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Sodium in PDB 6s2v: Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel

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

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

Protein crystallography data

The structure of Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel, PDB code: 6s2v 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) 40.77 / 2.96
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.737, 105.737, 241.455, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27.5

Other elements in 6s2v:

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

Manganese (Mn) 3 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel (pdb code 6s2v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel, PDB code: 6s2v:

Sodium binding site 1 out of 1 in 6s2v

Go back to Sodium Binding Sites List in 6s2v
Sodium binding site 1 out of 1 in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na406

b:56.9
occ:1.00
 O C:ARG24 2.8 0.2 1.0
OE1 C:GLU13 3.6 0.2 1.0
C C:ARG24 4.0 0.6 1.0
CG C:ARG28 4.1 94.1 1.0
CZ2 C:TRP9 4.2 84.4 1.0
CB C:ARG28 4.2 87.1 1.0
OE2 C:GLU13 4.3 0.9 1.0
CD C:GLU13 4.3 0.5 1.0
CA C:ALA25 4.7 95.4 1.0
NE1 C:TRP9 4.7 83.8 1.0
N C:ALA25 4.8 96.2 1.0
CE2 C:TRP9 4.8 85.0 1.0
CB C:ARG24 4.8 97.5 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 8 13:22:19 2024

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