Nickel in PDB 5tfz: Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Nickel and Diacrylate

The structure of Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Nickel and Diacrylate, PDB code: 5tfz was solved by N.J.Schnicker, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.17 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.352, 54.667, 118.335, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.4

The binding sites of Nickel atom in the Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Nickel and Diacrylate (pdb code 5tfz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Nickel and Diacrylate, PDB code: 5tfz:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Nickel and Diacrylate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Nickel and Diacrylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:38.7 occ:1.00 NE2 A:HIS58 2.2 23.4 1.0 O1 A:7BC202 2.3 47.9 1.0 O A:7BC202 2.4 49.8 1.0 NE2 A:HIS96 2.4 22.8 1.0 C A:7BC202 2.6 50.1 1.0 NE2 A:HIS56 2.7 22.6 1.0 OE2 A:GLU62 2.7 14.3 1.0 CE1 A:HIS96 3.1 20.8 1.0 CD2 A:HIS58 3.1 18.8 1.0 CE1 A:HIS58 3.2 23.4 1.0 CD2 A:HIS96 3.5 16.5 1.0 CD2 A:HIS56 3.6 22.6 1.0 CE1 A:HIS56 3.6 23.1 1.0 CD A:GLU62 3.6 19.6 1.0 OE1 A:GLU62 3.9 20.5 1.0 CE2 A:TYR122 3.9 39.6 1.0 OH A:TYR64 3.9 22.0 1.0 C1 A:7BC202 4.1 53.0 1.0 OH A:TYR122 4.2 45.1 1.0 CG A:HIS58 4.3 18.3 1.0 ND1 A:HIS58 4.3 22.6 1.0 ND1 A:HIS96 4.3 20.7 1.0 CZ A:TYR122 4.4 40.8 1.0 CG A:HIS96 4.5 20.5 1.0 ND1 A:HIS56 4.7 23.8 1.0 CG A:HIS56 4.7 20.7 1.0 CD2 A:TYR122 4.8 38.2 1.0 CZ A:PHE112 4.8 19.6 1.0 CZ A:TYR64 4.9 20.3 1.0 C2 A:7BC202 4.9 57.6 1.0 CE1 A:TYR64 5.0 17.3 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Nickel and Diacrylate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Nickel and Diacrylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni204 b:27.2 occ:1.00 NE2 B:HIS96 2.1 20.9 1.0 O B:7BC205 2.1 21.4 1.0 NE2 B:HIS58 2.1 21.2 1.0 O1 B:7BC205 2.3 28.7 1.0 NE2 B:HIS56 2.4 27.2 1.0 C B:7BC205 2.5 28.9 1.0 CE1 B:HIS96 2.7 19.7 1.0 OE2 B:GLU62 2.7 21.6 1.0 CE1 B:HIS58 3.0 23.1 1.0 CD2 B:HIS58 3.2 21.1 1.0 CD2 B:HIS56 3.2 25.1 1.0 CD2 B:HIS96 3.3 25.4 1.0 CE1 B:HIS56 3.4 24.0 1.0 CD B:GLU62 3.6 22.9 1.0 OE1 B:GLU62 3.8 22.6 1.0 ND1 B:HIS96 3.9 17.3 1.0 C1 B:7BC205 4.0 36.3 1.0 OH B:TYR64 4.0 20.1 1.0 ND1 B:HIS58 4.1 21.7 1.0 CE2 B:TYR122 4.2 24.9 1.0 CG B:HIS58 4.2 19.4 1.0 CG B:HIS96 4.2 23.8 1.0 CG B:HIS56 4.4 21.7 1.0 ND1 B:HIS56 4.4 26.5 1.0 OH B:TYR122 4.5 20.2 1.0 CZ B:TYR122 4.7 25.9 1.0 CZ B:PHE112 4.8 28.8 1.0 CZ B:TYR64 4.9 20.7 1.0 C2 B:7BC205 4.9 43.3 1.0 CE1 B:TYR64 5.0 14.0 1.0

N.J.Schnicker, S.M.De Silva, J.D.Todd, M.Dey. Structural and Biochemical Insights Into Dimethylsulfoniopropionate Cleavage By Cofactor-Bound Dddk From the Prolific Marine Bacterium Pelagibacter. Biochemistry V. 56 2873 2017.
ISSN: ISSN 1520-4995
PubMed: 28511016
DOI: 10.1021/ACS.BIOCHEM.7B00099