Zinc in PDB 5xkx: Crystal Structure of Wt Dddy

The structure of Crystal Structure of Wt Dddy, PDB code: 5xkx was solved by C.Y.Li, Y.Z.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.02 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.063, 72.070, 88.046, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 18.4

The binding sites of Zinc atom in the Crystal Structure of Wt Dddy (pdb code 5xkx). 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 Wt Dddy, PDB code: 5xkx:

Zinc binding site 1 out of 1 in the Crystal Structure of Wt Dddy


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 Wt Dddy within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:13.3 occ:1.00 OE2 A:GLU269 1.9 13.8 1.0 O A:ACT502 2.0 19.7 1.0 NE2 A:HIS265 2.1 12.1 1.0 NE2 A:HIS338 2.1 11.3 1.0 OXT A:ACT502 2.4 22.3 1.0 C A:ACT502 2.5 21.7 1.0 CD A:GLU269 2.8 13.2 1.0 CE1 A:HIS338 3.0 10.8 1.0 CD2 A:HIS265 3.0 12.1 1.0 OE1 A:GLU269 3.0 15.0 1.0 CE1 A:HIS265 3.1 12.8 1.0 CD2 A:HIS338 3.1 12.4 1.0 NE2 A:HIS263 3.6 12.5 1.0 CD2 A:HIS263 3.7 12.4 1.0 CH3 A:ACT502 3.9 22.9 1.0 NH2 A:ARG361 4.1 17.1 1.0 ND1 A:HIS338 4.1 11.6 1.0 ND1 A:HIS265 4.2 12.9 1.0 CG A:HIS265 4.2 12.2 1.0 CG A:GLU269 4.2 10.1 1.0 CG A:HIS338 4.2 12.1 1.0 CD2 A:PHE332 4.3 15.8 1.0 CE2 A:PHE332 4.5 15.2 1.0 CB A:GLU269 4.6 11.6 1.0 CE2 A:TYR271 4.6 12.8 1.0 OH A:TYR271 4.6 15.7 1.0 CE1 A:HIS263 4.8 12.6 1.0 CG A:HIS263 5.0 12.4 1.0 NE A:ARG361 5.0 13.8 1.0 CZ A:ARG361 5.0 16.2 1.0

C.Y.Li, D.Zhang, X.L.Chen, P.Wang, W.L.Shi, P.Y.Li, X.Y.Zhang, Q.L.Qin, J.D.Todd, Y.Z.Zhang. Mechanistic Insights Into Dimethylsulfoniopropionate Lyase Dddy, A New Member of the Cupin Superfamily. J. Mol. Biol. V. 429 3850 2017.
ISSN: ESSN 1089-8638
PubMed: 29106934
DOI: 10.1016/J.JMB.2017.10.022