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Zinc in PDB 4oc3: X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine

Enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine

All present enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine, PDB code: 4oc3 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) 29.52 / 1.79
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.566, 130.434, 159.017, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.1

Other elements in 4oc3:

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine also contains other interesting chemical elements:

Iodine (I) 1 atom
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 Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine (pdb code 4oc3). 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 Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine, PDB code: 4oc3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4oc3

Go back to Zinc Binding Sites List in 4oc3
Zinc binding site 1 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine


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 Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn816

b:21.7
occ:1.00
 O A:HOH1185 2.0 21.2 1.0
NE2 A:HIS553 2.1 15.7 1.0
OE2 A:GLU425 2.1 19.1 1.0
OD2 A:ASP387 2.1 23.6 1.0
OE1 A:GLU425 2.5 18.5 1.0
CD A:GLU425 2.7 20.7 1.0
OAC A:2QP820 2.7 20.8 1.0
CE1 A:HIS553 3.0 15.3 1.0
CG A:ASP387 3.0 20.0 1.0
CD2 A:HIS553 3.1 15.1 1.0
ZN A:ZN817 3.3 19.9 1.0
OD1 A:ASP387 3.3 17.1 1.0
CAZ A:2QP820 3.5 23.9 1.0
OE1 A:GLU424 4.0 18.1 1.0
NAV A:2QP820 4.1 23.1 1.0
CBF A:2QP820 4.1 23.9 1.0
CE1 A:TYR552 4.1 20.9 1.0
ND1 A:HIS553 4.1 15.1 1.0
O A:HOH916 4.2 20.1 1.0
CG A:GLU425 4.2 17.2 1.0
CG A:HIS553 4.2 16.9 1.0
CB A:ASP387 4.3 19.7 1.0
N A:2QP820 4.3 22.1 1.0
OH A:TYR552 4.4 22.8 1.0
CA A:2QP820 4.5 24.9 1.0
NE2 A:HIS377 4.6 17.6 1.0
CAY A:2QP820 4.7 31.8 1.0
CZ A:TYR552 4.7 19.1 1.0
CE1 A:HIS377 4.7 16.3 1.0
CD1 A:TRP381 4.8 17.9 1.0
NE1 A:TRP381 4.9 19.5 1.0
OD2 A:ASP453 4.9 20.9 1.0
OAF A:2QP820 4.9 32.9 1.0
CD A:GLU424 5.0 20.2 1.0
CD1 A:TYR552 5.0 20.9 1.0

Zinc binding site 2 out of 2 in 4oc3

Go back to Zinc Binding Sites List in 4oc3
Zinc binding site 2 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine


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 Cfibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Furan-2-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn817

b:19.9
occ:1.00
 OD2 A:ASP453 1.9 20.9 1.0
O A:HOH1185 1.9 21.2 1.0
OD1 A:ASP387 2.0 17.1 1.0
NE2 A:HIS377 2.0 17.6 1.0
CG A:ASP453 2.7 21.1 1.0
OD1 A:ASP453 2.8 22.8 1.0
CG A:ASP387 2.9 20.0 1.0
CE1 A:HIS377 3.0 16.3 1.0
CD2 A:HIS377 3.0 15.8 1.0
OD2 A:ASP387 3.2 23.6 1.0
ZN A:ZN816 3.3 21.7 1.0
OE1 A:GLU424 3.6 18.1 1.0
OE2 A:GLU425 3.6 19.1 1.0
CD A:GLU424 4.0 20.2 1.0
ND1 A:HIS377 4.1 17.1 1.0
OE2 A:GLU424 4.2 21.1 1.0
CG A:HIS377 4.2 15.1 1.0
CB A:ASP453 4.2 19.5 1.0
ND2 A:ASN519 4.2 20.7 1.0
CB A:ASP387 4.2 19.7 1.0
CB A:PRO388 4.3 17.3 1.0
CD A:GLU425 4.4 20.7 1.0
CA A:PRO388 4.6 17.1 1.0
CA A:ASP387 4.6 18.8 1.0
OAC A:2QP820 4.7 20.8 1.0
CAZ A:2QP820 4.7 23.9 1.0
C A:ASP387 4.7 18.7 1.0
N A:PRO388 4.7 18.1 1.0
OE1 A:GLU425 4.7 18.5 1.0
OG A:SER454 4.7 19.5 0.7
N A:2QP820 4.8 22.1 1.0
O A:HOH1181 4.8 32.9 1.0
OXT A:2QP820 4.9 26.5 1.0
CA A:2QP820 4.9 24.9 1.0
CG A:GLU424 5.0 15.5 1.0
C A:2QP820 5.0 25.4 1.0

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 03:38:56 2024

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