Zinc in PDB 5om9: Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor

All present enzymatic activity of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor:
3.4.17.1;

The structure of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor, PDB code: 5om9 was solved by P.Gallego, C.Granados, D.Fernandez, I.Pallares, G.Covaleda, F.X.Aviles, J.Vendrell, D.Reverter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.68 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.901, 52.544, 133.984, 90.00, 94.84, 90.00
R / Rfree (%)	15.4 / 21.2

The binding sites of Zinc atom in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor (pdb code 5om9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor, PDB code: 5om9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:9.7 occ:1.00 ND1 A:HIS196 2.0 6.4 1.0 ND1 A:HIS69 2.1 6.3 1.0 OE1 A:GLU72 2.2 6.5 1.0 OE2 A:GLU72 2.2 7.5 1.0 CD A:GLU72 2.5 4.5 1.0 S10 A:O2S401 2.7 22.3 1.0 CE1 A:HIS196 3.0 7.5 1.0 CE1 A:HIS69 3.0 6.3 1.0 CG A:HIS196 3.0 5.6 1.0 CG A:HIS69 3.1 6.1 1.0 CB A:HIS196 3.4 5.5 1.0 CB A:HIS69 3.4 4.5 1.0 C09 A:O2S401 3.7 16.9 1.0 O A:SER197 3.9 7.3 1.0 O A:HOH583 3.9 10.1 1.0 CG A:GLU72 4.0 6.6 1.0 NE2 A:HIS196 4.1 8.5 1.0 CD2 A:HIS196 4.1 6.7 1.0 NE2 A:HIS69 4.1 8.6 1.0 CA A:HIS196 4.2 5.3 1.0 CD2 A:HIS69 4.2 6.4 1.0 O A:HOH556 4.4 12.9 1.0 NH1 A:ARG127 4.4 13.2 1.0 O A:HOH531 4.5 25.2 1.0 N A:SER197 4.5 6.6 1.0 C11 A:O2S401 4.5 18.9 1.0 CA A:HIS69 4.7 5.0 1.0 OE1 A:GLU270 4.7 12.9 1.0 O03 A:O2S401 4.7 12.6 1.0 N A:HIS69 4.8 5.3 1.0 C A:HIS196 4.9 6.0 1.0 CB A:GLU72 4.9 6.0 1.0 C A:SER197 5.0 7.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:11.2 occ:1.00 ND1 B:HIS196 2.0 9.2 1.0 ND1 B:HIS69 2.1 6.7 1.0 OE2 B:GLU72 2.1 11.6 1.0 OE1 B:GLU72 2.3 8.6 1.0 S10 B:O2S401 2.5 23.1 1.0 CD B:GLU72 2.5 7.6 1.0 CE1 B:HIS196 2.9 10.0 1.0 CE1 B:HIS69 3.0 7.4 1.0 CG B:HIS196 3.1 6.3 1.0 CG B:HIS69 3.1 5.8 1.0 CB B:HIS69 3.4 5.2 1.0 CB B:HIS196 3.5 5.5 1.0 C09 B:O2S401 3.7 18.2 1.0 NE2 B:HIS196 4.1 7.8 1.0 O B:SER197 4.1 10.5 1.0 CG B:GLU72 4.1 7.1 1.0 CD2 B:HIS196 4.2 9.2 1.0 NE2 B:HIS69 4.2 7.8 1.0 O B:HOH622 4.2 11.0 1.0 O B:HOH533 4.2 14.3 1.0 CD2 B:HIS69 4.2 8.3 1.0 CA B:HIS196 4.3 4.8 1.0 NH1 B:ARG127 4.3 12.3 1.0 O B:HOH510 4.4 37.0 1.0 C11 B:O2S401 4.6 22.6 1.0 O01 B:O2S401 4.6 15.0 1.0 N B:SER197 4.6 6.0 1.0 CA B:HIS69 4.8 5.6 1.0 C02 B:O2S401 4.8 16.1 1.0 N B:HIS69 4.8 7.5 1.0 C04 B:O2S401 4.8 19.0 1.0 OE1 B:GLU270 4.9 21.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:11.8 occ:1.00 OE2 B:GLU302 1.9 22.4 1.0 NE2 B:HIS307 2.0 12.2 1.0 OE1 B:GLU302 2.7 12.4 1.0 CD B:GLU302 2.7 14.2 1.0 CE1 B:HIS307 3.0 14.4 1.0 CD2 B:HIS307 3.1 12.4 1.0 CB B:ASN306 3.9 13.9 1.0 O B:HOH501 4.0 0.6 0.5 ND2 B:ASN306 4.1 13.4 1.0 ND1 B:HIS307 4.1 16.5 1.0 CG B:HIS307 4.2 15.1 1.0 CG B:GLU302 4.3 14.8 1.0 CG B:ASN306 4.5 15.6 1.0 O B:GLU302 5.0 9.2 1.0

S.A.Testero, C.Granados, D.Fernandez, P.Gallego, G.Covaleda, D.Reverter, J.Vendrell, F.X.Aviles, I.Pallares, S.Mobashery. Discovery of Mechanism-Based Inactivators For Human Pancreatic Carboxypeptidase A From A Focused Synthetic Library. Acs Med Chem Lett V. 8 1122 2017.
ISSN: ISSN 1948-5875
PubMed: 29057062
DOI: 10.1021/ACSMEDCHEMLETT.7B00346