Zinc in PDB 3wc6: Carboxypeptidase B in Complex with 2ND Zinc

All present enzymatic activity of Carboxypeptidase B in Complex with 2ND Zinc:
3.4.17.2;

The structure of Carboxypeptidase B in Complex with 2ND Zinc, PDB code: 3wc6 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 / 1.65
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.050, 79.050, 100.719, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.9

The binding sites of Zinc atom in the Carboxypeptidase B in Complex with 2ND Zinc (pdb code 3wc6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Carboxypeptidase B in Complex with 2ND Zinc, PDB code: 3wc6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Carboxypeptidase B in Complex with 2ND Zinc


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 2ND Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.4 occ:1.00 OE1 A:GLU291 2.0 12.7 1.0 OE2 A:GLU85 2.1 16.5 1.0 O A:HOH665 2.2 20.6 1.0 OE2 A:GLU291 2.3 13.5 1.0 CD A:GLU291 2.5 15.3 1.0 CD A:GLU85 3.1 19.9 1.0 OE1 A:GLU85 3.3 21.9 1.0 NH2 A:ARG84 4.0 12.7 1.0 CG A:GLU291 4.0 10.5 1.0 NE1 A:TRP81 4.4 13.9 1.0 CG A:GLU85 4.4 14.6 1.0 O A:HOH526 4.5 13.9 1.0 O A:HOH566 4.6 22.8 1.0 CB A:GLU291 5.0 10.8 1.0 CZ2 A:TRP81 5.0 12.0 1.0

Zinc binding site 2 out of 7 in the Carboxypeptidase B in Complex with 2ND Zinc


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 2ND Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.3 occ:1.00 ND1 A:HIS196 2.1 9.1 1.0 ND1 A:HIS69 2.1 14.6 1.0 OE1 A:GLU72 2.2 11.3 1.0 OE2 A:GLU72 2.3 13.5 1.0 CD A:GLU72 2.6 11.3 1.0 CE1 A:HIS69 3.0 13.4 1.0 CE1 A:HIS196 3.0 10.9 1.0 CG A:HIS196 3.1 10.0 1.0 CG A:HIS69 3.1 12.9 1.0 CB A:HIS196 3.4 9.0 1.0 CB A:HIS69 3.5 9.4 1.0 ZN A:ZN408 3.6 68.5 1.0 O A:HOH539 4.0 11.4 1.0 O A:SER197 4.0 8.2 1.0 CG A:GLU72 4.1 11.1 1.0 NE2 A:HIS69 4.1 10.9 1.0 NE2 A:HIS196 4.1 11.7 1.0 CD2 A:HIS196 4.2 11.9 1.0 CD2 A:HIS69 4.2 12.2 1.0 CH3 A:ACT401 4.2 20.3 1.0 CA A:HIS196 4.3 9.7 1.0 O A:HOH593 4.4 17.2 1.0 OE2 A:GLU270 4.4 27.3 1.0 NH1 A:ARG127 4.5 18.9 1.0 N A:SER197 4.5 9.8 1.0 C A:ACT401 4.6 26.4 1.0 O A:ACT401 4.6 16.5 1.0 CA A:HIS69 4.8 9.3 1.0 OE1 A:GLU270 4.9 17.3 1.0 N A:HIS69 4.9 9.0 1.0 CB A:GLU72 4.9 7.7 1.0 C A:HIS196 4.9 10.5 1.0

Zinc binding site 3 out of 7 in the Carboxypeptidase B in Complex with 2ND Zinc


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 2ND Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:65.1 occ:1.00 O A:HOH853 2.2 26.2 1.0 OE2 A:GLU19 2.4 28.6 1.0 OE1 A:GLU19 2.7 26.0 1.0 CD A:GLU19 2.9 24.5 1.0 O A:HOH587 3.3 23.4 1.0 O A:HOH671 4.0 29.6 1.0 CG A:GLU19 4.4 20.1 1.0 NE1 A:TRP15 4.6 15.9 1.0 OD1 A:ASN45 4.6 21.5 1.0

