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Zinc in PDB 2amt: Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor

Enzymatic activity of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor

All present enzymatic activity of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor:
4.6.1.12;

Protein crystallography data

The structure of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor, PDB code: 2amt was solved by N.L.Ramsden, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.50 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.033, 115.269, 87.609, 90.00, 90.18, 90.00
R / Rfree (%) 24.3 / 28

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor (pdb code 2amt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor, PDB code: 2amt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2amt

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Zinc binding site 1 out of 6 in the Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1900

b:45.6
occ:1.00
 NE2 A:HIS10 2.1 35.5 1.0
OD2 A:ASP8 2.2 32.5 1.0
ND1 A:HIS42 2.4 34.3 1.0
O7 A:1AA1901 2.7 69.4 1.0
CG A:ASP8 2.9 32.1 1.0
CE1 A:HIS10 2.9 35.7 1.0
OD1 A:ASP8 3.0 32.2 1.0
CD2 A:HIS10 3.1 35.2 1.0
CE1 A:HIS42 3.2 34.1 1.0
CG A:HIS42 3.2 33.9 1.0
CE1 A:HIS34 3.4 49.4 1.0
NE2 A:HIS34 3.4 49.3 1.0
CB A:HIS42 3.5 33.5 1.0
P2 A:1AA1901 3.9 69.3 1.0
C7 A:1AA1901 3.9 70.6 0.0
O4 A:1AA1901 4.0 69.8 1.0
ND1 A:HIS10 4.0 35.5 1.0
CG A:HIS10 4.1 35.1 1.0
NE2 A:HIS42 4.1 34.2 1.0
CD2 A:HIS42 4.2 34.1 1.0
CB A:ASP8 4.3 31.8 1.0
O A:VAL9 4.6 33.3 1.0
ND1 A:HIS34 4.7 49.4 1.0
CD2 A:HIS34 4.8 49.3 1.0
O8 A:1AA1901 4.8 69.2 1.0

Zinc binding site 2 out of 6 in 2amt

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Zinc binding site 2 out of 6 in the Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2900

b:36.0
occ:1.00
 OD2 B:ASP8 2.1 22.8 1.0
NE2 B:HIS10 2.1 27.7 1.0
ND1 B:HIS42 2.2 22.4 1.0
O8 C:1AA2901 2.5 51.2 1.0
CG B:ASP8 2.8 22.9 1.0
OD1 B:ASP8 2.9 22.2 1.0
CE1 B:HIS10 2.9 27.8 1.0
CG B:HIS42 3.1 21.6 1.0
CE1 B:HIS42 3.1 22.5 1.0
CD2 B:HIS10 3.1 27.2 1.0
CB B:HIS42 3.4 21.1 1.0
P2 C:1AA2901 3.9 51.2 1.0
ND1 B:HIS10 4.0 27.9 1.0
NE2 B:HIS42 4.1 22.9 1.0
CG B:HIS10 4.2 27.5 1.0
CD2 B:HIS42 4.2 22.2 1.0
O5 C:1AA2901 4.2 55.9 1.0
CB B:ASP8 4.2 23.3 1.0
O B:HOH2935 4.4 23.7 1.0
O4 C:1AA2901 4.5 52.2 1.0
C2' C:1AA2901 4.5 57.5 1.0
CD1 B:ILE57 4.6 31.9 1.0
O3 C:1AA2901 4.8 48.8 1.0
OG B:SER35 4.9 41.5 1.0
O7 C:1AA2901 4.9 51.4 1.0
C8 C:1AA2901 4.9 54.8 1.0
O B:VAL9 4.9 25.4 1.0
CA B:HIS42 4.9 21.1 1.0

Zinc binding site 3 out of 6 in 2amt

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Zinc binding site 3 out of 6 in the Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3900

b:30.4
occ:1.00
 O8 C:1AA3901 2.0 48.5 1.0
OD2 C:ASP8 2.1 25.3 1.0
NE2 C:HIS10 2.1 27.7 1.0
ND1 C:HIS42 2.2 22.6 1.0
CG C:ASP8 2.8 25.8 1.0
OD1 C:ASP8 2.9 25.3 1.0
CD2 C:HIS10 3.0 27.6 1.0
CE1 C:HIS10 3.0 27.9 1.0
CG C:HIS42 3.1 22.0 1.0
CE1 C:HIS42 3.2 22.7 1.0
CB C:HIS42 3.3 21.6 1.0
P2 C:1AA3901 3.4 48.6 1.0
ND1 C:HIS10 4.1 28.2 1.0
CG C:HIS10 4.1 27.8 1.0
CB C:ASP8 4.2 26.1 1.0
O3 C:1AA3901 4.2 47.0 1.0
O7 C:1AA3901 4.2 48.5 1.0
CD2 C:HIS42 4.2 22.4 1.0
NE2 C:HIS42 4.2 22.9 1.0
O4 C:1AA3901 4.4 50.0 1.0
C8 C:1AA3901 4.5 53.1 1.0
O C:HOH3927 4.5 28.9 1.0
C7 C:1AA3901 4.5 51.8 1.0
O C:HOH3912 4.8 25.0 1.0
O C:ASP38 4.8 30.4 1.0
CA C:HIS42 4.9 21.6 1.0
CA C:VAL39 4.9 28.3 1.0
O C:VAL9 4.9 27.3 1.0

