Atomistry » Zinc » PDB 5olm-5ph9 » 5om9
Atomistry »
  Zinc »
    PDB 5olm-5ph9 »
      5om9 »

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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 5om9

Go back to Zinc Binding Sites List in 5om9
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 5om9

Go back to Zinc Binding Sites List in 5om9
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 5om9

Go back to Zinc Binding Sites List in 5om9
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

Reference:

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
Page generated: Wed Dec 16 06:39:02 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy