Magnesium in PDB 7o9f: Bacillus Subtilis Ffh in Complex with Ppgpp

The structure of Bacillus Subtilis Ffh in Complex with Ppgpp, PDB code: 7o9f was solved by L.Czech, C.-N.Mais, G.Bange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.12 / 2.51
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	163.28, 163.28, 93.47, 90, 90, 90
R / Rfree (%)	21.4 / 25.3

The binding sites of Magnesium atom in the Bacillus Subtilis Ffh in Complex with Ppgpp (pdb code 7o9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Bacillus Subtilis Ffh in Complex with Ppgpp, PDB code: 7o9f:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Bacillus Subtilis Ffh in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacillus Subtilis Ffh in Complex with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:67.6 occ:1.00 O3B A:G4P401 2.0 64.8 1.0 O A:HOH508 2.1 63.6 1.0 O A:HOH509 2.2 58.3 1.0 O A:HOH503 2.2 59.9 1.0 O A:HOH507 2.2 69.1 1.0 OG1 A:THR115 2.2 51.6 1.0 PB A:G4P401 3.2 61.8 1.0 CB A:THR115 3.3 57.7 1.0 O2B A:G4P401 3.5 78.4 1.0 N A:THR115 3.9 47.9 1.0 OD2 A:ASP139 4.1 68.1 1.0 NH1 A:ARG142 4.1 112.6 1.0 CA A:THR115 4.1 47.0 1.0 O1B A:G4P401 4.2 73.5 1.0 O2A A:G4P401 4.2 60.5 1.0 OD2 A:ASP191 4.2 60.9 1.0 O3A A:G4P401 4.3 67.8 1.0 OD1 A:ASP191 4.3 64.7 1.0 CG2 A:THR115 4.4 60.1 1.0 PA A:G4P401 4.5 53.6 1.0 O A:HOH501 4.5 72.0 1.0 OE1 A:GLN148 4.5 71.7 1.0 O1A A:G4P401 4.6 55.8 1.0 CB A:LYS114 4.6 53.7 1.0 CE A:LYS114 4.7 72.3 1.0 CG A:ASP191 4.7 66.7 1.0 C A:LYS114 4.9 56.9 1.0 CZ A:ARG142 5.0 107.5 1.0

Magnesium binding site 2 out of 3 in the Bacillus Subtilis Ffh in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacillus Subtilis Ffh in Complex with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:77.6 occ:1.00 O B:HOH504 1.9 78.6 1.0 OG1 B:THR115 2.0 57.1 1.0 O2B B:G4P401 2.0 67.7 1.0 O B:HOH506 2.2 61.6 1.0 O B:HOH501 2.3 69.1 1.0 CB B:THR115 3.2 58.2 1.0 PB B:G4P401 3.3 67.6 1.0 NH2 B:ARG142 3.4 114.2 1.0 O1B B:G4P401 3.6 75.2 1.0 N B:THR115 3.6 67.8 1.0 OD2 B:ASP191 3.7 67.8 1.0 CA B:THR115 4.0 72.9 1.0 OD2 B:ASP139 4.0 95.4 1.0 OD1 B:ASP191 4.0 75.2 1.0 O3B B:G4P401 4.1 76.8 1.0 CG B:ASP191 4.3 80.0 1.0 CB B:LYS114 4.3 70.7 1.0 CG2 B:THR115 4.4 68.0 1.0 O2A B:G4P401 4.5 70.7 1.0 O3A B:G4P401 4.5 71.1 1.0 CE B:LYS114 4.6 76.8 1.0 C B:LYS114 4.7 72.7 1.0 CZ B:ARG142 4.7 109.0 1.0 O1A B:G4P401 4.8 66.7 1.0 PA B:G4P401 4.9 87.9 1.0 OE1 B:GLN148 4.9 74.2 1.0 CA B:LYS114 5.0 69.2 1.0 O B:THR192 5.0 73.2 1.0 CG B:ASP139 5.0 83.4 1.0

Magnesium binding site 3 out of 3 in the Bacillus Subtilis Ffh in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacillus Subtilis Ffh in Complex with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:122.9 occ:1.00 OG1 C:THR115 2.6 131.7 1.0 O1B C:G4P401 2.7 121.8 1.0 NH1 C:ARG142 2.8 164.3 1.0 O3B C:G4P401 3.5 126.6 1.0 OD2 C:ASP139 3.5 153.7 1.0 PB C:G4P401 3.6 119.9 1.0 CZ C:ARG142 3.8 166.9 1.0 CB C:THR115 3.8 131.0 1.0 OE1 C:GLN148 4.1 134.3 1.0 OD2 C:ASP191 4.3 141.7 1.0 CD C:ARG142 4.3 161.8 1.0 NE C:ARG142 4.4 166.5 1.0 O2A C:G4P401 4.4 129.2 1.0 CG2 C:THR115 4.6 131.2 1.0 NH2 C:ARG142 4.6 163.2 1.0 O2B C:G4P401 4.6 127.7 1.0 CG C:ASP139 4.7 152.5 1.0 N C:THR115 4.7 126.0 1.0 O3A C:G4P401 4.7 121.2 1.0 PA C:G4P401 4.9 114.9 1.0 CA C:THR115 4.9 128.2 1.0 OD1 C:ASP191 4.9 153.7 1.0 O1A C:G4P401 4.9 117.0 1.0 CB C:ALA145 4.9 148.0 1.0

L.Czech, C.N.Mais, H.Kratzat, P.Sarmah, P.Giammarinaro, S.A.Freibert, H.F.Esser, J.Musial, O.Berninghausen, W.Steinchen, R.Beckmann, H.G.Koch, G.Bange. Inhibition of Srp-Dependent Protein Secretion By the Bacterial Alarmone (P)Ppgpp. Nat Commun V. 13 1069 2022.
ISSN: ESSN 2041-1723
PubMed: 35217658
DOI: 10.1038/S41467-022-28675-0