Zinc in PDB 3wc5: Carboxypeptidase B in Complex with DD9

All present enzymatic activity of Carboxypeptidase B in Complex with DD9:
3.4.17.2;

The structure of Carboxypeptidase B in Complex with DD9, PDB code: 3wc5 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)	15.00 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.359, 79.359, 100.583, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.4

The structure of Carboxypeptidase B in Complex with DD9 also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Zinc atom in the Carboxypeptidase B in Complex with DD9 (pdb code 3wc5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Carboxypeptidase B in Complex with DD9, PDB code: 3wc5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Carboxypeptidase B in Complex with DD9


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 DD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.5 occ:1.00 O A:HOH823 2.0 16.6 1.0 OE1 A:GLU291 2.0 11.1 1.0 OE2 A:GLU85 2.1 10.4 1.0 OE2 A:GLU291 2.3 13.2 1.0 CD A:GLU291 2.5 12.9 1.0 CD A:GLU85 3.0 16.1 1.0 OE1 A:GLU85 3.3 17.8 1.0 NH2 A:ARG84 4.0 11.6 1.0 CG A:GLU291 4.1 10.7 1.0 NE1 A:TRP81 4.3 11.7 1.0 CG A:GLU85 4.3 13.1 1.0 O A:HOH542 4.4 12.2 1.0 O A:HOH728 4.5 22.8 1.0 CZ2 A:TRP81 5.0 11.5 1.0

Zinc binding site 2 out of 3 in the Carboxypeptidase B in Complex with DD9


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 DD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:11.2 occ:1.00 OE1 A:GLU72 2.0 8.7 1.0 ND1 A:HIS69 2.1 8.4 1.0 ND1 A:HIS196 2.1 11.1 1.0 SED A:DDK403 2.4 10.6 1.0 OE2 A:GLU72 2.5 9.1 1.0 CD A:GLU72 2.6 6.2 1.0 CE1 A:HIS69 3.0 9.3 1.0 CE1 A:HIS196 3.1 10.7 1.0 CG A:HIS196 3.1 8.6 1.0 CG A:HIS69 3.1 9.6 1.0 CAF A:DDK403 3.3 10.4 1.0 CB A:HIS196 3.4 7.3 1.0 CB A:HIS69 3.6 7.6 1.0 O A:HOH574 3.9 10.8 1.0 ZN A:ZN404 3.9 12.2 1.0 O A:SER197 4.0 8.2 1.0 CG A:GLU72 4.1 9.5 1.0 NE2 A:HIS69 4.2 8.8 1.0 NE2 A:HIS196 4.2 11.2 1.0 CD2 A:HIS196 4.2 8.1 1.0 CA A:HIS196 4.2 7.6 1.0 CD2 A:HIS69 4.2 10.1 1.0 NH1 A:ARG127 4.3 12.0 1.0 N A:SER197 4.5 7.8 1.0 OAB A:DDK403 4.6 12.8 1.0 CAL A:DDK403 4.7 9.6 1.0 O A:HOH566 4.7 14.5 1.0 OE1 A:GLU270 4.7 11.8 1.0 CAK A:DDK403 4.7 11.6 1.0 CA A:HIS69 4.8 8.6 1.0 N A:HIS69 4.9 8.8 1.0 CB A:GLU72 4.9 5.8 1.0 C A:HIS196 4.9 8.1 1.0

Zinc binding site 3 out of 3 in the Carboxypeptidase B in Complex with DD9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Carboxypeptidase B in Complex with DD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:12.2 occ:1.00 O2 A:CAC405 1.9 12.5 1.0 O A:SER197 2.1 8.2 1.0 OE1 A:GLU270 2.2 11.8 1.0 OE2 A:GLU270 2.2 12.1 1.0 SED A:DDK403 2.4 10.6 1.0 CD A:GLU270 2.5 10.2 1.0 C A:SER197 2.8 8.7 1.0 N A:TYR198 3.2 8.2 1.0 AS A:CAC405 3.3 14.8 1.0 CAF A:DDK403 3.4 10.4 1.0 C2 A:CAC405 3.5 18.6 1.0 O A:TYR198 3.7 10.7 1.0 OE2 A:GLU72 3.9 9.1 1.0 ZN A:ZN402 3.9 11.2 1.0 CA A:SER197 4.0 8.1 1.0 CG A:GLU270 4.0 7.0 1.0 N A:SER197 4.1 7.8 1.0 CD A:GLU72 4.1 6.2 1.0 OE1 A:GLU72 4.3 8.7 1.0 CB A:HIS196 4.3 7.3 1.0 CAL A:DDK403 4.3 9.6 1.0 O1 A:CAC405 4.3 16.5 1.0 CA A:TYR198 4.4 8.0 1.0 C A:TYR198 4.4 9.8 1.0 CE1 A:PHE279 4.6 11.9 1.0 C1 A:CAC405 4.6 15.8 1.0 CB A:GLU270 4.8 7.9 1.0 C A:HIS196 4.9 8.1 1.0

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