Magnesium in PDB 5cyo: High Resolution Septin 9 Gtpase Domain in Complex with Gdp

The structure of High Resolution Septin 9 Gtpase Domain in Complex with Gdp, PDB code: 5cyo was solved by S.S.Matos, D.A.Leonardo, H.M.Pereira, E.Horjales, A.P.U.Araujo, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.29 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.497, 78.049, 77.443, 90.00, 105.92, 90.00
R / Rfree (%)	18.3 / 22.8

The binding sites of Magnesium atom in the High Resolution Septin 9 Gtpase Domain in Complex with Gdp (pdb code 5cyo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the High Resolution Septin 9 Gtpase Domain in Complex with Gdp, PDB code: 5cyo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the High Resolution Septin 9 Gtpase Domain 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 High Resolution Septin 9 Gtpase Domain in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:28.1 occ:1.00 O2B A:GDP301 2.0 22.0 1.0 OG A:SER37 2.1 26.1 1.0 O A:HOH413 2.1 21.7 1.0 OG1 A:THR64 2.1 30.2 1.0 O A:HOH420 2.2 22.3 1.0 O A:HOH423 2.2 23.8 1.0 CB A:SER37 3.1 26.9 1.0 CB A:THR64 3.2 27.3 1.0 PB A:GDP301 3.2 22.4 1.0 O1B A:GDP301 3.4 23.1 1.0 N A:THR64 3.8 25.8 1.0 N A:SER37 3.8 24.0 1.0 O A:HOH473 3.9 36.7 1.0 OD2 A:ASP87 4.0 24.5 1.0 O1A A:GDP301 4.0 21.8 1.0 CA A:SER37 4.0 29.2 1.0 OD1 A:ASP87 4.1 28.2 1.0 CA A:THR64 4.1 33.0 1.0 O3B A:GDP301 4.1 20.6 1.0 O A:HOH459 4.2 36.4 1.0 CG2 A:THR64 4.3 24.4 1.0 O3A A:GDP301 4.4 23.9 1.0 CG A:ASP87 4.4 26.3 1.0 PA A:GDP301 4.5 21.7 1.0 O A:PRO62 4.6 28.0 1.0 O2A A:GDP301 4.6 20.1 1.0 O A:HOH417 4.7 47.6 1.0 NZ A:LYS36 4.7 25.5 1.0 O A:THR88 4.8 27.9 1.0 C A:LYS63 4.8 27.4 1.0 CB A:LYS36 4.8 24.3 1.0 C A:LYS36 4.9 23.6 1.0

Magnesium binding site 2 out of 2 in the High Resolution Septin 9 Gtpase Domain 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 High Resolution Septin 9 Gtpase Domain in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:29.2 occ:1.00 OG B:SER37 2.0 28.6 1.0 O1B B:GDP301 2.0 26.2 1.0 O B:HOH407 2.1 24.5 1.0 O B:HOH444 2.1 26.0 1.0 O B:HOH419 2.1 28.5 1.0 OG1 B:THR64 2.2 30.0 1.0 CB B:SER37 3.1 30.8 1.0 PB B:GDP301 3.2 28.6 1.0 CB B:THR64 3.3 28.5 1.0 O3B B:GDP301 3.4 25.4 1.0 N B:SER37 3.8 32.0 1.0 OD2 B:ASP87 3.8 33.4 1.0 N B:THR64 3.9 32.9 1.0 CA B:SER37 4.0 32.7 1.0 O2A B:GDP301 4.0 25.8 1.0 OD1 B:ASP87 4.0 29.4 1.0 O B:HOH446 4.2 36.7 1.0 CA B:THR64 4.2 32.2 1.0 O2B B:GDP301 4.2 25.0 1.0 O B:HOH425 4.2 44.9 1.0 CG B:ASP87 4.3 32.6 1.0 O3A B:GDP301 4.4 32.7 1.0 CG2 B:THR64 4.4 25.2 1.0 PA B:GDP301 4.5 28.6 1.0 O B:PRO62 4.5 39.3 1.0 O1A B:GDP301 4.6 26.9 1.0 NZ B:LYS36 4.8 25.8 1.0 CB B:LYS36 4.8 23.1 1.0 O B:THR88 4.9 33.2 1.0 C B:LYS36 4.9 29.9 1.0 C B:LYS63 4.9 35.9 1.0

S.S.Matos, D.A.Leonardo, H.M.Pereira, E.Horjales, A.P.U.Araujo, R.C.Garratt. High Resolution Septin 9 Gtpase Domain in Complex with Gdp To Be Published.