Zinc in PDB 5jc6: Carboxypeptidase B with 2-Nd Zinc and Acetate Ion

All present enzymatic activity of Carboxypeptidase B with 2-Nd Zinc and Acetate Ion:
3.4.17.2;

The structure of Carboxypeptidase B with 2-Nd Zinc and Acetate Ion, PDB code: 5jc6 was solved by V.I.Timofeev, V.K.Akparov, I.P.Kuranova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.65 / 1.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.580, 79.580, 100.510, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.8

The binding sites of Zinc atom in the Carboxypeptidase B with 2-Nd Zinc and Acetate Ion (pdb code 5jc6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Carboxypeptidase B with 2-Nd Zinc and Acetate Ion, PDB code: 5jc6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Carboxypeptidase B with 2-Nd Zinc and Acetate Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Carboxypeptidase B with 2-Nd Zinc and Acetate Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:8.7 occ:1.00 O A:HOH549 1.9 12.4 1.0 ND1 A:HIS69 2.1 9.0 1.0 ND1 A:HIS196 2.1 7.2 1.0 OE2 A:GLU72 2.2 8.0 1.0 OE1 A:GLU72 2.3 10.0 1.0 CD A:GLU72 2.6 8.1 1.0 CE1 A:HIS69 3.0 9.1 1.0 CE1 A:HIS196 3.0 8.9 1.0 CG A:HIS196 3.1 7.3 1.0 CG A:HIS69 3.1 8.5 1.0 ZN A:ZN402 3.4 18.0 1.0 CB A:HIS196 3.4 6.7 1.0 O A:ACT406 3.5 15.3 1.0 CB A:HIS69 3.5 7.8 1.0 O A:SER197 3.9 7.7 1.0 O A:HOH667 4.0 11.2 1.0 CG A:GLU72 4.1 7.8 1.0 C A:ACT406 4.1 17.2 1.0 NE2 A:HIS69 4.1 8.4 1.0 NE2 A:HIS196 4.2 8.4 1.0 CD2 A:HIS69 4.2 8.7 1.0 CD2 A:HIS196 4.2 7.8 1.0 CA A:HIS196 4.2 6.0 1.0 N A:SER197 4.4 5.9 1.0 O A:HOH507 4.4 17.6 1.0 OE2 A:GLU270 4.6 14.1 1.0 OXT A:ACT406 4.6 13.4 1.0 NH1 A:ARG127 4.6 15.3 1.0 CH3 A:ACT406 4.7 17.3 1.0 OE1 A:GLU270 4.8 11.1 1.0 CA A:HIS69 4.8 7.3 1.0 C A:HIS196 4.9 5.5 1.0 N A:HIS69 4.9 7.7 1.0 CB A:GLU72 4.9 7.1 1.0 C A:SER197 5.0 6.7 1.0

Zinc binding site 2 out of 5 in the Carboxypeptidase B with 2-Nd Zinc and Acetate Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Carboxypeptidase B with 2-Nd Zinc and Acetate Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:18.0 occ:1.00 O A:HOH549 1.7 12.4 1.0 OE2 A:GLU270 1.9 14.1 1.0 O A:ACT406 2.0 15.3 1.0 CD A:GLU270 2.8 12.1 1.0 C A:ACT406 3.0 17.2 1.0 OE1 A:GLU270 3.0 11.1 1.0 ZN A:ZN401 3.4 8.7 1.0 CH3 A:ACT406 3.5 17.3 1.0 O A:HOH513 3.8 23.2 1.0 ND1 A:HIS196 4.0 7.2 1.0 CB A:HIS196 4.1 6.7 1.0 O A:SER197 4.1 7.7 1.0 OXT A:ACT406 4.1 13.4 1.0 CG A:GLU270 4.2 10.0 1.0 CG A:HIS196 4.3 7.3 1.0 OH A:TYR248 4.3 28.5 1.0 OE1 A:GLU72 4.6 10.0 1.0 C A:SER197 4.7 6.7 1.0 CD1 A:ILE247 4.8 25.4 1.0 ND1 A:HIS69 4.8 9.0 1.0 OE2 A:GLU72 4.9 8.0 1.0 CE1 A:HIS69 4.9 9.1 1.0 CE1 A:HIS196 4.9 8.9 1.0

Zinc binding site 3 out of 5 in the Carboxypeptidase B with 2-Nd Zinc and Acetate Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Carboxypeptidase B with 2-Nd Zinc and Acetate Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:10.7 occ:1.00 O A:HOH526 2.1 14.2 1.0 OE2 A:GLU85 2.1 11.6 1.0 OE1 A:GLU291 2.1 10.0 1.0 OE2 A:GLU291 2.3 10.0 1.0 CD A:GLU291 2.5 10.1 1.0 CD A:GLU85 3.0 11.7 1.0 OE1 A:GLU85 3.3 14.5 1.0 NH2 A:ARG84 3.9 12.2 1.0 CG A:GLU291 4.0 9.1 1.0 NE1 A:TRP81 4.3 8.9 1.0 CG A:GLU85 4.4 11.4 1.0 O A:HOH530 4.4 11.5 1.0 CB A:GLU291 5.0 8.1 1.0 CZ2 A:TRP81 5.0 9.1 1.0

Zinc binding site 4 out of 5 in the Carboxypeptidase B with 2-Nd Zinc and Acetate Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Carboxypeptidase B with 2-Nd Zinc and Acetate Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:50.2 occ:1.00 O A:HOH630 2.1 27.8 1.0 OE1 A:GLU19 2.3 24.9 1.0 OE2 A:GLU19 2.6 25.5 1.0 CD A:GLU19 2.8 21.0 1.0 O A:HOH628 3.0 27.3 1.0 O A:HOH664 3.6 21.1 1.0 CG A:GLU19 4.3 18.0 1.0 OD1 A:ASN45 4.5 19.6 1.0 NE1 A:TRP15 4.5 14.1 1.0

Zinc binding site 5 out of 5 in the Carboxypeptidase B with 2-Nd Zinc and Acetate Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Carboxypeptidase B with 2-Nd Zinc and Acetate Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:37.8 occ:1.00 ND1 A:HIS7 2.3 15.3 1.0 CG A:HIS7 3.2 14.7 1.0 CE1 A:HIS7 3.3 14.0 1.0 CB A:HIS7 3.4 16.1 1.0 O A:HIS7 3.4 18.3 1.0 C A:HIS7 3.7 15.4 1.0 O A:HOH631 4.1 16.9 1.0 CA A:HIS7 4.2 13.4 1.0 N A:SER8 4.3 13.9 1.0 CE2 A:TYR9 4.3 10.9 1.0 CD2 A:HIS7 4.3 13.2 1.0 CD1 A:TRP21 4.3 11.5 1.0 NE2 A:HIS7 4.4 12.7 1.0 CA A:SER8 4.5 14.2 1.0 CD2 A:TYR9 4.6 10.3 1.0 CZ A:TYR9 4.8 9.7 1.0 O A:HOH681 4.8 30.2 1.0 NE1 A:TRP21 4.9 11.7 1.0 N A:HIS7 4.9 15.3 1.0

V.Akparov, V.Timofeev, I.Khaliullin, V.Svedas, I.Kuranova. Structure of the Carboxypeptidase B Complex with N-Sulfamoyl-L-Phenylalanine - A Transition State Analog of Non-Specific Substrate. J. Biomol. Struct. Dyn. V. 36 956 2018.
ISSN: ESSN 1538-0254
PubMed: 28274181
DOI: 10.1080/07391102.2017.1304242