J.Elkins, C.Gileadi, N.Burgess, S.Colebrook, O.Gileadi, O.Fedorov, G.Bunkoczi, F.Von Delft, D.Doyle, M.Sundstrom, C.Arrowsmith, J.Weigelt, A.Edwards. Crystal Structure of the Human RAC3 in Complex with Gdp To Be Published.