Nickel in PDB 8qfr: Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic)

The structure of Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic), PDB code: 8qfr was solved by C.M.Vasseur, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.36 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.633, 59.088, 134.446, 90, 90, 90
R / Rfree (%)	17.9 / 22

The structure of Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic) also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	3 atoms

The binding sites of Nickel atom in the Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic) (pdb code 8qfr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic), PDB code: 8qfr:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:20.5 occ:1.00 NE2 A:HIS134 2.0 17.6 1.0 NE2 A:HIS90 2.0 16.0 1.0 S15 A:LW8302 2.1 28.8 0.7 NE2 A:HIS88 2.1 14.9 1.0 O A:HOH442 2.6 20.7 1.0 O A:HOH401 2.9 27.8 1.0 CE1 A:HIS134 2.9 14.8 1.0 CE1 A:HIS90 3.0 18.4 1.0 CD2 A:HIS88 3.0 15.9 1.0 CD2 A:HIS90 3.0 14.6 1.0 CD2 A:HIS134 3.1 16.2 1.0 CE1 A:HIS88 3.1 17.4 1.0 C14 A:LW8302 3.4 33.9 0.7 H15 A:LW8302 3.8 46.0 0.7 N11 A:LW8302 4.0 38.3 0.7 ND1 A:HIS134 4.0 14.3 1.0 ND1 A:HIS90 4.1 17.4 1.0 CG A:HIS90 4.1 17.1 1.0 CG A:HIS88 4.2 17.9 1.0 ND1 A:HIS88 4.2 19.0 1.0 CG A:HIS134 4.2 13.6 1.0 OH A:TYR149 4.3 21.4 1.0 N13 A:LW8302 4.6 38.3 0.7 CZ A:PHE128 4.7 17.1 1.0 CE1 A:TYR149 4.7 17.7 1.0 H16 A:LW8302 4.9 46.0 0.7 CZ A:TYR149 5.0 20.6 1.0

Nickel binding site 2 out of 2 in the Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni204 b:18.4 occ:1.00 NE2 B:HIS90 2.0 19.2 1.0 NE2 B:HIS134 2.0 17.2 1.0 O B:ACT202 2.0 14.2 0.8 O B:HOH302 2.1 24.4 1.0 NE2 B:HIS88 2.2 18.2 1.0 OXT B:ACT202 2.4 18.3 0.8 C B:ACT202 2.4 14.0 0.8 CE1 B:HIS90 2.9 18.3 1.0 CE1 B:HIS134 3.0 18.1 1.0 CD2 B:HIS134 3.1 16.9 1.0 CD2 B:HIS90 3.1 14.6 1.0 CE1 B:HIS88 3.1 20.5 1.0 CD2 B:HIS88 3.2 16.3 1.0 CH3 B:ACT202 3.8 22.3 0.8 ND1 B:HIS90 4.0 13.1 1.0 ND1 B:HIS134 4.1 16.9 1.0 H3 B:ACT202 4.1 26.8 0.8 CG B:HIS90 4.2 14.9 1.0 CG B:HIS134 4.2 16.7 1.0 H1 B:ACT202 4.2 26.8 0.8 ND1 B:HIS88 4.2 17.6 1.0 CG B:HIS88 4.3 18.2 1.0 H2 B:ACT202 4.3 26.8 0.8 OH B:TYR149 4.5 19.3 1.0 CE1 B:TYR149 4.6 15.5 1.0 CZ B:PHE128 4.6 18.5 1.0

E.Nalivaiko, C.M.Vasseur, F.P.Seebeck. Ergothioneine Dioxygenase From Thermocatellispora Tengchongensis in Complex with Nickel and Substrate (Anaerobic) To Be Published.