Zinc in PDB 5y4k: Crystal Structure of Dddy Mutant Y260A

The structure of Crystal Structure of Dddy Mutant Y260A, PDB code: 5y4k was solved by Y.Z.Zhang, C.Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.42 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.841, 72.646, 89.547, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 18.8

The binding sites of Zinc atom in the Crystal Structure of Dddy Mutant Y260A (pdb code 5y4k). 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 Dddy Mutant Y260A, PDB code: 5y4k:

Zinc binding site 1 out of 1 in the Crystal Structure of Dddy Mutant Y260A


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 Dddy Mutant Y260A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:13.5 occ:1.00 OXT A:AKR502 2.0 16.1 1.0 OE2 A:GLU269 2.0 12.0 1.0 NE2 A:HIS265 2.1 10.3 1.0 NE2 A:HIS338 2.1 11.8 1.0 O A:AKR502 2.3 17.9 1.0 C A:AKR502 2.5 21.2 1.0 CD A:GLU269 2.9 15.2 1.0 CE1 A:HIS338 3.0 9.8 1.0 CD2 A:HIS265 3.1 12.1 1.0 CE1 A:HIS265 3.1 11.0 1.0 CD2 A:HIS338 3.1 12.6 1.0 OE1 A:GLU269 3.2 13.6 1.0 CA A:AKR502 3.9 26.2 1.0 NH2 A:ARG361 4.0 17.4 1.0 ND1 A:HIS338 4.2 11.8 1.0 ND1 A:HIS265 4.2 11.2 1.0 CG A:HIS338 4.2 10.8 1.0 CG A:HIS265 4.2 11.6 1.0 CG A:GLU269 4.3 11.9 1.0 CD2 A:PHE332 4.5 9.0 1.0 CE2 A:PHE332 4.6 13.5 1.0 OH A:TYR271 4.6 12.9 1.0 CB A:HIS263 4.6 18.4 1.0 ND1 A:HIS263 4.6 23.9 1.0 CB A:AKR502 4.6 26.8 1.0 CB A:GLU269 4.7 10.7 1.0 CE2 A:TYR271 4.8 11.1 1.0 CZ A:ARG361 5.0 15.9 1.0 NE A:ARG361 5.0 12.6 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