Zinc in PDB 5wvu: Crystal Structure of Carboxypeptidase From Thermus Thermophilus

All present enzymatic activity of Crystal Structure of Carboxypeptidase From Thermus Thermophilus:
3.4.17.19;

The structure of Crystal Structure of Carboxypeptidase From Thermus Thermophilus, PDB code: 5wvu was solved by M.Okai, K.Nagata, M.Tanokura, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.25 / 2.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	170.100, 233.700, 124.400, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.4

The binding sites of Zinc atom in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus (pdb code 5wvu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus, PDB code: 5wvu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus


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 Carboxypeptidase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:53.1 occ:1.00 NE2 A:HIS280 2.3 31.5 1.0 OE1 A:GLU306 2.4 35.5 1.0 NE2 A:HIS276 2.5 32.6 1.0 CE1 A:HIS280 3.2 28.3 1.0 CD2 A:HIS276 3.3 29.6 1.0 CD A:GLU306 3.3 33.5 1.0 CD2 A:HIS280 3.4 28.0 1.0 CE1 A:HIS276 3.5 35.8 1.0 OE2 A:GLU306 3.5 45.4 1.0 OG A:SER309 3.8 33.5 1.0 CB A:SER309 4.2 28.6 1.0 ND1 A:HIS280 4.4 29.4 1.0 CG A:HIS280 4.5 32.1 1.0 CG A:HIS276 4.5 30.8 1.0 ND1 A:HIS276 4.5 35.1 1.0 CG A:GLU306 4.7 35.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Carboxypeptidase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:83.7 occ:1.00 OE1 B:GLU306 2.3 54.7 1.0 NE2 B:HIS280 2.5 49.5 1.0 CE1 B:HIS276 2.6 53.6 1.0 CD B:GLU306 3.2 56.7 1.0 NE2 B:HIS276 3.2 51.5 1.0 CE1 B:HIS280 3.4 45.1 1.0 OE2 B:GLU306 3.4 59.1 1.0 CD2 B:HIS280 3.5 48.1 1.0 ND1 B:HIS276 3.6 53.4 1.0 OG B:SER309 3.9 50.8 1.0 CD2 B:HIS276 4.4 48.5 1.0 CB B:SER309 4.4 45.6 1.0 ND1 B:HIS280 4.5 47.5 1.0 CG B:GLU306 4.6 52.8 1.0 CG B:HIS280 4.6 48.9 1.0 CG B:HIS276 4.6 46.9 1.0 OE2 B:GLU277 4.9 53.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Carboxypeptidase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:61.3 occ:1.00 NE2 C:HIS280 2.0 41.6 1.0 NE2 C:HIS276 2.5 54.0 1.0 OE1 C:GLU306 2.6 50.0 1.0 OE2 C:GLU306 2.7 57.4 1.0 CE1 C:HIS280 2.7 41.6 1.0 CD C:GLU306 3.0 49.7 1.0 CD2 C:HIS280 3.1 45.4 1.0 CD2 C:HIS276 3.3 51.0 1.0 CE1 C:HIS276 3.6 50.7 1.0 CE1 C:TYR430 3.6 48.1 1.0 OG C:SER309 3.8 44.6 1.0 ND1 C:HIS280 3.9 42.9 1.0 OH C:TYR430 4.0 44.5 1.0 CG C:HIS280 4.2 44.6 1.0 CB C:SER309 4.3 44.2 1.0 CZ C:TYR430 4.3 48.7 1.0 CG C:HIS276 4.4 54.8 1.0 CG C:GLU306 4.5 41.2 1.0 ND1 C:HIS276 4.5 58.3 1.0 CD1 C:TYR430 4.6 47.9 1.0 OH C:TYR426 4.8 52.7 1.0 OE2 C:GLU277 4.9 39.2 1.0

M.Okai, A.Yamamura, K.Hayakawa, S.Tsutsui, K.I.Miyazono, W.C.Lee, K.Nagata, Y.Inoue, M.Tanokura. Insight Into the Transition Between the Open and Closed Conformations of Thermus Thermophilus Carboxypeptidase. Biochem. Biophys. Res. V. 484 787 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28161633
DOI: 10.1016/J.BBRC.2017.01.167