Zinc binding site 4 out of 7 in the Carboxypeptidase B in Complex with 2ND Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Carboxypeptidase B in Complex with 2ND Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:43.5 occ:1.00 OE2 A:GLU28 2.0 30.5 1.0 CD A:GLU28 2.8 27.8 1.0 OE1 A:GLU28 2.9 29.8 1.0 NE2 A:GLN24 4.1 32.2 1.0 CG A:GLN24 4.1 20.9 1.0 CG A:GLU28 4.2 22.8 1.0 CD A:GLN24 4.6 26.9 1.0

Zinc binding site 5 out of 7 in the Carboxypeptidase B in Complex with 2ND Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Carboxypeptidase B in Complex with 2ND Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:87.5 occ:1.00 OE2 A:GLU98 2.6 34.5 1.0 OE1 A:GLU98 2.8 36.9 1.0 CD A:GLU98 3.0 32.2 1.0 O A:HOH756 3.4 44.6 1.0 O A:HOH793 3.5 35.1 1.0 O A:HOH803 3.8 29.9 1.0 O A:HOH730 4.2 39.6 1.0 NZ A:LYS102 4.5 30.3 1.0 CG A:GLU98 4.6 19.4 1.0

Zinc binding site 6 out of 7 in the Carboxypeptidase B in Complex with 2ND Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Carboxypeptidase B in Complex with 2ND Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:29.8 occ:1.00 ND1 A:HIS7 2.1 15.4 1.0 CE1 A:HIS7 3.0 17.9 1.0 CG A:HIS7 3.1 16.2 1.0 O A:HIS7 3.3 19.8 1.0 CB A:HIS7 3.5 19.2 1.0 C A:HIS7 3.7 19.2 1.0 NE2 A:HIS7 4.2 15.3 1.0 CA A:HIS7 4.2 19.1 1.0 CD2 A:HIS7 4.2 15.8 1.0 O A:HOH829 4.3 26.8 1.0 N A:SER8 4.3 15.5 1.0 CD1 A:TRP21 4.3 12.1 1.0 CE2 A:TYR9 4.4 17.1 1.0 CA A:SER8 4.4 14.7 1.0 CD2 A:TYR9 4.7 16.6 1.0 CZ A:TYR9 4.8 19.3 1.0 N A:HIS7 4.9 22.8 1.0 N A:TYR9 4.9 14.5 1.0 C A:SER8 4.9 15.2 1.0 NE1 A:TRP21 4.9 13.4 1.0

Zinc binding site 7 out of 7 in the Carboxypeptidase B in Complex with 2ND Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Carboxypeptidase B in Complex with 2ND Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:68.5 occ:1.00 OE1 A:GLU270 2.5 17.3 1.0 O A:SER197 2.5 8.2 1.0 OE2 A:GLU270 2.8 27.3 1.0 CD A:GLU270 2.9 19.8 1.0 C A:SER197 3.1 9.9 1.0 N A:TYR198 3.5 11.2 1.0 ZN A:ZN403 3.6 13.3 1.0 OE2 A:GLU72 3.7 13.5 1.0 O A:TYR198 4.0 14.9 1.0 CH3 A:ACT401 4.0 20.3 1.0 CD A:GLU72 4.1 11.3 1.0 N A:SER197 4.1 9.8 1.0 CA A:SER197 4.2 10.5 1.0 CB A:HIS196 4.2 9.0 1.0 OE1 A:GLU72 4.2 11.3 1.0 CG A:GLU270 4.4 13.3 1.0 CA A:TYR198 4.7 10.4 1.0 C A:TYR198 4.7 13.2 1.0 ND1 A:HIS196 4.7 9.1 1.0 CE1 A:PHE279 4.8 13.7 1.0 CG A:HIS196 4.9 10.0 1.0 O A:HOH593 4.9 17.2 1.0 C A:ACT401 4.9 26.4 1.0 C A:HIS196 4.9 10.5 1.0 O A:HOH736 5.0 22.5 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