Zinc in PDB 2zxc: Ceramidase Complexed with C2

All present enzymatic activity of Ceramidase Complexed with C2:
3.5.1.23;

The structure of Ceramidase Complexed with C2, PDB code: 2zxc was solved by H.Okano, T.Inoue, N.Okino, Y.Kakuta, H.Matsumura, M.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.97 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.741, 65.800, 340.339, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.8

The structure of Ceramidase Complexed with C2 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Ceramidase Complexed with C2 (pdb code 2zxc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Ceramidase Complexed with C2, PDB code: 2zxc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Ceramidase Complexed with C2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ceramidase Complexed with C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn647 b:25.6 occ:1.00 OE1 A:GLU411 1.8 19.1 1.0 O A:HOH686 1.9 43.2 1.0 NE2 A:HIS204 2.0 16.0 1.0 NE2 A:HIS97 2.2 16.3 1.0 OH A:TYR448 2.4 15.1 1.0 CD A:GLU411 2.6 19.6 1.0 OE2 A:GLU411 2.7 24.6 1.0 CE1 A:HIS204 2.9 15.4 1.0 CD2 A:HIS204 3.0 13.9 1.0 CE1 A:HIS97 3.1 17.5 1.0 CD2 A:HIS97 3.2 17.2 1.0 CZ A:TYR448 3.3 15.3 1.0 C19 A:2ED701 3.7 56.7 1.0 OH A:TYR441 3.9 16.5 1.0 CE2 A:TYR448 3.9 14.0 1.0 ND1 A:HIS204 4.0 13.9 1.0 CG A:GLU411 4.0 20.9 1.0 O2 A:2ED701 4.0 58.3 1.0 CG A:HIS204 4.0 14.1 1.0 CE1 A:TYR448 4.2 15.0 1.0 NE2 A:HIS99 4.2 19.0 1.0 CE1 A:HIS99 4.2 20.9 1.0 NH2 A:ARG160 4.3 21.3 1.0 ND1 A:HIS97 4.3 16.6 1.0 CG A:HIS97 4.3 16.8 1.0 C18 A:2ED701 4.4 58.8 1.0 CE1 A:TYR441 4.6 13.4 1.0 NH1 A:ARG160 4.7 23.1 1.0 CB A:GLU411 4.7 21.5 1.0 CZ A:TYR441 4.8 15.4 1.0 OH A:TYR445 4.9 14.3 1.0 CZ A:ARG160 4.9 21.1 1.0

Zinc binding site 2 out of 2 in the Ceramidase Complexed with C2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ceramidase Complexed with C2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn647 b:26.4 occ:1.00 OE1 B:GLU411 1.8 18.3 1.0 NE2 B:HIS204 1.9 14.5 1.0 NE2 B:HIS97 2.1 17.9 1.0 O B:HOH678 2.3 49.0 1.0 OH B:TYR448 2.4 19.2 1.0 CD B:GLU411 2.6 20.1 1.0 CE1 B:HIS204 2.8 13.3 1.0 OE2 B:GLU411 2.8 23.4 1.0 CD2 B:HIS204 3.0 13.4 1.0 CE1 B:HIS97 3.0 18.7 1.0 CD2 B:HIS97 3.2 18.6 1.0 CZ B:TYR448 3.3 17.6 1.0 C19 B:2ED702 3.6 57.0 1.0 ND1 B:HIS204 3.9 14.0 1.0 CE2 B:TYR448 3.9 15.4 1.0 OH B:TYR441 4.0 18.3 1.0 CG B:GLU411 4.0 21.7 1.0 CG B:HIS204 4.0 12.7 1.0 O2 B:2ED702 4.1 58.8 1.0 ND1 B:HIS97 4.2 17.5 1.0 CE1 B:TYR448 4.2 18.3 1.0 NE2 B:HIS99 4.2 20.0 1.0 C18 B:2ED702 4.3 59.0 1.0 CE1 B:HIS99 4.3 22.7 1.0 NH2 B:ARG160 4.3 19.7 1.0 CG B:HIS97 4.3 18.0 1.0 CE1 B:TYR441 4.6 13.7 1.0 NH1 B:ARG160 4.7 19.8 1.0 CB B:GLU411 4.8 22.3 1.0 CZ B:TYR441 4.8 18.2 1.0 OH B:TYR445 4.9 13.1 1.0 CZ B:ARG160 4.9 20.8 1.0

T.Inoue, N.Okino, Y.Kakuta, A.Hijikata, H.Okano, H.M.Goda, M.Tani, N.Sueyoshi, K.Kambayashi, H.Matsumura, Y.Kai, M.Ito. Mechanistic Insights Into the Hydrolysis and Synthesis of Ceramide By Neutral Ceramidase. J.Biol.Chem. V. 284 9566 2009.
ISSN: ISSN 0021-9258
PubMed: 19088069
DOI: 10.1074/JBC.M808232200