Atomistry » Zinc » PDB 4o6p-4ojo » 4oc2
Atomistry »
  Zinc »
    PDB 4o6p-4ojo »
      4oc2 »

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: Wed Dec 16 05:38:28 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