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Zinc in PDB 4oc1: X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid

Enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid

All present enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid, PDB code: 4oc1 was solved by J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.Pomper, J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.396, 130.353, 158.944, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.3

Other elements in 4oc1:

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid also contains other interesting chemical elements:

Iodine (I) 2 atoms
Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid (pdb code 4oc1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid, PDB code: 4oc1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4oc1

Go back to Zinc Binding Sites List in 4oc1
Zinc binding site 1 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn814

b:19.4
occ:1.00
 O A:HOH1427 2.0 18.0 1.0
NE2 A:HIS553 2.0 17.4 1.0
OE2 A:GLU425 2.1 17.8 1.0
OD2 A:ASP387 2.1 20.0 1.0
OE1 A:GLU425 2.5 16.9 1.0
OAC A:2QS818 2.5 16.0 0.6
CD A:GLU425 2.6 16.7 1.0
CE1 A:HIS553 2.9 16.9 1.0
CG A:ASP387 3.0 19.3 1.0
CD2 A:HIS553 3.1 16.8 1.0
OAC A:2QS818 3.2 20.1 0.4
CAX A:2QS818 3.3 15.6 0.6
ZN A:ZN815 3.3 18.9 1.0
OD1 A:ASP387 3.3 18.0 1.0
NAT A:2QS818 3.8 14.2 0.6
CBD A:2QS818 3.9 13.8 0.6
CAX A:2QS818 3.9 20.7 0.4
CE1 A:TYR552 4.0 17.6 1.0
ND1 A:HIS553 4.1 17.3 1.0
N A:2QS818 4.1 16.2 0.6
OE1 A:GLU424 4.1 18.4 1.0
O A:HOH916 4.2 19.8 1.0
CG A:GLU425 4.2 16.1 1.0
CG A:HIS553 4.2 17.2 1.0
CB A:ASP387 4.3 18.9 1.0
OH A:TYR552 4.4 19.8 1.0
CA A:2QS818 4.4 18.3 0.6
CAW A:2QS818 4.5 19.9 0.6
NAT A:2QS818 4.5 18.8 0.4
NE2 A:HIS377 4.5 16.1 1.0
CZ A:TYR552 4.6 20.1 1.0
CBD A:2QS818 4.6 17.2 0.4
N A:2QS818 4.7 19.9 0.4
CD1 A:TRP381 4.7 20.1 1.0
CE1 A:HIS377 4.7 15.4 1.0
OAB A:2QS818 4.8 20.5 0.6
NE1 A:TRP381 4.8 18.0 1.0
OD2 A:ASP453 4.8 20.6 1.0
CA A:2QS818 4.9 21.4 0.4
OAB A:2QS818 4.9 22.7 0.4
CD1 A:TYR552 5.0 19.6 1.0

Zinc binding site 2 out of 2 in 4oc1

Go back to Zinc Binding Sites List in 4oc1
Zinc binding site 2 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn815

b:18.9
occ:1.00
 OD2 A:ASP453 1.9 20.6 1.0
O A:HOH1427 1.9 18.0 1.0
NE2 A:HIS377 2.0 16.1 1.0
OD1 A:ASP387 2.0 18.0 1.0
CG A:ASP453 2.7 21.2 1.0
OD1 A:ASP453 2.8 25.0 1.0
CG A:ASP387 2.9 19.3 1.0
CE1 A:HIS377 3.0 15.4 1.0
CD2 A:HIS377 3.0 15.5 1.0
OD2 A:ASP387 3.2 20.0 1.0
ZN A:ZN814 3.3 19.4 1.0
OE2 A:GLU425 3.6 17.8 1.0
OE1 A:GLU424 3.7 18.4 1.0
CD A:GLU424 4.1 18.2 1.0
ND1 A:HIS377 4.1 17.4 1.0
CB A:ASP453 4.2 19.1 1.0
CG A:HIS377 4.2 16.0 1.0
CB A:ASP387 4.2 18.9 1.0
ND2 A:ASN519 4.2 17.3 1.0
OE2 A:GLU424 4.3 20.1 1.0
CB A:PRO388 4.3 17.1 1.0
CD A:GLU425 4.3 16.7 1.0
CAX A:2QS818 4.4 15.6 0.6
N A:2QS818 4.4 16.2 0.6
CA A:PRO388 4.5 16.9 1.0
CA A:ASP387 4.6 17.4 1.0
OAC A:2QS818 4.6 16.0 0.6
C A:ASP387 4.6 18.0 1.0
N A:PRO388 4.6 17.6 1.0
OE1 A:GLU425 4.7 16.9 1.0
CA A:2QS818 4.7 18.3 0.6
O A:HOH1406 4.8 29.9 1.0
OXT A:2QS818 4.8 20.5 0.6
OG A:SER454 4.8 22.6 1.0
NAT A:2QS818 4.8 14.2 0.6
C A:2QS818 4.8 19.3 0.6

Reference:

J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.G.Pomper, J.Lubkowski, C.Barinka. Structural Characterization of P1'-Diversified Urea-Based Inhibitors of Glutamate Carboxypeptidase II. Bioorg.Med.Chem.Lett. V. 24 2340 2014.
ISSN: ISSN 0960-894X
PubMed: 24731280
DOI: 10.1016/J.BMCL.2014.03.066
Page generated: Sun Oct 27 03:37:51 2024

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