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Zinc in PDB 1dce: Crystal Structure of Rab Geranylgeranyltransferase From Rat Brain

Protein crystallography data

The structure of Crystal Structure of Rab Geranylgeranyltransferase From Rat Brain, PDB code: 1dce was solved by H.Zhang, M.C.Seabra, H.Deisenhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.864, 77.439, 121.775, 74.60, 79.91, 67.89
R / Rfree (%) 21.5 / 26.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rab Geranylgeranyltransferase From Rat Brain (pdb code 1dce). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Rab Geranylgeranyltransferase From Rat Brain, PDB code: 1dce:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1dce

Go back to Zinc Binding Sites List in 1dce
Zinc binding site 1 out of 2 in the Crystal Structure of Rab Geranylgeranyltransferase From Rat Brain


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 Rab Geranylgeranyltransferase From Rat Brain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn900

b:32.2
occ:1.00
NE2 B:HIS290 2.0 30.0 1.0
OD2 B:ASP238 2.2 30.8 1.0
OD1 B:ASP238 2.2 30.5 1.0
SG B:CYS240 2.3 29.3 1.0
NE2 A:HIS2 2.3 44.8 1.0
CG B:ASP238 2.7 29.9 1.0
CD2 B:HIS290 2.9 29.6 1.0
CD2 A:HIS2 3.0 45.9 1.0
CE1 B:HIS290 3.1 29.7 1.0
CB B:CYS240 3.3 27.9 1.0
CE1 A:HIS2 3.5 46.9 1.0
N B:CYS240 3.9 25.7 1.0
CB B:ASP280 3.9 32.4 1.0
CB B:ASP238 4.0 27.0 1.0
CG B:HIS290 4.1 31.1 1.0
ND1 B:HIS290 4.1 30.9 1.0
CA B:CYS240 4.1 28.3 1.0
CG A:HIS2 4.2 48.7 1.0
CE2 B:PHE289 4.3 30.1 1.0
ND1 A:HIS2 4.4 47.6 1.0
CA B:ASP280 4.6 33.0 1.0
O B:HOH1036 4.8 40.4 1.0
N B:TYR241 4.8 29.1 1.0
N B:VAL239 4.9 29.4 1.0
C B:CYS240 5.0 26.8 1.0
CD2 B:PHE289 5.0 32.1 1.0

Zinc binding site 2 out of 2 in 1dce

Go back to Zinc Binding Sites List in 1dce
Zinc binding site 2 out of 2 in the Crystal Structure of Rab Geranylgeranyltransferase From Rat Brain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rab Geranylgeranyltransferase From Rat Brain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn950

b:35.4
occ:1.00
NE2 D:HIS290 2.1 31.1 1.0
OD2 D:ASP238 2.2 37.1 1.0
OD1 D:ASP238 2.2 39.4 1.0
SG D:CYS240 2.3 30.6 1.0
NE2 C:HIS2 2.3 48.2 1.0
CG D:ASP238 2.6 37.8 1.0
CD2 C:HIS2 2.9 49.2 1.0
CD2 D:HIS290 3.0 30.3 1.0
CB D:CYS240 3.1 31.1 1.0
CE1 D:HIS290 3.1 28.2 1.0
CE1 C:HIS2 3.5 51.0 1.0
N D:CYS240 3.9 30.9 1.0
CB D:ASP280 4.0 36.7 1.0
CB D:ASP238 4.0 35.8 1.0
CE2 D:PHE289 4.1 35.1 1.0
CA D:CYS240 4.1 29.6 1.0
CG D:HIS290 4.1 30.2 1.0
ND1 D:HIS290 4.2 30.1 1.0
CG C:HIS2 4.2 50.8 1.0
ND1 C:HIS2 4.4 49.5 1.0
CA D:ASP280 4.6 36.3 1.0
CD2 D:PHE289 4.7 36.0 1.0
N D:TYR241 4.9 31.9 1.0
C D:CYS240 5.0 31.5 1.0
N D:VAL239 5.0 32.6 1.0

Reference:

H.Zhang, M.C.Seabra, J.Deisenhofer. Crystal Structure of Rab Geranylgeranyltransferase at 2.0 A Resolution. Structure Fold.Des. V. 8 241 2000.
ISSN: ISSN 0969-2126
PubMed: 10745007
DOI: 10.1016/S0969-2126(00)00102-7
Page generated: Mon Jan 25 16:08:20 2021

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