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

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

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

Protein crystallography data

The structure of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Nipp, PDB code: 1nfs 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 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.982, 71.493, 91.441, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 26

Other elements in 1nfs:

The structure of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Nipp 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 Nipp (pdb code 1nfs). 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 Nipp, PDB code: 1nfs:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1nfs

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


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 Nipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:29.4
occ:1.00
 O7 A:DED301 1.8 41.7 1.0
O2 A:DED301 1.9 23.2 1.0
O A:HOH508 1.9 21.5 1.0
OE2 A:GLU87 2.0 36.3 1.0
O A:HOH509 2.1 28.4 1.0
O A:CYS67 2.1 30.3 1.0
CD A:GLU87 2.9 35.7 1.0
OE1 A:GLU87 3.1 34.2 1.0
P8 A:DED301 3.2 37.0 1.0
C A:CYS67 3.2 33.0 1.0
P4 A:DED301 3.3 30.0 1.0
O9 A:DED301 3.7 37.8 1.0
O5 A:DED301 3.8 28.8 1.0
N A:CYS67 3.8 30.8 1.0
CA A:CYS67 4.0 33.5 1.0
O1 A:DED301 4.0 30.9 1.0
O A:HOH507 4.1 32.9 1.0
N A:GLY68 4.2 30.7 1.0
O3 A:DED301 4.2 37.3 1.0
O6 A:DED301 4.2 31.7 1.0
CG A:GLU87 4.3 27.4 1.0
NH2 A:ARG83 4.3 39.7 1.0
CA A:GLY68 4.3 34.1 1.0
OE1 A:GLU135 4.3 33.4 1.0
NE A:ARG83 4.4 34.3 1.0
CB A:CYS67 4.4 32.6 1.0
NH1 A:ARG51 4.4 21.4 1.0
O A:HOH503 4.5 26.1 1.0
CG2 A:VAL66 4.8 29.4 1.0
CZ A:ARG83 4.8 36.3 1.0
NZ A:LYS55 4.9 27.7 1.0
C A:VAL66 5.0 28.5 1.0

Magnesium binding site 2 out of 2 in 1nfs

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


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 Nipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:46.8
occ:1.00
 O7 B:DED302 1.7 56.6 1.0
OE2 B:GLU87 1.9 39.7 1.0
O B:HOH523 2.0 35.8 1.0
O B:HOH522 2.1 26.5 1.0
O2 B:DED302 2.3 40.9 1.0
O B:CYS67 2.5 29.3 1.0
CD B:GLU87 2.9 35.7 1.0
OE1 B:GLU87 3.1 35.1 1.0
P8 B:DED302 3.2 54.9 1.0
C B:CYS67 3.5 33.7 1.0
P4 B:DED302 3.7 51.7 1.0
NH2 B:ARG83 3.8 42.0 1.0
O6 B:DED302 3.9 58.8 1.0
O9 B:DED302 3.9 49.8 1.0
O5 B:DED302 4.0 58.5 1.0
N B:CYS67 4.0 32.6 1.0
O B:HOH515 4.1 31.1 1.0
NE B:ARG83 4.1 35.6 1.0
O1 B:DED302 4.2 42.5 1.0
O B:HOH519 4.2 31.2 1.0
CG B:GLU87 4.2 27.8 1.0
CA B:CYS67 4.2 32.5 1.0
NH1 B:ARG51 4.3 24.0 1.0
CZ B:ARG83 4.4 35.8 1.0
OE1 B:GLU135 4.5 36.0 1.0
N B:GLY68 4.5 33.7 1.0
CB B:CYS67 4.6 32.6 1.0
NZ B:LYS55 4.6 31.5 1.0
CA B:GLY68 4.6 36.6 1.0
O3 B:DED302 4.7 72.5 1.0
CE B:LYS55 5.0 33.9 1.0
CG2 B:VAL66 5.0 32.0 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: Sun Aug 10 01:37:44 2025

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