Magnesium in PDB 3syn: Crystal Structure of Flhf in Complex with Its Activator

The structure of Crystal Structure of Flhf in Complex with Its Activator, PDB code: 3syn was solved by G.Bange, N.Kuemmerer, K.Wild, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.09 / 3.06
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.790, 63.360, 114.500, 92.26, 100.96, 94.25
R / Rfree (%)	18.1 / 23.9

The structure of Crystal Structure of Flhf in Complex with Its Activator also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Aluminium	(Al)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Flhf in Complex with Its Activator (pdb code 3syn). 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 Flhf in Complex with Its Activator, PDB code: 3syn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Flhf in Complex with Its Activator


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 Flhf in Complex with Its Activator within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg367 b:14.7 occ:1.00 O3B A:GDP1 2.3 12.2 1.0 OG1 A:THR189 2.3 22.2 1.0 O A:HOH9 2.4 18.1 1.0 O A:HOH373 2.5 20.8 1.0 F2 A:AF3368 3.0 10.2 1.0 O1B A:GDP1 3.0 11.8 1.0 F3 A:AF3368 3.0 18.2 1.0 PB A:GDP1 3.2 15.2 1.0 AL A:AF3368 3.3 15.5 1.0 OD2 A:ASP213 3.6 22.4 1.0 CB A:THR189 3.6 23.4 1.0 OD2 A:ASP259 3.7 29.8 1.0 N A:THR189 4.0 9.2 1.0 O A:THR260 4.0 13.3 1.0 O2B A:GDP1 4.1 14.6 1.0 OD1 A:ASP259 4.2 23.2 1.0 CG A:ASP259 4.3 24.2 1.0 CA A:THR189 4.3 19.0 1.0 CE A:LYS188 4.5 11.2 1.0 O3A A:GDP1 4.6 14.4 1.0 NZ A:LYS188 4.6 13.0 1.0 CG A:ASP213 4.7 21.2 1.0 CB A:LYS188 4.7 8.3 1.0 CG2 A:THR189 4.7 7.0 1.0 F1 A:AF3368 4.7 34.2 1.0 O2A A:GDP1 4.8 16.8 1.0 OE1 A:GLN222 4.9 21.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Flhf in Complex with Its Activator


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 Flhf in Complex with Its Activator within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg367 b:10.8 occ:1.00 O B:HOH373 2.1 13.9 1.0 O B:HOH29 2.4 9.2 1.0 O2B B:GDP2 2.6 7.8 1.0 F3 B:AF3368 2.7 19.8 1.0 F2 B:AF3368 2.8 7.9 1.0 OG1 B:THR189 2.8 16.3 1.0 O B:HOH374 3.0 26.7 1.0 AL B:AF3368 3.1 24.5 1.0 OD2 B:ASP213 3.2 12.0 1.0 O3B B:GDP2 3.3 11.5 1.0 PB B:GDP2 3.4 10.1 1.0 O B:THR260 3.7 14.7 1.0 OD2 B:ASP259 4.0 24.6 1.0 O1B B:GDP2 4.0 7.9 1.0 O B:HOH46 4.0 8.7 1.0 CB B:THR189 4.2 20.1 1.0 CE B:LYS188 4.3 10.8 1.0 OD1 B:ASP259 4.3 25.1 1.0 NZ B:LYS188 4.3 10.8 1.0 CG B:ASP213 4.3 20.3 1.0 N B:THR189 4.3 9.5 1.0 CG B:ASP259 4.5 20.1 1.0 F1 B:AF3368 4.7 31.5 1.0 CB B:ASP213 4.7 21.6 1.0 CB B:LYS188 4.8 8.1 1.0 C B:THR260 4.8 14.3 1.0 CA B:THR189 4.8 17.2 1.0 O3A B:GDP2 4.8 13.6 1.0 N B:GLY262 4.8 10.3 1.0 CB B:ALA219 5.0 11.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Flhf in Complex with Its Activator


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 Flhf in Complex with Its Activator within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg367 b:23.1 occ:1.00 O C:HOH373 2.3 14.8 1.0 OG1 C:THR189 2.4 18.4 1.0 O C:HOH372 2.5 22.2 1.0 O2B C:GDP3 2.8 6.9 1.0 F2 C:AF3368 2.9 15.6 1.0 OD2 C:ASP213 3.0 24.6 1.0 O3B C:GDP3 3.5 20.9 1.0 AL C:AF3368 3.6 27.8 1.0 OD2 C:ASP259 3.6 29.8 1.0 F3 C:AF3368 3.6 16.6 1.0 PB C:GDP3 3.8 10.0 1.0 CB C:THR189 3.8 17.8 1.0 CG C:ASP213 4.1 23.2 1.0 O C:THR260 4.2 12.1 1.0 CB C:ALA219 4.2 10.8 1.0 CG C:ASP259 4.3 25.0 1.0 OD1 C:ASP259 4.4 28.9 1.0 CB C:ASP213 4.4 15.5 1.0 O D:HOH33 4.4 15.6 1.0 N C:THR189 4.6 11.6 1.0 OE1 C:GLN222 4.6 22.0 1.0 CG2 C:THR189 4.6 8.5 1.0 CA C:THR189 4.7 16.7 1.0 O3A C:GDP3 4.8 15.4 1.0 O1B C:GDP3 5.0 11.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Flhf in Complex with Its Activator


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 Flhf in Complex with Its Activator within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg367 b:4.2 occ:1.00 O D:HOH26 2.4 21.5 1.0 O D:HOH40 2.4 11.6 1.0 O2B D:GDP4 2.6 8.5 1.0 OG1 D:THR189 2.7 17.4 1.0 F2 D:AF3368 2.8 13.6 1.0 F3 D:AF3368 2.9 23.0 1.0 OD2 D:ASP213 3.0 21.6 1.0 AL D:AF3368 3.1 15.9 1.0 O3B D:GDP4 3.5 13.7 1.0 PB D:GDP4 3.6 8.9 1.0 O D:HOH372 3.9 22.6 1.0 OD2 D:ASP259 4.0 27.6 1.0 CB D:THR189 4.1 17.8 1.0 O D:THR260 4.1 13.7 1.0 CG D:ASP213 4.2 21.3 1.0 CB D:ALA219 4.5 12.2 1.0 O1B D:GDP4 4.6 5.5 1.0 OD1 D:ASP259 4.6 22.6 1.0 N D:THR189 4.6 11.1 1.0 CB D:ASP213 4.6 19.2 1.0 CG D:ASP259 4.6 21.3 1.0 F1 D:AF3368 4.7 31.7 1.0 O3A D:GDP4 4.8 14.4 1.0 OE1 D:GLN222 4.8 21.3 1.0 CE D:LYS188 4.9 12.2 1.0 CA D:THR189 4.9 14.9 1.0 NZ D:LYS188 4.9 11.5 1.0 CG2 D:THR189 5.0 6.9 1.0

G.Bange, N.Kummerer, P.Grudnik, R.Lindner, G.Petzold, D.Kressler, E.Hurt, K.Wild, I.Sinning. Structural Basis For the Molecular Evolution of Srp-Gtpase Activation By Protein. Nat.Struct.Mol.Biol. V. 18 1376 2011.
ISSN: ISSN 1545-9993
PubMed: 22056770
DOI: 10.1038/NSMB.2141