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Zinc in PDB 3hxd: Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9)

Enzymatic activity of Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9)

All present enzymatic activity of Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9):
2.5.1.60;

Protein crystallography data

The structure of Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9), PDB code: 3hxd was solved by Z.Guo, K.Alexandrov, H.Waldmann, R.S.Goody, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.837, 90.786, 115.100, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.2

Other elements in 3hxd:

The structure of Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9) (pdb code 3hxd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9), PDB code: 3hxd:

Zinc binding site 1 out of 1 in 3hxd

Go back to Zinc Binding Sites List in 3hxd
Zinc binding site 1 out of 1 in the Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Engineered Rabggtase in Complex with A Peptidomimetic Inhibitor (Compound 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn332

b:55.3
occ:1.00
 NBF B:BD7334 2.1 65.2 1.0
OD2 B:ASP238 2.2 39.2 1.0
SG B:CYS240 2.3 38.1 0.5
NE2 B:HIS290 2.3 27.3 1.0
SG B:CYS240 2.6 35.2 0.5
OD1 B:ASP238 2.7 36.7 1.0
CG B:ASP238 2.8 36.0 1.0
CAV B:BD7334 3.0 66.7 1.0
CAW B:BD7334 3.1 64.5 1.0
CD2 B:HIS290 3.2 29.1 1.0
CB B:CYS240 3.3 33.1 0.5
CE1 B:HIS290 3.4 28.6 1.0
CB B:CYS240 3.4 37.1 0.5
CE1 B:PHE289 4.0 30.2 1.0
NBB B:BD7334 4.1 66.8 1.0
CBP B:BD7334 4.2 65.3 1.0
CB B:ASP238 4.2 33.9 1.0
O B:HOH480 4.2 50.4 1.0
N B:CYS240 4.3 33.4 0.5
CB B:ASP280 4.3 36.0 1.0
N B:CYS240 4.3 35.9 0.5
CA B:CYS240 4.3 33.4 0.5
CG B:HIS290 4.4 27.2 1.0
CA B:CYS240 4.5 37.1 0.5
ND1 B:HIS290 4.5 27.4 1.0
CD1 B:PHE289 4.7 30.2 1.0
N B:TYR241 4.7 33.4 0.5
O B:HOH400 4.9 63.8 1.0
CE1 B:TYR241 4.9 43.0 0.5
C B:CYS240 4.9 33.1 0.5

Reference:

K.T.Tan, E.Guiu-Rozas, R.S.Bon, Z.Guo, C.Delon, S.Wetzel, S.Arndt, K.Alexandrov, H.Waldmann, R.S.Goody, Y.W.Wu, W.Blankenfeldt. Design, Synthesis, and Characterization of Peptide-Based Rab Geranylgeranyl Transferase Inhibitors J.Med.Chem. V. 52 8025 2009.
ISSN: ISSN 0022-2623
PubMed: 19894725
DOI: 10.1021/JM901117D
Page generated: Sat Oct 26 06:45:13 2024

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