Zinc in PDB 5tg0: Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Iron and Zinc

The structure of Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Iron and Zinc, PDB code: 5tg0 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)	27.53 / 1.44
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	55.065, 85.416, 54.380, 90.00, 90.00, 90.00
R / Rfree (%)	11 / 14

The structure of Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Iron and Zinc also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Iron and Zinc (pdb code 5tg0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Iron and Zinc, PDB code: 5tg0:

Zinc binding site 1 out of 1 in the Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Iron and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Dimethylsulfoniopropionate (Dmsp) Lyase Dddk Complexed with Iron and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:9.0 occ:0.37 FE A:FE201 1.3 10.2 0.6 O A:HOH321 1.6 15.3 0.6 NE2 A:HIS58 1.9 16.4 1.0 O A:HOH321 2.1 12.8 0.4 NE2 A:HIS96 2.2 12.9 1.0 OE1 A:GLU62 2.5 10.0 0.4 NE2 A:HIS56 2.7 15.0 1.0 CD2 A:HIS58 2.8 16.7 1.0 HE1 A:HIS96 2.8 16.1 1.0 CE1 A:HIS96 2.8 13.4 1.0 HD2 A:HIS58 2.9 20.0 1.0 CE1 A:HIS58 3.0 14.2 1.0 OE1 A:GLU62 3.0 13.6 0.6 OE2 A:GLU62 3.1 13.4 0.6 HE1 A:HIS58 3.3 17.1 1.0 OH A:TYR64 3.3 17.2 1.0 CD A:GLU62 3.4 13.0 0.6 CD2 A:HIS96 3.5 11.6 1.0 CD2 A:HIS56 3.5 12.9 1.0 HD2 A:HIS56 3.5 15.4 1.0 CD A:GLU62 3.5 9.9 0.4 CE1 A:HIS56 3.7 16.5 1.0 HD2 A:HIS96 3.8 13.9 1.0 HZ A:PHE112 3.9 11.5 1.0 OE2 A:GLU62 3.9 10.1 0.4 HE1 A:HIS56 3.9 19.8 1.0 CG A:HIS58 3.9 13.8 1.0 HE2 A:TYR122 4.0 21.2 0.9 ND1 A:HIS58 4.0 13.1 1.0 ND1 A:HIS96 4.1 12.8 1.0 O A:HOH348 4.4 26.5 1.0 CG A:HIS96 4.4 12.0 1.0 O A:HOH302 4.5 28.9 1.0 CZ A:TYR64 4.5 13.9 1.0 HG21 A:ILE90 4.5 11.9 1.0 CE2 A:TYR122 4.6 17.6 0.9 CG A:HIS56 4.7 13.2 1.0 HE1 A:TYR64 4.7 12.9 1.0 CZ A:PHE112 4.7 9.6 1.0 ND1 A:HIS56 4.7 14.3 1.0 CG A:GLU62 4.8 10.8 0.6 HD1 A:HIS96 4.8 15.4 1.0 HD1 A:HIS58 4.8 15.8 1.0 HE1 A:PHE112 4.8 11.4 1.0 HB3 A:GLU62 4.8 10.5 0.4 HH A:TYR122 4.9 25.3 0.9 HB2 A:GLU62 4.9 10.5 0.4 CG A:GLU62 4.9 9.8 0.4 HB3 A:GLU62 4.9 10.6 0.6 HB2 A:GLU62 4.9 10.6 0.6 HD2 A:TYR122 4.9 21.1 0.9 HG13 A:ILE90 5.0 13.1 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