Magnesium in PDB 6mqk: Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp

The structure of Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp, PDB code: 6mqk was solved by D.K.S.V.Castro, H.M.Pereira, J.Brandao-Neto, A.P.U.Ulian, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.59 / 2.19
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.960, 69.250, 88.230, 75.45, 89.46, 76.43
R / Rfree (%)	18.4 / 22.9

The binding sites of Magnesium atom in the Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp (pdb code 6mqk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp, PDB code: 6mqk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Gtpase Domain of Human Septin 12 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 Gtpase Domain of Human Septin 12 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:44.4 occ:1.00 OG A:SER63 2.0 40.0 1.0 O1B A:GDP401 2.0 40.6 1.0 O A:HOH506 2.1 36.6 1.0 O A:HOH508 2.1 47.1 1.0 O A:HOH516 2.4 35.8 1.0 OG1 A:THR89 2.5 84.0 1.0 CG2 A:THR89 3.1 85.2 1.0 CB A:SER63 3.1 37.6 1.0 CB A:THR89 3.3 85.5 1.0 PB A:GDP401 3.5 39.2 1.0 N A:THR89 3.6 84.7 1.0 OD2 A:ASP112 3.8 47.6 1.0 O3B A:GDP401 3.8 37.3 1.0 N A:SER63 3.9 35.6 1.0 CA A:SER63 4.1 36.3 1.0 O A:PRO87 4.1 85.6 1.0 CA A:THR89 4.1 86.5 1.0 O2A A:GDP401 4.2 38.0 1.0 O2B A:GDP401 4.2 41.3 1.0 OD1 A:ASP112 4.2 49.8 1.0 CG A:ASP112 4.4 48.0 1.0 O3A A:GDP401 4.6 41.7 1.0 C A:GLN88 4.7 85.5 1.0 O A:THR113 4.8 53.0 1.0 PA A:GDP401 4.8 43.1 1.0 CA A:GLN88 4.9 85.8 1.0 NZ A:LYS62 5.0 36.6 1.0 O1A A:GDP401 5.0 45.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Gtpase Domain of Human Septin 12 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 Gtpase Domain of Human Septin 12 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:33.3 occ:1.00 O1B B:GDP401 2.0 29.8 1.0 OG B:SER63 2.0 49.7 1.0 O B:HOH509 2.1 33.1 1.0 O B:HOH517 2.1 33.7 1.0 OG1 B:THR89 2.1 56.6 1.0 O B:HOH513 2.1 38.5 1.0 CB B:SER63 3.2 41.9 1.0 CB B:THR89 3.2 55.6 1.0 PB B:GDP401 3.3 38.6 1.0 O2B B:GDP401 3.5 33.4 1.0 N B:THR89 3.8 61.2 1.0 N B:SER63 3.8 36.5 1.0 OD2 B:ASP112 3.9 42.5 1.0 O2A B:GDP401 4.0 35.8 1.0 O B:HOH520 4.0 42.6 1.0 CA B:SER63 4.0 38.1 1.0 OD1 B:ASP112 4.1 42.8 1.0 CA B:THR89 4.1 57.5 1.0 O B:PRO87 4.2 70.2 1.0 O3B B:GDP401 4.2 28.5 1.0 CG2 B:THR89 4.3 50.5 1.0 O3A B:GDP401 4.4 38.0 1.0 CG B:ASP112 4.4 41.2 1.0 PA B:GDP401 4.6 39.2 1.0 C B:GLN88 4.8 62.9 1.0 O1A B:GDP401 4.8 35.1 1.0 O B:THR113 4.8 39.0 1.0 C B:LYS62 4.9 36.0 1.0 CB B:LYS62 5.0 33.7 1.0 NZ B:LYS62 5.0 41.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Gtpase Domain of Human Septin 12 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 Gtpase Domain of Human Septin 12 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:47.8 occ:1.00 O C:HOH514 2.0 38.7 1.0 OG1 C:THR89 2.1 85.5 1.0 O C:HOH518 2.2 41.5 1.0 O C:HOH512 2.2 36.5 1.0 OG C:SER63 2.3 39.3 1.0 O3B C:GDP401 2.6 38.5 1.0 CB C:THR89 3.0 88.1 1.0 N C:THR89 3.2 95.3 1.0 CB C:SER63 3.6 38.0 1.0 O1B C:GDP401 3.7 39.9 1.0 CA C:THR89 3.7 92.4 1.0 PB C:GDP401 3.7 37.4 1.0 O C:PRO87 4.0 95.9 1.0 OD2 C:ASP112 4.0 40.6 1.0 CG2 C:THR89 4.2 87.0 1.0 C C:GLN88 4.3 98.2 1.0 OD1 C:ASP112 4.3 39.1 1.0 N C:SER63 4.3 33.2 1.0 O2A C:GDP401 4.4 34.5 1.0 CA C:GLN88 4.5 98.4 1.0 CG C:ASP112 4.5 40.0 1.0 CA C:SER63 4.5 37.1 1.0 O2B C:GDP401 4.6 34.3 1.0 O C:THR113 4.7 53.2 1.0 C C:THR89 4.9 93.5 1.0 O3A C:GDP401 5.0 40.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Gtpase Domain of Human Septin 12 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 Gtpase Domain of Human Septin 12 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:42.7 occ:1.00 O D:HOH517 2.0 47.0 1.0 O D:HOH522 2.0 35.8 1.0 OG D:SER63 2.1 40.4 1.0 O D:HOH506 2.3 40.9 1.0 O3B D:GDP401 2.3 36.8 1.0 CB D:SER63 3.1 37.6 1.0 PB D:GDP401 3.5 33.5 1.0 O1B D:GDP401 3.5 34.3 1.0 OD2 D:ASP112 4.0 44.4 1.0 N D:SER63 4.0 34.7 1.0 O2A D:GDP401 4.0 34.3 1.0 O D:THR86 4.1 67.2 1.0 CA D:SER63 4.2 37.9 1.0 O D:PRO87 4.3 60.4 1.0 OD1 D:ASP112 4.5 41.6 1.0 O3A D:GDP401 4.5 35.5 1.0 O2B D:GDP401 4.5 27.9 1.0 PA D:GDP401 4.5 37.0 1.0 CG2 D:THR86 4.6 69.8 1.0 CG D:ASP112 4.6 43.7 1.0 O1A D:GDP401 4.7 35.8 1.0 NE2 A:HIS170 4.8 43.6 1.0 CB D:THR86 4.8 69.1 1.0 O D:HOH541 4.9 45.7 1.0 C D:PRO87 4.9 66.0 1.0 CE1 A:HIS170 4.9 44.5 1.0 C D:THR86 5.0 68.4 1.0

D.K.S.V.Castro, H.M.Pereira, J.Brandao-Neto, A.P.U.Ulian, R.C.Garratt. Crystal Structure of Gtpase Domain of Human Septin 12 To Be Published.