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Zinc in PDB 1h48: The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product

Enzymatic activity of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product

All present enzymatic activity of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product:
4.6.1.12;

Protein crystallography data

The structure of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product, PDB code: 1h48 was solved by L.E.Kemp, M.S.Alphey, C.S.Bond, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 198.122, 150.287, 57.559, 90.00, 106.52, 90.00
R / Rfree (%) 20.2 / 23.6

Other elements in 1h48:

The structure of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product (pdb code 1h48). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product, PDB code: 1h48:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1h48

Go back to Zinc Binding Sites List in 1h48
Zinc binding site 1 out of 6 in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:50.5
occ:1.00
 OD2 A:ASP8 1.9 37.4 1.0
ND1 A:HIS42 2.0 37.4 1.0
OA2 A:CDI201 2.2 91.2 1.0
NE2 A:HIS10 2.2 42.0 1.0
PA A:CDI201 2.3 92.5 1.0
OB1 A:CDI201 2.4 90.6 1.0
OA1 A:CDI201 2.7 91.6 1.0
CE1 A:HIS42 2.9 37.9 1.0
CG A:ASP8 3.0 35.9 1.0
CE1 A:HIS10 3.1 42.7 1.0
CG A:HIS42 3.1 35.1 1.0
CD2 A:HIS10 3.2 40.9 1.0
OD1 A:ASP8 3.2 40.7 1.0
CB A:HIS42 3.5 34.3 1.0
PB A:CDI201 3.9 90.4 1.0
OA3 A:CDI201 3.9 92.0 1.0
NE2 A:HIS42 4.1 37.6 1.0
CD2 A:HIS42 4.2 34.1 1.0
ND1 A:HIS10 4.2 46.3 1.0
CG A:HIS10 4.3 40.8 1.0
CB A:ASP8 4.3 35.1 1.0
OB3 A:CDI201 4.4 88.6 1.0
C5 A:CDI201 4.4 88.4 1.0
CD1 A:ILE57 4.5 60.6 1.0
C1 A:CDI201 4.6 91.0 1.0
OB2 A:CDI201 4.7 90.0 1.0
O A:VAL9 4.8 37.0 1.0
O A:HOH325 4.9 60.0 1.0
OB4 A:CDI201 4.9 90.5 1.0

Zinc binding site 2 out of 6 in 1h48

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Zinc binding site 2 out of 6 in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn903

b:58.9
occ:1.00
 OD2 B:ASP8 2.1 38.0 1.0
ND1 B:HIS42 2.2 43.2 1.0
NE2 B:HIS10 2.2 43.5 1.0
OA2 B:CDI902 2.5 75.0 0.5
OB1 B:CDI902 2.6 74.5 0.5
CG B:ASP8 3.0 37.8 1.0
CE1 B:HIS10 3.0 46.5 1.0
CE1 B:HIS42 3.1 42.6 1.0
OD1 B:ASP8 3.1 40.3 1.0
PA B:CDI902 3.2 75.8 0.5
CG B:HIS42 3.2 40.0 1.0
CD2 B:HIS10 3.3 42.5 1.0
CB B:HIS42 3.6 37.3 1.0
PB B:CDI902 3.9 72.7 0.5
OB3 B:CDI902 4.1 72.5 0.5
ND1 B:HIS10 4.1 45.7 1.0
NE2 B:HIS42 4.2 42.6 1.0
OA3 B:CDI902 4.2 75.7 0.5
C1 B:CDI902 4.3 75.4 0.5
CD2 B:HIS42 4.3 41.8 1.0
CG B:HIS10 4.3 41.1 1.0
OA1 B:CDI902 4.3 75.4 0.5
CB B:ASP8 4.5 36.9 1.0
OB2 B:CDI902 4.8 73.0 0.5
C5 B:CDI902 4.8 74.5 0.5
O B:VAL9 4.8 37.3 1.0
OB4 B:CDI902 4.9 74.3 0.5

Zinc binding site 3 out of 6 in 1h48

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Zinc binding site 3 out of 6 in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn903

b:43.7
occ:1.00
 OA2 C:CDI902 2.0 79.3 1.0
OD2 C:ASP8 2.1 35.2 1.0
NE2 C:HIS10 2.1 40.7 1.0
ND1 C:HIS42 2.2 27.4 1.0
PA C:CDI902 2.5 80.8 1.0
OB1 C:CDI902 2.6 80.3 1.0
CE1 C:HIS10 3.0 42.4 1.0
CG C:ASP8 3.0 33.5 1.0
OA1 C:CDI902 3.0 81.2 1.0
CE1 C:HIS42 3.0 27.7 1.0
OD1 C:ASP8 3.1 35.7 1.0
CD2 C:HIS10 3.1 37.4 1.0
CG C:HIS42 3.3 28.6 1.0
CB C:HIS42 3.7 29.6 1.0
O A:HOH301 4.0 51.6 1.0
OA3 C:CDI902 4.1 81.4 1.0
ND1 C:HIS10 4.1 41.7 1.0
PB C:CDI902 4.1 79.7 1.0
CG C:HIS10 4.2 38.6 1.0
NE2 C:HIS42 4.2 26.6 1.0
CD2 C:HIS42 4.3 27.4 1.0
CB C:ASP8 4.4 32.4 1.0
OB3 C:CDI902 4.6 78.5 1.0
O2P A:C5P203 4.6 78.3 1.0
CD1 C:ILE57 4.7 47.8 1.0
C1 C:CDI902 4.7 80.0 1.0
O C:VAL9 4.8 34.5 1.0
C5 C:CDI902 4.8 79.3 1.0
OB2 C:CDI902 4.8 78.9 1.0
O C:HOH1029 4.9 45.4 1.0

