Zinc in PDB 3wab: Carboxypeptidase B in Complex with DD2

All present enzymatic activity of Carboxypeptidase B in Complex with DD2:
3.4.17.2;

The structure of Carboxypeptidase B in Complex with DD2, PDB code: 3wab 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 / 2.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.314, 79.314, 100.342, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 27.8

The structure of Carboxypeptidase B in Complex with DD2 also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Zinc atom in the Carboxypeptidase B in Complex with DD2 (pdb code 3wab). 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 DD2, PDB code: 3wab:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Carboxypeptidase B in Complex with DD2


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 DD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.9 occ:1.00 OE2 A:GLU85 2.3 18.0 1.0 OE1 A:GLU291 2.3 14.0 1.0 OE2 A:GLU291 2.4 16.8 1.0 CD A:GLU291 2.7 17.9 1.0 CD A:GLU85 3.1 13.5 1.0 OE1 A:GLU85 3.2 16.4 1.0 NH2 A:ARG84 4.1 8.5 1.0 CG A:GLU291 4.2 17.8 1.0 O A:HOH681 4.4 17.2 1.0 NE1 A:TRP81 4.4 24.6 1.0 CG A:GLU85 4.5 15.3 1.0 CZ2 A:TRP81 4.9 16.8 1.0

Zinc binding site 2 out of 3 in the Carboxypeptidase B in Complex with DD2


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 DD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:17.5 occ:1.00 ND1 A:HIS69 2.2 16.4 1.0 ND1 A:HIS196 2.2 10.0 1.0 OE2 A:GLU72 2.2 9.7 1.0 OE1 A:GLU72 2.4 23.2 1.0 S9 A:DDW403 2.5 11.3 1.0 CD A:GLU72 2.7 6.7 1.0 CE1 A:HIS69 3.1 5.8 1.0 CG A:HIS196 3.1 9.2 1.0 CG A:HIS69 3.2 36.5 1.0 CE1 A:HIS196 3.2 11.3 1.0 CB A:HIS196 3.3 7.1 1.0 C8 A:DDW403 3.4 15.0 1.0 CB A:HIS69 3.6 1.6 1.0 ZN A:ZN404 3.9 18.3 1.0 O A:HOH705 4.0 12.1 1.0 CG A:GLU72 4.2 7.8 1.0 CA A:HIS196 4.2 12.7 1.0 O12 A:DDW403 4.2 9.9 1.0 NE2 A:HIS69 4.2 11.1 1.0 O A:SER197 4.2 34.4 1.0 CD2 A:HIS196 4.3 11.3 1.0 NE2 A:HIS196 4.3 19.6 1.0 CD2 A:HIS69 4.3 15.3 1.0 N A:SER197 4.4 14.1 1.0 NH1 A:ARG127 4.4 22.0 1.0 O A:HOH525 4.7 13.0 1.0 C7 A:DDW403 4.7 15.6 1.0 OE1 A:GLU270 4.7 14.9 1.0 C10 A:DDW403 4.7 21.7 1.0 N A:HIS69 4.8 7.7 1.0 CA A:HIS69 4.8 4.5 1.0 C A:HIS196 4.9 7.0 1.0 CB A:GLU72 4.9 9.0 1.0

Zinc binding site 3 out of 3 in the Carboxypeptidase B in Complex with DD2


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 DD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:18.3 occ:1.00 O1 A:CAC405 2.2 31.8 1.0 OE1 A:GLU270 2.3 14.9 1.0 O A:SER197 2.5 34.4 1.0 S9 A:DDW403 2.5 11.3 1.0 OE2 A:GLU270 2.5 9.9 1.0 CD A:GLU270 2.7 16.3 1.0 C A:SER197 2.8 11.4 1.0 N A:TYR198 3.1 12.2 1.0 AS A:CAC405 3.3 22.7 1.0 O2 A:CAC405 3.3 24.3 1.0 C8 A:DDW403 3.3 15.0 1.0 OE1 A:GLU72 3.5 23.2 1.0 O A:TYR198 3.6 11.0 1.0 N A:SER197 3.8 14.1 1.0 ZN A:ZN402 3.9 17.5 1.0 CA A:SER197 3.9 13.7 1.0 CD A:GLU72 4.0 6.7 1.0 CA A:TYR198 4.2 15.2 1.0 CG A:GLU270 4.2 5.1 1.0 CB A:HIS196 4.3 7.1 1.0 C7 A:DDW403 4.3 15.6 1.0 OE2 A:GLU72 4.3 9.7 1.0 C2 A:CAC405 4.4 17.9 1.0 C A:TYR198 4.4 20.9 1.0 CE1 A:PHE279 4.5 8.9 1.0 C1 A:CAC405 4.8 17.6 1.0 C A:HIS196 4.8 7.0 1.0 CG A:GLU72 4.9 7.8 1.0 CB A:GLU270 5.0 11.0 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