Zinc in PDB 3wc7: Carboxypeptidase B in Complex with EF6265

All present enzymatic activity of Carboxypeptidase B in Complex with EF6265:
3.4.17.2;

The structure of Carboxypeptidase B in Complex with EF6265, PDB code: 3wc7 was solved by N.Yoshimoto, T.Itoh, Y.Inaba, K.Yamamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.02 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.360, 79.360, 100.160, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 20.7

The binding sites of Zinc atom in the Carboxypeptidase B in Complex with EF6265 (pdb code 3wc7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Carboxypeptidase B in Complex with EF6265, PDB code: 3wc7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Carboxypeptidase B in Complex with EF6265


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Carboxypeptidase B in Complex with EF6265 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:26.8 occ:1.00 OE1 A:GLU291 2.0 27.7 1.0 O A:HOH641 2.1 33.7 1.0 OE2 A:GLU85 2.1 28.6 1.0 OE2 A:GLU291 2.3 27.7 1.0 CD A:GLU291 2.5 28.5 1.0 CD A:GLU85 3.0 29.1 1.0 OE1 A:GLU85 3.3 29.4 1.0 NH2 A:ARG84 3.9 27.4 1.0 CG A:GLU291 4.1 27.9 1.0 NE1 A:TRP81 4.3 27.1 1.0 O A:HOH538 4.4 29.9 1.0 CG A:GLU85 4.4 27.6 1.0 O A:HOH621 4.5 33.4 1.0 CZ2 A:TRP81 5.0 27.9 1.0

Zinc binding site 2 out of 2 in the Carboxypeptidase B in Complex with EF6265


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Carboxypeptidase B in Complex with EF6265 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:22.9 occ:1.00 OE2 A:GLU72 2.1 24.3 1.0 O19 A:EF1403 2.1 35.5 0.5 ND1 A:HIS196 2.1 26.1 1.0 O19 A:EF1403 2.1 35.5 0.5 ND1 A:HIS69 2.1 25.6 1.0 OE1 A:GLU72 2.6 23.7 1.0 CD A:GLU72 2.7 23.6 1.0 O18 A:EF1403 2.7 29.7 0.5 O18 A:EF1403 2.7 29.7 0.5 P13 A:EF1403 2.8 30.9 0.5 P13 A:EF1403 2.8 30.9 0.5 CE1 A:HIS69 3.0 24.8 1.0 CE1 A:HIS196 3.0 25.7 1.0 CG A:HIS196 3.1 26.1 1.0 CG A:HIS69 3.2 25.8 1.0 CB A:HIS196 3.5 25.4 1.0 CB A:HIS69 3.6 25.6 1.0 NH1 A:ARG127 4.0 25.4 1.0 C12 A:EF1403 4.0 32.1 0.5 C12 A:EF1403 4.1 32.1 0.5 O A:HOH574 4.1 29.6 1.0 NE2 A:HIS69 4.1 25.4 1.0 NE2 A:HIS196 4.2 25.9 1.0 CG A:GLU72 4.2 25.5 1.0 O A:SER197 4.2 26.2 1.0 C17 A:EF1403 4.2 30.1 0.5 C17 A:EF1403 4.2 30.1 0.5 CD2 A:HIS196 4.2 24.9 1.0 CD2 A:HIS69 4.3 24.8 1.0 C20 A:EF1403 4.3 34.3 0.5 C20 A:EF1403 4.3 34.3 0.5 O A:HOH507 4.3 27.3 1.0 O23 A:EF1403 4.4 41.5 0.5 O23 A:EF1403 4.4 41.5 0.5 C21 A:EF1403 4.4 37.4 0.5 C21 A:EF1403 4.4 37.4 0.5 CA A:HIS196 4.5 25.4 1.0 N A:SER197 4.7 25.6 1.0 CA A:HIS69 4.9 26.3 1.0 CZ A:ARG127 4.9 25.4 1.0 N10 A:EF1403 4.9 30.6 0.5 OE1 A:GLU270 5.0 25.2 1.0 N10 A:EF1403 5.0 30.7 0.5

N.Yoshimoto, T.Itoh, Y.Inaba, H.Ishii, K.Yamamoto. Structural Basis For Inhibition of Carboxypeptidase B By Selenium-Containing Inhibitor: Selenium Coordinates to Zinc in Enzyme J.Med.Chem. 2013.
ISSN: ISSN 0022-2623
PubMed: 24010887
DOI: 10.1021/JM400816V