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Sodium in PDB 4ngt: Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor

Enzymatic activity of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor

All present enzymatic activity of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor:
3.4.17.21;

Protein crystallography data

The structure of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor, PDB code: 4ngt was solved by J.Tykvart, P.Pachl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.19 / 2.31
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.543, 130.297, 159.864, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.3

Other elements in 4ngt:

The structure of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor (pdb code 4ngt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor, PDB code: 4ngt:

Sodium binding site 1 out of 1 in 4ngt

Go back to Sodium Binding Sites List in 4ngt
Sodium binding site 1 out of 1 in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na814

b:29.2
occ:0.75
 O A:HOH1022 2.6 25.9 1.0
OG A:SER513 2.7 22.9 1.0
O A:VAL464 3.0 17.0 1.0
OD1 A:ASP465 3.1 20.7 1.0
CB A:SER513 3.2 22.4 1.0
BR A:J42815 3.4 39.8 0.5
N A:SER513 3.4 25.1 1.0
C57 A:J42815 3.6 37.9 0.5
CG A:ARG463 3.9 24.0 1.0
C A:VAL464 3.9 18.6 1.0
CA A:SER513 3.9 22.1 1.0
C A:J42815 3.9 36.1 0.5
N A:VAL464 4.1 21.9 1.0
CG A:ASP465 4.2 21.8 1.0
CD A:ARG463 4.3 22.4 1.0
C A:ILE512 4.4 25.6 1.0
NE A:ARG463 4.4 23.9 1.0
CG A:ARG511 4.4 32.8 1.0
CD A:ARG511 4.4 33.7 1.0
O A:HOH1016 4.5 20.1 1.0
CA A:ILE512 4.6 27.7 1.0
N A:ASP465 4.6 18.0 1.0
CA A:VAL464 4.6 20.5 1.0
C18 A:J42815 4.7 37.3 0.5
O A:HOH1149 4.7 32.1 1.0
CB A:ARG463 4.7 23.2 1.0
CA A:ARG463 4.7 21.0 1.0
O A:ARG511 4.7 26.5 1.0
C17 A:J42815 4.7 40.1 0.5
C A:ARG463 4.8 21.3 1.0
C18 A:J42815 4.8 76.3 0.5
CA A:ASP465 4.9 18.4 1.0
O8 A:J42815 5.0 71.4 0.5
OD2 A:ASP465 5.0 21.1 1.0
C A:ARG511 5.0 28.0 1.0

Reference:

J.Tykvart, J.Schimer, J.Barinkova, P.Pachl, L.Postova-Slavetinska, P.Majer, J.Konvalinka, P.Sacha. Rational Design of Urea-Based Glutamate Carboxypeptidase II (Gcpii) Inhibitors As Versatile Tools For Specific Drug Targeting and Delivery Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
DOI: 10.1016/J.BMC.2014.05.061
Page generated: Tue Dec 15 06:55:18 2020

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