Magnesium in PDB 4ku4: Crystal Structure of A Ras-Like Protein From Cryphonectria Parasitica in Complex with Gdp

The structure of Crystal Structure of A Ras-Like Protein From Cryphonectria Parasitica in Complex with Gdp, PDB code: 4ku4 was solved by C.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.795, 52.595, 53.234, 114.62, 93.01, 90.05
R / Rfree (%)	19.3 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of A Ras-Like Protein From Cryphonectria Parasitica in Complex with Gdp (pdb code 4ku4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Ras-Like Protein From Cryphonectria Parasitica in Complex with Gdp, PDB code: 4ku4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A Ras-Like Protein From Cryphonectria Parasitica 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 A Ras-Like Protein From Cryphonectria Parasitica in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:9.4 occ:1.00 O A:HOH404 2.1 11.7 1.0 O A:HOH403 2.2 11.4 1.0 O1B A:GDP301 2.2 8.9 1.0 OG1 A:THR25 2.2 7.7 1.0 O A:HOH402 2.2 13.5 1.0 O A:HOH401 2.2 12.7 1.0 H A:THR25 3.2 15.5 1.0 HB A:THR25 3.3 9.8 1.0 CB A:THR25 3.3 8.0 1.0 PB A:GDP301 3.4 7.9 1.0 O3B A:GDP301 3.5 12.5 1.0 O A:HOH487 3.9 22.1 1.0 HB2 A:LYS24 3.9 12.1 1.0 N A:THR25 3.9 12.7 1.0 HB2 A:ALA67 3.9 29.4 1.0 OD2 A:ASP65 4.0 11.7 1.0 HE2 A:LYS24 4.0 16.3 1.0 HG3 A:GLU45 4.1 26.4 1.0 CA A:THR25 4.2 9.2 1.0 O2A A:GDP301 4.2 7.2 1.0 OD1 A:ASP65 4.2 11.5 1.0 OD1 A:ASP41 4.2 9.7 1.0 OE2 A:GLU45 4.3 25.9 1.0 O A:HOH411 4.3 11.7 1.0 HG21 A:THR25 4.4 7.3 1.0 O2B A:GDP301 4.4 5.4 1.0 CG2 A:THR25 4.4 5.9 1.0 O A:THR66 4.4 11.7 1.0 O3A A:GDP301 4.5 7.6 1.0 HA A:THR25 4.5 11.3 1.0 CG A:ASP65 4.5 11.1 1.0 HG2 A:GLU45 4.5 26.4 1.0 HZ1 A:LYS24 4.7 12.9 1.0 PA A:GDP301 4.7 9.1 1.0 CG A:GLU45 4.7 22.1 1.0 HH22 B:ARG149 4.7 10.0 1.0 HG23 A:THR25 4.8 7.3 1.0 CB A:ALA67 4.8 24.8 1.0 O1A A:GDP301 4.8 11.1 1.0 O A:HOH410 4.8 20.3 1.0 HZ3 A:LYS24 4.8 12.9 1.0 CB A:LYS24 4.8 10.0 1.0 CE A:LYS24 4.9 13.7 1.0 O A:HOH511 4.9 26.5 1.0 HB1 A:ALA67 5.0 29.4 1.0 CD A:GLU45 5.0 29.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A Ras-Like Protein From Cryphonectria Parasitica 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 A Ras-Like Protein From Cryphonectria Parasitica in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:23.1 occ:1.00 O A:HOH409 2.0 30.6 1.0 O A:HOH408 2.1 26.0 1.0 O A:HOH405 2.1 19.0 1.0 OD2 A:ASP46 2.2 26.8 1.0 O A:HOH406 2.2 24.6 1.0 O A:HOH407 2.2 26.2 1.0 CG A:ASP46 3.1 24.2 1.0 HD23 A:LEU44 3.4 30.0 0.0 HD21 A:LEU44 3.6 30.0 0.0 OD1 A:ASP46 3.6 17.8 1.0 HA A:ASP46 3.8 16.2 1.0 CD2 A:LEU44 3.9 25.1 0.0 HG A:LEU44 4.0 30.0 1.0 O A:LEU44 4.1 15.1 1.0 O A:HOH493 4.2 27.2 1.0 CB A:ASP46 4.2 19.5 1.0 O A:GLU45 4.4 14.2 1.0 CA A:ASP46 4.4 13.4 1.0 HH A:TYR40 4.4 14.2 1.0 HB3 A:ASP46 4.5 23.6 1.0 CG A:LEU44 4.5 25.1 1.0 HG3 A:PRO42 4.6 16.6 1.0 HD22 A:LEU44 4.7 30.0 0.0 HB2 A:PRO42 4.8 21.4 1.0 O A:HOH647 4.8 31.3 1.0 C A:GLU45 4.8 15.3 1.0 N A:ASP46 4.8 17.9 1.0 O A:HOH507 4.8 32.6 1.0 O A:HOH449 5.0 24.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A Ras-Like Protein From Cryphonectria Parasitica 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 A Ras-Like Protein From Cryphonectria Parasitica in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:10.4 occ:1.00 O1B B:GDP600 2.1 6.9 1.0 O B:HOH703 2.1 9.2 1.0 O B:HOH702 2.2 9.1 1.0 OG1 B:THR25 2.2 7.6 1.0 O B:HOH704 2.2 11.0 1.0 O B:HOH701 2.2 17.3 1.0 H B:THR25 3.3 11.7 1.0 PB B:GDP600 3.3 8.8 1.0 HB B:THR25 3.3 10.4 1.0 CB B:THR25 3.3 8.7 1.0 O3B B:GDP600 3.5 9.9 1.0 O B:HOH760 3.9 21.4 1.0 N B:THR25 3.9 9.7 1.0 HB2 B:LYS24 3.9 11.3 1.0 OD2 B:ASP65 4.0 10.8 1.0 HG3 B:GLU45 4.1 20.0 1.0 HE2 B:LYS24 4.1 12.4 1.0 CA B:THR25 4.2 12.8 1.0 O2A B:GDP600 4.2 8.3 1.0 OE2 B:GLU45 4.2 18.7 1.0 OD1 B:ASP65 4.2 8.9 1.0 OD1 B:ASP41 4.3 14.6 1.0 O2B B:GDP600 4.3 7.1 1.0 O B:HOH705 4.3 18.1 1.0 O B:HOH706 4.3 12.2 1.0 HG21 B:THR25 4.4 10.7 1.0 O3A B:GDP600 4.4 9.3 1.0 HG2 B:GLU45 4.4 20.0 1.0 CG2 B:THR25 4.4 9.0 1.0 HA B:THR25 4.5 15.4 1.0 CG B:ASP65 4.5 10.1 1.0 HZ1 B:LYS24 4.6 15.4 1.0 O B:THR66 4.6 11.8 1.0 CG B:GLU45 4.6 17.0 1.0 PA B:GDP600 4.6 9.1 1.0 HZ3 B:LYS24 4.7 15.4 1.0 HG23 B:THR25 4.8 10.7 1.0 O1A B:GDP600 4.8 12.2 1.0 CB B:LYS24 4.8 9.3 1.0 O B:HOH838 4.8 25.4 1.0 NZ B:LYS24 4.9 12.9 1.0 CD B:GLU45 4.9 23.1 1.0 CE B:LYS24 4.9 10.4 1.0 C B:LYS24 5.0 10.3 1.0 HB3 B:LYS24 5.0 11.3 1.0

C.Chen, G.Choi. Crystal Structure of A Ras-Like Protein From Cryphonectria Parasitica in Complex with Gdp To Be Published.