Manganese in PDB 6s2v: 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;

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

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

Chlorine	(Cl)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Manganese 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 Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel, PDB code: 6s2v:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:98.7 occ:1.00 OD2 A:ASP146 2.0 1.0 1.0 NE2 A:HIS52 2.0 0.4 1.0 OD2 A:ASP77 2.3 0.7 1.0 NE2 A:HIS76 2.4 0.5 1.0 CD2 A:HIS52 3.0 0.2 1.0 CE1 A:HIS52 3.1 0.2 1.0 CG A:ASP146 3.1 95.4 1.0 CD2 A:HIS76 3.1 0.7 1.0 CG A:ASP77 3.2 0.9 1.0 CE1 A:HIS76 3.5 0.1 1.0 OD1 A:ASP77 3.5 0.7 1.0 OD1 A:ASP146 3.8 98.3 1.0 OH A:TYR49 4.1 0.3 1.0 CB A:ASP146 4.1 78.9 1.0 CG A:HIS52 4.1 0.2 1.0 ND1 A:HIS52 4.2 0.3 1.0 CG A:HIS76 4.3 0.1 1.0 ND1 A:HIS76 4.5 0.7 1.0 CB A:ASP77 4.6 0.9 1.0 OD1 A:ASN150 4.7 0.9 1.0 CA A:ASP146 4.9 76.7 1.0

Manganese binding site 2 out of 3 in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:0.8 occ:1.00 NE2 B:HIS76 2.2 0.2 1.0 OD1 B:ASP146 2.3 0.8 1.0 NE2 B:HIS52 2.6 0.7 1.0 OD2 B:ASP146 2.8 0.8 1.0 OD2 B:ASP77 2.8 0.2 1.0 CD2 B:HIS76 2.8 0.5 1.0 CG B:ASP146 2.8 0.3 1.0 CE1 B:HIS52 3.4 0.3 1.0 CE1 B:HIS76 3.5 0.9 1.0 CD2 B:HIS52 3.7 0.9 1.0 CG B:ASP77 3.9 0.8 1.0 CG B:HIS76 4.1 0.8 1.0 CB B:ASP146 4.2 0.8 1.0 OH B:TYR49 4.3 0.0 1.0 OD1 B:ASP77 4.3 0.5 1.0 ND2 B:ASN150 4.4 0.2 1.0 ND1 B:HIS76 4.4 0.6 1.0 ND1 B:HIS52 4.6 0.9 1.0 CG B:HIS52 4.7 0.3 1.0 OD1 B:ASN150 4.8 0.2 1.0

Manganese binding site 3 out of 3 in the Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the N-Terminal Catalytic Region of T. Thermophilus Rel within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:73.0 occ:1.00 OD1 C:ASP146 2.1 84.7 1.0 NE2 C:HIS52 2.1 61.3 1.0 NE2 C:HIS76 2.3 67.5 1.0 OD2 C:ASP77 2.6 91.2 1.0 CE1 C:HIS52 3.0 61.0 1.0 CD2 C:HIS52 3.1 61.8 1.0 CG C:ASP146 3.1 82.9 1.0 CD2 C:HIS76 3.2 68.0 1.0 OD1 C:ASP77 3.2 87.4 1.0 CE1 C:HIS76 3.3 67.3 1.0 CG C:ASP77 3.3 86.1 1.0 OD2 C:ASP146 3.6 89.3 1.0 OH C:TYR49 3.9 68.9 1.0 ND1 C:HIS52 4.1 61.8 1.0 CG C:HIS52 4.1 60.4 1.0 ND2 C:ASN150 4.2 87.8 1.0 CB C:ASP146 4.4 66.8 1.0 CG C:HIS76 4.4 67.3 1.0 ND1 C:HIS76 4.4 68.5 1.0 CB C:ASP77 4.8 76.5 1.0 OD1 C:ASN150 4.8 87.5 1.0 OE2 C:GLU104 4.8 0.8 1.0 CA C:ASP146 4.9 64.5 1.0 CG C:ASN150 5.0 95.8 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