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Manganese 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:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total only one binding site of Manganese was determined in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel Bound to Ppgpp, PDB code: 6s2t:

Manganese binding site 1 out of 1 in 6s2t

Go back to Manganese Binding Sites List in 6s2t
Manganese 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 Manganese with other atoms in the Mn 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:Mn404

b:99.5
occ:1.00
 OD2 A:ASP146 2.1 77.8 1.0
OD2 A:ASP77 2.3 91.3 1.0
NE2 A:HIS52 2.4 58.4 1.0
O1C A:G4P401 2.5 0.2 1.0
NE2 A:HIS76 2.8 55.6 1.0
CG A:ASP77 3.1 78.3 1.0
OD1 A:ASP77 3.2 76.7 1.0
CG A:ASP146 3.3 72.5 1.0
CE1 A:HIS52 3.3 58.1 1.0
CD2 A:HIS52 3.3 58.8 1.0
CD2 A:HIS76 3.4 56.0 1.0
OD1 A:ASP146 3.8 74.1 1.0
PC A:G4P401 3.9 0.5 1.0
CE1 A:HIS76 4.0 55.3 1.0
OH A:TYR49 4.0 86.7 1.0
O A:HOH511 4.1 67.9 1.0
O3' A:G4P401 4.3 0.5 1.0
ND1 A:HIS52 4.4 59.0 1.0
O2' A:G4P401 4.4 0.2 1.0
CG A:HIS52 4.4 57.8 1.0
CB A:ASP146 4.5 60.2 1.0
CB A:ASP77 4.5 61.9 1.0
CG A:HIS76 4.6 54.7 1.0
ND2 A:ASN150 4.6 91.8 1.0
OE2 A:GLU104 4.7 60.6 1.0
O3C A:G4P401 4.8 0.2 1.0
O2C A:G4P401 4.8 0.3 1.0
ND1 A:HIS76 4.9 56.1 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: Sun Oct 6 07:05:10 2024

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