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Zinc in PDB 3dst: Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate

Enzymatic activity of Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate

All present enzymatic activity of Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate:
2.5.1.60;

Protein crystallography data

The structure of Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate, PDB code: 3dst was solved by Z.Guo, S.Yu, R.S.Goody, K.Alexandrov, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.21 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.264, 90.618, 114.478, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22

Other elements in 3dst:

The structure of Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate (pdb code 3dst). 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 Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate, PDB code: 3dst:

Zinc binding site 1 out of 1 in 3dst

Go back to Zinc Binding Sites List in 3dst
Zinc binding site 1 out of 1 in the Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex with Geranylgeranyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn332

b:51.3
occ:1.00
 NE2 B:HIS290 2.4 37.4 1.0
SG B:CYS240 2.4 35.9 1.0
OD2 B:ASP238 2.4 35.1 1.0
OD1 B:ASP238 2.7 34.7 1.0
CG B:ASP238 2.8 33.4 1.0
CB B:CYS240 3.2 33.4 1.0
CD2 B:HIS290 3.2 39.5 1.0
CE1 B:HIS290 3.4 39.1 1.0
C4 B:GRG334 3.8 48.4 1.0
CE1 B:PHE289 3.9 39.5 1.0
CB B:ASP238 4.2 32.1 1.0
N B:CYS240 4.3 31.7 1.0
CA B:CYS240 4.4 32.7 1.0
CB B:ASP280 4.4 44.4 1.0
CG B:HIS290 4.4 37.8 1.0
ND1 B:HIS290 4.5 37.2 1.0
CD1 B:PHE289 4.6 37.9 1.0
CZ B:PHE289 4.9 39.5 1.0

Reference:

Z.Guo, Y.-W.Wu, D.Das, C.Delon, J.Cramer, S.Yu, S.Thuns, N.Lupilova, H.Waldmann, L.Brunsveld, R.S.Goody, K.Alexandrov, W.Blankenfeldt. Structures of Rabggtase-Substrate/Product Complexes Provide Insights Into the Evolution of Protein Prenylation Embo J. V. 27 2444 2008.
ISSN: ISSN 0261-4189
PubMed: 18756270
DOI: 10.1038/EMBOJ.2008.164
Page generated: Thu Oct 24 12:19:48 2024

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