Magnesium in PDB 4z54: High Resolution Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix in Complex with Gdp

The structure of High Resolution Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix in Complex with Gdp, PDB code: 4z54 was solved by N.F.Valadares, J.N.Macedo, H.M.Pereira, J.Brandao-Neto, S.O.Matos, D.A.Leonardo, 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)	41.08 / 1.83
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.410, 44.550, 78.950, 99.29, 100.77, 108.39
R / Rfree (%)	17 / 19.9

The binding sites of Magnesium atom in the High Resolution Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix in Complex with Gdp (pdb code 4z54). 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 Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix in Complex with Gdp, PDB code: 4z54:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the High Resolution Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix 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 Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:22.8 occ:1.00 O2B A:GDP401 2.0 24.0 1.0 O A:HOH559 2.0 30.0 1.0 OG1 A:THR102 2.1 24.6 1.0 O A:HOH542 2.1 20.5 1.0 OG A:SER75 2.1 22.9 1.0 O A:HOH564 2.1 23.5 1.0 CB A:SER75 3.1 21.6 1.0 CB A:THR102 3.2 22.2 1.0 PB A:GDP401 3.2 20.3 1.0 O A:HOH589 3.4 30.0 1.0 O1B A:GDP401 3.4 23.5 1.0 N A:THR102 3.7 22.6 1.0 N A:SER75 3.9 19.3 1.0 OD2 A:ASP125 4.0 30.9 1.0 CA A:SER75 4.1 24.2 1.0 CA A:THR102 4.1 27.6 1.0 OD1 A:ASP125 4.1 29.4 1.0 O1A A:GDP401 4.1 22.4 1.0 O3B A:GDP401 4.2 16.9 1.0 CG2 A:THR102 4.3 21.9 1.0 O3A A:GDP401 4.4 17.7 1.0 O A:PRO100 4.4 26.0 1.0 CG A:ASP125 4.4 30.5 1.0 PA A:GDP401 4.6 19.9 1.0 O A:HOH624 4.6 38.9 1.0 NZ A:LYS74 4.6 19.5 1.0 C A:LYS101 4.7 27.4 1.0 O2A A:GDP401 4.8 21.2 1.0 O A:THR126 4.8 22.1 1.0 CB A:LYS74 4.9 23.3 1.0 NE2 B:HIS183 5.0 23.6 1.0 C A:LYS74 5.0 22.9 1.0

Magnesium binding site 2 out of 2 in the High Resolution Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix 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 Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:26.4 occ:1.00 O B:HOH561 2.0 26.1 1.0 O1B B:GDP401 2.0 23.1 1.0 OG B:SER75 2.1 21.7 1.0 O B:HOH543 2.1 26.0 1.0 OG1 B:THR102 2.2 28.0 1.0 O B:HOH601 2.2 24.9 1.0 CB B:SER75 3.2 21.7 1.0 PB B:GDP401 3.2 22.1 1.0 CB B:THR102 3.3 24.8 1.0 O3B B:GDP401 3.4 21.8 1.0 O B:HOH594 3.6 36.2 1.0 N B:THR102 3.8 24.6 1.0 N B:SER75 3.9 23.5 1.0 OD2 B:ASP125 4.1 28.6 1.0 CA B:SER75 4.1 21.5 1.0 O2A B:GDP401 4.1 23.7 1.0 CA B:THR102 4.2 27.8 1.0 O2B B:GDP401 4.2 17.2 1.0 OD1 B:ASP125 4.2 26.9 1.0 O3A B:GDP401 4.3 21.8 1.0 CG2 B:THR102 4.4 27.2 1.0 O B:PRO100 4.4 30.9 1.0 O B:HOH577 4.4 35.8 1.0 CG B:ASP125 4.5 30.5 1.0 NZ B:LYS74 4.5 25.9 1.0 O B:THR126 4.5 22.7 1.0 PA B:GDP401 4.6 22.4 1.0 C B:LYS101 4.8 27.9 1.0 O1A B:GDP401 4.8 20.8 1.0 NE2 A:HIS183 4.8 42.4 1.0 CB B:LYS74 4.8 21.6 1.0 C B:LYS74 4.9 23.7 1.0 CA B:LYS101 5.0 31.7 1.0

N.F.Valadares, J.N.Macedo, H.M.Pereira, J.Brandao-Neto, S.O.Matos, D.A.Leonardo, A.P.U.Araujo, R.C.Garratt. High Resolution Human SEPTIN3 Gtpase Domain with Alpha-Zero Helix in Complex with Gdp To Be Published.