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Magnesium in PDB 6s2t: Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp

Enzymatic activity of Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp

All present enzymatic activity of Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp:
2.7.6.5;

Protein crystallography data

The structure of Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp, PDB code: 6s2t 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) 62.17 / 2.75
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 87.927, 87.927, 184.252, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22

Other elements in 6s2t:

The structure of Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp (pdb code 6s2t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp, PDB code: 6s2t:

Magnesium binding site 1 out of 1 in 6s2t

Go back to Magnesium Binding Sites List in 6s2t
Magnesium binding site 1 out of 1 in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to 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 N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:50.8
occ:1.00
 OD1 A:ASP146 2.4 74.1 1.0
NH1 A:ARG147 2.6 60.2 1.0
O3C A:G4P401 2.9 0.2 1.0
O3D A:G4P401 3.2 0.7 1.0
OD1 A:ASN150 3.4 86.0 1.0
PD A:G4P401 3.4 0.8 1.0
NZ A:LYS143 3.6 43.7 1.0
O2D A:G4P401 3.6 0.2 1.0
CA A:ARG147 3.7 58.1 1.0
CG A:ASP146 3.7 72.5 1.0
CE A:LYS143 3.7 49.6 1.0
N A:ARG147 3.8 58.5 1.0
CG A:ASN150 3.8 97.1 1.0
CZ A:ARG147 3.8 75.5 1.0
CB A:ARG147 3.9 56.3 1.0
O1C A:G4P401 4.1 0.2 1.0
PC A:G4P401 4.2 0.5 1.0
C A:ASP146 4.2 62.8 1.0
CD A:ARG147 4.2 68.5 1.0
CB A:ASN150 4.3 69.9 1.0
O A:ASP146 4.5 63.5 1.0
NE A:ARG147 4.5 66.8 1.0
OD2 A:ASP146 4.5 77.8 1.0
CB A:ASP146 4.5 60.2 1.0
ND2 A:ASN150 4.6 91.8 1.0
CG A:ARG147 4.7 62.2 1.0
NH2 A:ARG147 4.8 61.6 1.0
O1D A:G4P401 4.8 0.2 1.0
O2C A:G4P401 4.9 0.3 1.0
O A:LYS143 4.9 55.2 1.0

Reference:

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
Page generated: Tue Oct 1 17:36:39 2024

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