Zinc binding site 4 out of 6 in 2amt

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Zinc binding site 4 out of 6 in the Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4900

b:37.7
occ:1.00
 OD2 D:ASP8 2.0 22.5 1.0
NE2 D:HIS10 2.1 26.3 1.0
ND1 D:HIS42 2.2 20.4 0.6
O7 E:1AA4901 2.8 61.9 1.0
CG D:ASP8 2.9 22.1 1.0
CE1 D:HIS10 3.0 26.3 1.0
OD1 D:ASP8 3.1 22.0 1.0
CD2 D:HIS10 3.1 25.9 1.0
CE1 D:HIS42 3.1 20.4 0.6
CG D:HIS42 3.1 20.2 0.6
P2 E:1AA4901 3.3 62.0 1.0
O4 E:1AA4901 3.3 62.7 1.0
O8 E:1AA4901 3.4 61.8 1.0
CB D:HIS42 3.4 20.1 0.6
ND1 D:HIS10 4.1 26.4 1.0
CG D:HIS10 4.1 25.8 1.0
NE2 D:HIS42 4.2 20.7 0.6
CD2 D:HIS42 4.2 20.3 0.6
CB D:ASP8 4.3 22.3 1.0
C7 E:1AA4901 4.5 63.9 1.0
O5 E:1AA4901 4.6 65.8 1.0
O D:HOH8908 4.8 19.0 1.0
O D:VAL9 4.8 23.8 1.0
O3 E:1AA4901 4.9 59.8 1.0
CA D:VAL39 4.9 24.8 1.0
C8 E:1AA4901 4.9 64.8 1.0
CA D:HIS42 4.9 20.1 0.5
O D:ASP38 5.0 26.2 1.0

Zinc binding site 5 out of 6 in 2amt

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Zinc binding site 5 out of 6 in the Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn5900

b:34.1
occ:1.00
 O8 E:1AA5901 1.9 54.3 1.0
NE2 E:HIS10 2.0 28.4 1.0
ND1 E:HIS42 2.1 18.8 0.6
OD2 E:ASP8 2.1 23.3 1.0
CG E:ASP8 2.8 23.9 1.0
CE1 E:HIS10 2.9 27.8 1.0
OD1 E:ASP8 2.9 24.1 1.0
CE1 E:HIS42 3.0 18.6 0.6
CD2 E:HIS10 3.0 28.2 1.0
CG E:HIS42 3.1 18.6 0.6
P2 E:1AA5901 3.4 54.6 1.0
CB E:HIS42 3.4 18.7 0.6
ND1 E:HIS10 4.0 28.5 1.0
CG E:HIS10 4.1 28.0 1.0
NE2 E:HIS42 4.1 18.4 0.6
O3 E:1AA5901 4.1 53.0 1.0
O4 E:1AA5901 4.2 55.7 1.0
CD2 E:HIS42 4.2 18.5 0.6
CB E:ASP8 4.2 24.2 1.0
O7 E:1AA5901 4.4 54.8 1.0
O E:HOH5912 4.4 34.4 1.0
C8 E:1AA5901 4.7 58.5 1.0
O E:VAL9 4.7 26.5 1.0
O E:ASP38 4.8 27.0 1.0
OG E:SER35 4.8 39.2 1.0
CA E:HIS42 4.9 18.8 0.5
CA E:VAL39 5.0 24.6 1.0

Zinc binding site 6 out of 6 in 2amt

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Zinc binding site 6 out of 6 in the Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with A Cdp Derived Fluorescent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn6900

b:46.5
occ:1.00
 O8 D:1AA6901 2.0 70.9 1.0
ND1 F:HIS42 2.2 32.3 1.0
OD2 F:ASP8 2.2 28.7 1.0
NE2 F:HIS10 2.3 31.0 1.0
CE1 F:HIS10 2.8 31.2 1.0
CG F:ASP8 2.9 28.5 1.0
OD1 F:ASP8 2.9 28.0 1.0
CE1 F:HIS42 3.1 32.5 1.0
CG F:HIS42 3.2 31.9 1.0
CD2 F:HIS10 3.3 31.0 1.0
P2 D:1AA6901 3.4 71.2 1.0
CB F:HIS42 3.5 31.3 1.0
ND1 F:HIS10 3.9 31.5 1.0
O7 D:1AA6901 4.1 71.0 1.0
O F:HOH6913 4.2 51.6 1.0
O4 D:1AA6901 4.2 71.7 1.0
CG F:HIS10 4.2 31.0 1.0
NE2 F:HIS42 4.2 32.4 1.0
CB F:ASP8 4.3 28.7 1.0
CD2 F:HIS42 4.3 32.4 1.0
O3 D:1AA6901 4.5 69.6 1.0
C8 D:1AA6901 4.6 73.6 1.0
OG F:SER35 4.9 43.6 1.0
O F:VAL9 4.9 29.8 1.0

Reference:

C.M.Crane, J.Kaiser, N.L.Ramsden, S.Lauw, F.Rohdich, W.Eisenreich, W.N.Hunter, A.Bacher, F.Diederich. Fluorescent Inhibitors For Ispf, An Enzyme in the Non-Mevalonate Pathway For Isoprenoid Biosynthesis and A Potential Target For Antimalarial Therapy. Angew.Chem.Int.Ed.Engl. V. 45 1069 2006.
ISSN: ISSN 1433-7851
PubMed: 16392111
DOI: 10.1002/ANIE.200503003
Page generated: Wed Oct 16 21:41:56 2024

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