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Zinc in PDB 1jy8: 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf)

Protein crystallography data

The structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf), PDB code: 1jy8 was solved by S.Steinbacher, J.Kaiser, J.Wungsintaweekul, S.Hecht, W.Eisenreich, S.Gerhardt, A.Bacher, F.Rohdich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 144.630, 144.630, 144.630, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25.5

Zinc Binding Sites:

The binding sites of Zinc atom in the 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) (pdb code 1jy8). 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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf), PDB code: 1jy8:

Zinc binding site 1 out of 1 in 1jy8

Go back to Zinc Binding Sites List in 1jy8
Zinc binding site 1 out of 1 in the 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:36.1
occ:1.00
OD1 A:ASP8 1.9 30.8 1.0
OA2 A:CDI421 1.9 36.9 1.0
ND1 A:HIS42 2.0 25.6 1.0
NE2 A:HIS10 2.0 29.8 1.0
CG A:ASP8 2.8 29.2 1.0
CE1 A:HIS42 2.9 24.6 1.0
OD2 A:ASP8 2.9 28.8 1.0
CE1 A:HIS10 2.9 28.8 1.0
CD2 A:HIS10 2.9 28.4 1.0
OB1 A:CDI421 3.0 49.2 1.0
CG A:HIS42 3.1 23.5 1.0
PA A:CDI421 3.2 41.2 1.0
CB A:HIS42 3.5 23.6 1.0
OA1 A:CDI421 4.0 42.5 1.0
ND1 A:HIS10 4.0 26.7 1.0
NE2 A:HIS42 4.0 21.8 1.0
CG A:HIS10 4.1 28.5 1.0
CD2 A:HIS42 4.1 23.8 1.0
CB A:ASP8 4.2 26.0 1.0
O A:HOH507 4.3 36.6 1.0
PB A:CDI421 4.3 50.5 1.0
OA3 A:CDI421 4.4 46.7 1.0
O A:HOH501 4.5 39.4 1.0
H A:VAL9 4.6 0.0 0.0
O A:VAL9 4.6 29.0 1.0
H1 A:HOH511 4.6 0.0 0.0
H2 A:HOH507 4.6 0.0 0.0
H1 A:HOH501 4.7 0.0 0.0
H2 A:HOH501 4.7 0.0 0.0
O3P A:C5P669 4.7 55.9 1.0
OB3 A:CDI421 4.8 45.7 1.0
HD1 A:HIS10 4.9 0.0 0.0
HE2 A:HIS42 4.9 0.0 0.0
CA A:VAL39 5.0 28.2 1.0
O A:ASP38 5.0 31.4 1.0
O A:HOH511 5.0 32.4 1.0

Reference:

S.Steinbacher, J.Kaiser, J.Wungsintaweekul, S.Hecht, W.Eisenreich, S.Gerhardt, A.Bacher, F.Rohdich. Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase Involved in Mevalonate-Independent Biosynthesis of Isoprenoids. J.Mol.Biol. V. 316 79 2002.
ISSN: ISSN 0022-2836
PubMed: 11829504
DOI: 10.1006/JMBI.2001.5341
Page generated: Wed Dec 16 02:54:11 2020

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