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Zinc in PDB 4oc2: X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine

Enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]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 Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]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 Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine, PDB code: 4oc2 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) 29.47 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.338, 130.247, 159.073, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.8

Other elements in 4oc2:

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]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 Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine (pdb code 4oc2). 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 Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine, PDB code: 4oc2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4oc2

Go back to Zinc Binding Sites List in 4oc2
Zinc binding site 1 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]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 Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn817

b:22.5
occ:1.00
 O A:HOH1348 2.0 20.7 1.0
NE2 A:HIS553 2.0 18.8 1.0
OD2 A:ASP387 2.1 23.6 1.0
OE2 A:GLU425 2.1 20.3 1.0
OE1 A:GLU425 2.4 19.5 1.0
CD A:GLU425 2.6 19.3 1.0
OAD A:2QQ821 2.7 22.8 1.0
CE1 A:HIS553 3.0 20.5 1.0
CG A:ASP387 3.0 20.1 1.0
CD2 A:HIS553 3.1 18.9 1.0
ZN A:ZN818 3.3 22.0 1.0
OD1 A:ASP387 3.3 20.4 1.0
CAX A:2QQ821 3.5 27.3 1.0
CA A:2QQ821 3.9 26.6 1.0
N A:2QQ821 4.0 25.7 1.0
CE1 A:TYR552 4.1 21.6 1.0
OE1 A:GLU424 4.1 19.5 1.0
ND1 A:HIS553 4.1 19.2 1.0
CG A:GLU425 4.1 20.0 1.0
O A:HOH915 4.1 21.8 1.0
CG A:HIS553 4.2 19.1 1.0
CB A:ASP387 4.3 21.1 1.0
NAU A:2QQ821 4.3 23.9 1.0
OH A:TYR552 4.4 21.7 1.0
NE2 A:HIS377 4.6 18.8 1.0
CBC A:2QQ821 4.6 26.2 1.0
C A:2QQ821 4.7 28.4 1.0
CZ A:TYR552 4.7 20.3 1.0
CE1 A:HIS377 4.7 19.8 1.0
CD1 A:TRP381 4.7 20.5 1.0
NE1 A:TRP381 4.8 21.7 1.0
OD2 A:ASP453 4.8 22.5 1.0
OXT A:2QQ821 4.9 28.4 1.0

Zinc binding site 2 out of 2 in 4oc2

Go back to Zinc Binding Sites List in 4oc2
Zinc binding site 2 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]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 Ceibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxybut- 3-Yn-1-Yl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn818

b:22.0
occ:1.00
 OD2 A:ASP453 1.9 22.5 1.0
OD1 A:ASP387 1.9 20.4 1.0
O A:HOH1348 1.9 20.7 1.0
NE2 A:HIS377 2.0 18.8 1.0
CG A:ASP453 2.7 23.1 1.0
OD1 A:ASP453 2.8 25.4 1.0
CG A:ASP387 2.9 20.1 1.0
CE1 A:HIS377 2.9 19.8 1.0
CD2 A:HIS377 3.1 19.2 1.0
OD2 A:ASP387 3.3 23.6 1.0
ZN A:ZN817 3.3 22.5 1.0
OE2 A:GLU425 3.6 20.3 1.0
OE1 A:GLU424 3.7 19.5 1.0
CD A:GLU424 4.0 22.1 1.0
ND1 A:HIS377 4.1 19.2 1.0
CB A:ASP453 4.2 21.9 1.0
CG A:HIS377 4.2 17.0 1.0
CB A:ASP387 4.2 21.1 1.0
OE2 A:GLU424 4.2 23.2 1.0
ND2 A:ASN519 4.2 18.9 1.0
CB A:PRO388 4.2 20.2 1.0
CD A:GLU425 4.3 19.3 1.0
CA A:PRO388 4.5 19.2 1.0
CA A:ASP387 4.5 20.9 1.0
CAX A:2QQ821 4.6 27.3 1.0
OAD A:2QQ821 4.6 22.8 1.0
C A:ASP387 4.6 21.0 1.0
N A:PRO388 4.6 20.5 1.0
OE1 A:GLU425 4.7 19.5 1.0
OG A:SER454 4.7 20.9 0.7
NAU A:2QQ821 4.7 23.9 1.0
O A:HOH1349 4.7 32.6 1.0
CBC A:2QQ821 4.9 26.2 1.0
OAC A:2QQ821 4.9 29.4 1.0
N A:2QQ821 5.0 25.7 1.0
CG A:GLU424 5.0 18.2 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 03:37:51 2024

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