Zinc binding site 4 out of 6 in 1h48

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Zinc binding site 4 out of 6 in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:58.4
occ:1.00
 NE2 D:HIS10 2.1 43.9 1.0
OB1 D:CDI201 2.1 66.8 0.5
PA D:CDI201 2.1 68.6 0.5
OD2 D:ASP8 2.1 48.9 1.0
ND1 D:HIS42 2.1 39.8 1.0
OA2 D:CDI201 2.2 65.9 0.5
OA1 D:CDI201 2.3 66.8 0.5
CE1 D:HIS42 3.0 35.2 1.0
CE1 D:HIS10 3.0 46.4 1.0
CG D:ASP8 3.0 44.5 1.0
CD2 D:HIS10 3.1 45.2 1.0
CG D:HIS42 3.2 39.7 1.0
OD1 D:ASP8 3.2 47.1 1.0
PB D:CDI201 3.6 64.3 0.5
CB D:HIS42 3.6 39.9 1.0
OA3 D:CDI201 3.7 68.5 0.5
ND1 D:HIS10 4.1 46.8 1.0
NE2 D:HIS42 4.1 38.0 1.0
CG D:HIS10 4.2 44.2 1.0
OB2 D:CDI201 4.2 64.8 0.5
OB3 D:CDI201 4.2 65.8 0.5
CD2 D:HIS42 4.3 37.3 1.0
C5 D:CDI201 4.4 66.5 0.5
CB D:ASP8 4.4 43.8 1.0
C1 D:CDI201 4.6 67.9 0.5
OB4 D:CDI201 4.7 65.8 0.5
O D:VAL9 4.8 43.6 1.0

Zinc binding site 5 out of 6 in 1h48

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Zinc binding site 5 out of 6 in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn903

b:73.4
occ:1.00
 ND1 E:HIS42 2.0 48.6 1.0
OA2 E:CDI902 2.2 73.2 0.5
NE2 E:HIS10 2.3 59.2 1.0
OD2 E:ASP8 2.4 54.2 1.0
OB1 E:CDI902 2.5 71.8 0.5
CE1 E:HIS10 2.7 61.0 1.0
CE1 E:HIS42 2.7 51.5 1.0
PA E:CDI902 2.8 74.0 0.5
OD1 E:ASP8 3.1 54.2 1.0
CG E:ASP8 3.1 51.7 1.0
CG E:HIS42 3.2 52.8 1.0
CD2 E:HIS10 3.5 58.4 1.0
OA1 E:CDI902 3.6 73.2 0.5
CB E:HIS42 3.7 53.0 1.0
ND1 E:HIS10 3.8 58.9 1.0
NE2 E:HIS42 3.9 51.7 1.0
PB E:CDI902 4.0 69.9 0.5
OA3 E:CDI902 4.1 73.3 0.5
CD2 E:HIS42 4.2 51.1 1.0
CG E:HIS10 4.3 56.5 1.0
OB3 E:CDI902 4.3 68.8 0.5
C1 E:CDI902 4.5 72.5 0.5
CB E:ASP8 4.6 49.9 1.0
O E:VAL9 4.7 52.0 1.0
OB2 E:CDI902 4.7 68.2 0.5
C5 E:CDI902 4.8 70.7 0.5
O2P F:C5P901 4.9 0.9 1.0

Zinc binding site 6 out of 6 in 1h48

Go back to Zinc Binding Sites List in 1h48
Zinc binding site 6 out of 6 in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn903

b:51.0
occ:1.00
 OD2 F:ASP8 2.1 42.4 1.0
ND1 F:HIS42 2.1 32.3 1.0
NE2 F:HIS10 2.2 44.9 1.0
OA2 F:CDI902 2.3 58.3 0.5
OB1 F:CDI902 2.6 55.7 0.5
CE1 F:HIS10 2.9 44.4 1.0
CG F:ASP8 2.9 39.4 1.0
CE1 F:HIS42 3.0 30.4 1.0
PA F:CDI902 3.0 59.2 0.5
OD1 F:ASP8 3.1 40.9 1.0
CG F:HIS42 3.3 33.0 1.0
CD2 F:HIS10 3.3 42.7 1.0
CB F:HIS42 3.7 35.2 1.0
OA3 F:CDI902 4.0 59.5 0.5
PB F:CDI902 4.0 52.9 0.5
ND1 F:HIS10 4.1 45.0 1.0
NE2 F:HIS42 4.1 30.6 1.0
C1 F:CDI902 4.2 58.2 0.5
OA1 F:CDI902 4.2 58.3 0.5
CG F:HIS10 4.3 42.1 1.0
CD2 F:HIS42 4.3 28.9 1.0
OB3 F:CDI902 4.3 52.6 0.5
CB F:ASP8 4.4 37.5 1.0
C5 F:CDI902 4.6 54.7 0.5
O F:VAL9 4.8 38.8 1.0
OB2 F:CDI902 4.8 53.1 0.5

Reference:

L.E.Kemp, M.S.Alphey, C.S.Bond, M.Ferguson, S.Hecht, A.Bacher, W.Eisenreich, F.Rohdich, W.N.Hunter. The Identification of Isoprenoids That Bind in the Intersubunit Cavity of Escherichia Coli 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase By Complementary Biophysical Methods Acta Crystallogr.,Sect.D V. 61 45 2005.
ISSN: ISSN 0907-4449
PubMed: 15608374
DOI: 10.1107/S0907444904025971
Page generated: Wed Dec 16 02:50:52 2020

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