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Manganese 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:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with Nipp, PDB code: 1nfs:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 1nfs

Go back to Manganese Binding Sites List in 1nfs
Manganese 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 Manganese with other atoms in the Mn 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:Mn201

b:25.7
occ:1.00
 OE2 A:GLU116 1.8 27.7 1.0
NE2 A:HIS32 2.0 33.2 1.0
NE2 A:HIS69 2.1 37.6 1.0
OE2 A:GLU114 2.1 31.2 1.0
NE2 A:HIS25 2.1 33.4 1.0
OE1 A:GLU114 2.4 30.6 1.0
CD A:GLU114 2.6 33.2 1.0
CD A:GLU116 2.9 31.5 1.0
CD2 A:HIS69 3.0 33.9 1.0
CE1 A:HIS32 3.0 34.8 1.0
CD2 A:HIS32 3.0 36.4 1.0
CD2 A:HIS25 3.1 36.5 1.0
CE1 A:HIS25 3.1 35.7 1.0
CE1 A:HIS69 3.1 38.9 1.0
CG A:GLU116 3.5 31.8 1.0
OE1 A:GLU116 3.9 29.1 1.0
CG A:GLU114 4.1 30.9 1.0
ND1 A:HIS32 4.1 37.0 1.0
CG A:HIS69 4.2 34.7 1.0
CG A:HIS32 4.2 36.8 1.0
ND1 A:HIS69 4.2 33.5 1.0
ND1 A:HIS25 4.2 35.1 1.0
CG A:HIS25 4.2 35.2 1.0
O A:HOH506 4.2 39.5 1.0
CB A:GLU114 4.8 27.9 1.0
C10 A:DED301 4.9 39.6 1.0
CG1 A:VAL6 4.9 33.8 1.0

Manganese binding site 2 out of 2 in 1nfs

Go back to Manganese Binding Sites List in 1nfs
Manganese 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 Manganese with other atoms in the Mn 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:Mn201

b:34.9
occ:1.00
 NE2 B:HIS25 2.0 38.1 1.0
NE2 B:HIS32 2.0 33.2 1.0
OE2 B:GLU116 2.0 30.7 1.0
NE2 B:HIS69 2.0 36.5 1.0
OE2 B:GLU114 2.2 34.5 1.0
OE1 B:GLU114 2.5 32.7 1.0
CD B:GLU114 2.7 33.6 1.0
CE1 B:HIS25 2.9 37.0 1.0
CD2 B:HIS69 2.9 33.9 1.0
CD2 B:HIS32 3.0 37.3 1.0
CE1 B:HIS32 3.0 35.6 1.0
CD2 B:HIS25 3.0 39.0 1.0
CD B:GLU116 3.0 31.6 1.0
CE1 B:HIS69 3.1 39.1 1.0
CG B:GLU116 3.6 30.6 1.0
ND1 B:HIS25 4.0 39.9 1.0
OE1 B:GLU116 4.1 30.0 1.0
ND1 B:HIS32 4.1 36.5 1.0
CG B:HIS25 4.1 36.6 1.0
CG B:HIS69 4.1 34.0 1.0
CG B:HIS32 4.1 38.7 1.0
ND1 B:HIS69 4.1 33.9 1.0
CG B:GLU114 4.2 32.6 1.0
C10 B:DED302 4.6 49.2 1.0
CB B:ALA34 4.9 32.1 1.0
C11 B:DED302 4.9 44.9 1.0
CB B:GLU114 4.9 30.7 1.0
CB B:GLU116 5.0 29.6 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: Tue Dec 15 03:53:16 2020

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