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Fluorine in PDB 3d7d: A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor

Enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor

All present enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor:
3.4.17.21;

Protein crystallography data

The structure of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor, PDB code: 3d7d was solved by J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.69
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.930, 130.497, 159.187, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.9

Other elements in 3d7d:

The structure of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor (pdb code 3d7d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor, PDB code: 3d7d:

Fluorine binding site 1 out of 1 in 3d7d

Go back to Fluorine Binding Sites List in 3d7d
Fluorine binding site 1 out of 1 in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:46.8
occ:1.00
 F21 A:FBD1 0.0 46.8 1.0
C20 A:FBD1 1.4 44.3 1.0
C22 A:FBD1 2.3 42.6 1.0
C19 A:FBD1 2.4 40.9 1.0
O A:HOH2384 2.5 43.7 1.0
NH2 A:ARG463 3.3 30.4 1.0
CZ A:ARG463 3.4 29.9 1.0
OD2 A:ASP465 3.5 33.1 1.0
NH2 A:ARG534 3.5 23.0 1.0
NE A:ARG463 3.6 30.4 1.0
O A:HOH2347 3.6 46.3 1.0
C23 A:FBD1 3.6 43.5 1.0
C18 A:FBD1 3.7 42.0 1.0
CZ A:ARG534 3.8 23.2 1.0
O A:HOH2385 3.9 47.8 1.0
NH1 A:ARG463 4.0 30.4 1.0
O A:HOH1858 4.0 21.8 1.0
C17 A:FBD1 4.2 43.9 1.0
NH1 A:ARG534 4.4 23.0 1.0
CD A:ARG463 4.4 24.3 1.0
NE A:ARG534 4.4 22.3 1.0
CG A:ASP465 4.5 27.0 1.0
CD A:ARG534 4.7 21.6 1.0
O A:HOH1939 4.7 26.3 1.0
O A:HOH2386 4.8 34.4 1.0
OD1 A:ASP465 4.9 32.0 1.0

Reference:

C.Barinka, Y.Byun, C.L.Dusich, S.R.Banerjee, Y.Chen, M.Castanares, A.P.Kozikowski, R.C.Mease, M.G.Pomper, J.Lubkowski. Interactions Between Human Glutamate Carboxypeptidase II and Urea-Based Inhibitors: Structural Characterization J.Med.Chem. V. 51 7737 2008.
ISSN: ISSN 0022-2623
PubMed: 19053759
DOI: 10.1021/JM800765E
Page generated: Mon Jul 14 15:48:26 2025

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