Magnesium in PDB 6s2u: Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp

All present enzymatic activity of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp:
2.7.6.5;

The structure of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp, PDB code: 6s2u was solved by A.Garcia-Pino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.36 / 2.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.739, 50.346, 86.057, 90.00, 111.00, 90.00
R / Rfree (%)	21.4 / 24.8

The structure of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp (pdb code 6s2u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp, PDB code: 6s2u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:39.6 occ:1.00 O10 A:GN3403 2.2 0.0 1.0 O9 A:GN3403 2.2 0.5 1.0 P2 A:GN3403 2.7 0.2 1.0 C5' A:AMP402 2.8 75.7 1.0 O5' A:AMP402 3.0 73.1 1.0 O3P A:AMP402 3.3 75.6 1.0 O1P A:AMP402 3.5 71.2 1.0 P A:AMP402 3.5 73.1 1.0 O8 A:GN3403 3.6 0.4 1.0 C8 A:AMP402 3.6 88.7 1.0 O A:HOH502 3.9 47.8 1.0 C4' A:AMP402 4.0 80.0 1.0 C7 A:GN3403 4.1 0.1 1.0 N4 A:GN3403 4.1 0.7 1.0 C8 A:GN3403 4.3 0.6 1.0 NH2 A:ARG249 4.3 67.0 1.0 O4' A:AMP402 4.4 81.2 1.0 N7 A:AMP402 4.4 90.0 1.0 O A:HOH501 4.5 30.0 1.0 C3' A:AMP402 4.6 82.5 1.0 N9 A:AMP402 4.6 87.8 1.0 O14 A:GN3403 4.6 0.8 1.0 C2' A:AMP402 4.6 86.2 1.0 C1' A:AMP402 4.8 85.1 1.0 CZ A:ARG249 5.0 82.7 1.0 NE A:ARG249 5.0 78.0 1.0

Magnesium binding site 2 out of 2 in the Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Catalytic Domain of T. Thermophilus Rel in Complex with Amp and Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:29.8 occ:1.00 O7 A:GN3403 2.4 100.0 1.0 O5 A:GN3403 2.5 99.4 1.0 P1 A:GN3403 3.0 99.2 1.0 NH1 A:ARG316 3.8 55.2 1.0 O A:HOH509 4.0 42.4 1.0 O6 A:GN3403 4.0 96.4 1.0 O4 A:GN3403 4.2 1.0 1.0 CZ A:ARG316 4.8 78.8 1.0 NH2 A:ARG316 4.8 71.6 1.0

H.Tamman, K.Van Nerom, H.Takada, N.Vandenberk, D.Scholl, Y.Polikanov, J.Hofkens, A.Talavera, V.Hauryliuk, J.Hendrix, A.Garcia-Pino. A Nucleotide-Switch Mechanism Mediates Opposing Catalytic Activities of Rel Enzymes. Nat.Chem.Biol. V. 16 834 2020.
ISSN: ESSN 1552-4469
PubMed: 32393900
DOI: 10.1038/S41589-020-0520-2