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Magnesium in PDB 1nfz: Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp

Enzymatic activity of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp

All present enzymatic activity of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp:
5.3.3.2;

Protein crystallography data

The structure of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp, PDB code: 1nfz was solved by J.Wouters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.100, 72.110, 91.520, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.7

Other elements in 1nfz:

The structure of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp (pdb code 1nfz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp, PDB code: 1nfz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1nfz

Go back to Magnesium Binding Sites List in 1nfz
Magnesium binding site 1 out of 2 in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:25.9
occ:1.00
 O7 A:EIP301 2.0 18.3 1.0
O2 A:EIP301 2.0 21.7 1.0
O A:HOH509 2.1 28.4 1.0
O A:HOH508 2.1 21.5 1.0
O A:CYS67 2.1 21.1 1.0
OE2 A:GLU87 2.2 23.7 1.0
CD A:GLU87 3.1 24.3 1.0
P4 A:EIP301 3.2 25.1 1.0
P8 A:EIP301 3.2 28.3 1.0
C A:CYS67 3.2 24.9 1.0
O5 A:EIP301 3.3 25.6 1.0
OE1 A:GLU87 3.3 21.4 1.0
O1 A:EIP301 3.8 26.7 1.0
O9 A:EIP301 3.8 28.5 1.0
N A:CYS67 3.9 18.6 1.0
CA A:CYS67 4.0 24.2 1.0
CB A:CYS67 4.1 31.1 1.0
NH2 A:ARG83 4.2 23.8 1.0
N A:GLY68 4.2 20.8 1.0
O6 A:EIP301 4.2 33.6 1.0
O3 A:EIP301 4.2 22.8 1.0
CA A:GLY68 4.3 19.5 1.0
NE A:ARG83 4.3 24.2 1.0
OE1 A:GLU135 4.4 22.2 1.0
NH1 A:ARG51 4.4 21.0 1.0
CG A:GLU87 4.5 19.8 1.0
O A:HOH507 4.6 21.4 1.0
O A:HOH503 4.6 25.9 1.0
CZ A:ARG83 4.7 29.5 1.0
NZ A:LYS55 4.8 19.6 1.0

Magnesium binding site 2 out of 2 in 1nfz

Go back to Magnesium Binding Sites List in 1nfz
Magnesium binding site 2 out of 2 in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Eipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:27.5
occ:1.00
 O7 B:EIP302 1.9 24.5 1.0
O2 B:EIP302 2.0 26.3 1.0
OE2 B:GLU87 2.1 25.8 1.0
O B:HOH519 2.2 17.3 1.0
O B:HOH520 2.2 27.7 1.0
O B:CYS67 2.2 20.9 1.0
CD B:GLU87 3.1 23.9 1.0
P8 B:EIP302 3.2 37.3 1.0
P4 B:EIP302 3.2 32.4 1.0
C B:CYS67 3.3 23.9 1.0
O5 B:EIP302 3.4 33.6 1.0
OE1 B:GLU87 3.5 24.7 1.0
O9 B:EIP302 3.7 31.6 1.0
O1 B:EIP302 3.8 42.3 1.0
NH2 B:ARG83 4.0 26.6 1.0
CA B:CYS67 4.1 24.4 1.0
N B:CYS67 4.1 20.6 1.0
CB B:CYS67 4.2 30.5 1.0
O6 B:EIP302 4.2 37.6 1.0
NE B:ARG83 4.2 25.1 1.0
NH1 B:ARG51 4.2 18.0 1.0
N B:GLY68 4.3 19.9 1.0
O3 B:EIP302 4.3 25.9 1.0
O B:HOH512 4.3 16.5 1.0
CA B:GLY68 4.4 20.4 1.0
OE1 B:GLU135 4.4 26.7 1.0
O B:HOH516 4.4 21.7 1.0
CG B:GLU87 4.4 23.1 1.0
CZ B:ARG83 4.6 31.2 1.0
NZ B:LYS55 4.7 21.1 1.0
CE B:LYS55 4.9 23.8 1.0

Reference:

J.Wouters, Y.Oudjama, S.J.Barkley, C.Tricot, V.Stalon, L.Droogmans, C.D.Poulter. Catalytic Mechanism of Escherichia Coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 As Suggested By Crystal Structures of Complexes with Transition State Analogues and Irreversible Inhibitors J.Biol.Chem. V. 278 11903 2003.
ISSN: ISSN 0021-9258
PubMed: 12540835
DOI: 10.1074/JBC.M212823200
Page generated: Mon Dec 14 06:32:15 2020

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