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Manganese in PDB 1q54: Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp

Enzymatic activity of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp

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

Protein crystallography data

The structure of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp, PDB code: 1q54 was solved by J.Wouters, Y.Oudjama, S.Ghosh, V.Stalon, L.Droogmans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.830, 71.350, 91.490, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.6

Other elements in 1q54:

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

Bromine (Br) 4 atoms
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 the Bromohydrine of Ipp (pdb code 1q54). 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 the Bromohydrine of Ipp, PDB code: 1q54:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 1q54

Go back to Manganese Binding Sites List in 1q54
Manganese binding site 1 out of 2 in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp


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 the Bromohydrine of Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:25.4
occ:1.00
 NE2 A:HIS25 2.0 21.6 1.0
NE2 A:HIS69 2.0 28.4 1.0
NE2 A:HIS32 2.1 30.0 1.0
OE2 A:GLU116 2.2 33.5 1.0
OE2 A:GLU114 2.2 33.4 1.0
OE1 A:GLU114 2.4 33.4 1.0
CD A:GLU114 2.6 35.7 1.0
CE1 A:HIS25 2.9 26.7 1.0
CE1 A:HIS69 2.9 29.5 1.0
CE1 A:HIS32 2.9 31.7 1.0
CD2 A:HIS25 3.0 23.1 1.0
CD2 A:HIS32 3.1 30.4 1.0
CD2 A:HIS69 3.1 26.3 1.0
CD A:GLU116 3.3 35.9 1.0
CG A:GLU116 3.9 34.7 1.0
O1 A:BHI301 4.0 31.4 0.5
ND1 A:HIS25 4.0 23.3 1.0
ND1 A:HIS69 4.1 28.2 1.0
ND1 A:HIS32 4.1 35.5 1.0
CG A:HIS25 4.1 25.1 1.0
CG A:GLU114 4.1 28.8 1.0
CG A:HIS69 4.2 25.6 1.0
CG A:HIS32 4.2 31.0 1.0
OE1 A:GLU116 4.3 39.9 1.0
O A:HOH507 4.4 30.2 1.0
C12 A:BHI301 4.5 31.0 0.5
C12 A:BHI301 4.7 32.7 0.5
C13 A:BHI301 4.8 37.1 0.5
CG1 A:VAL6 4.9 29.6 1.0
CB A:GLU114 4.9 29.6 1.0

Manganese binding site 2 out of 2 in 1q54

Go back to Manganese Binding Sites List in 1q54
Manganese binding site 2 out of 2 in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp


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 the Bromohydrine of Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:27.2
occ:1.00
 NE2 B:HIS25 2.0 25.5 1.0
NE2 B:HIS32 2.0 32.9 1.0
NE2 B:HIS69 2.0 28.7 1.0
OE2 B:GLU116 2.2 34.3 1.0
OE2 B:GLU114 2.2 30.3 1.0
OE1 B:GLU114 2.5 33.8 1.0
CD B:GLU114 2.7 34.5 1.0
CE1 B:HIS25 2.8 26.5 1.0
CE1 B:HIS32 2.9 33.6 1.0
CE1 B:HIS69 2.9 30.0 1.0
CD2 B:HIS32 3.1 30.5 1.0
CD2 B:HIS69 3.1 28.4 1.0
CD2 B:HIS25 3.1 25.1 1.0
CD B:GLU116 3.3 35.9 1.0
CG B:GLU116 3.8 34.2 1.0
ND1 B:HIS25 4.0 29.1 1.0
ND1 B:HIS32 4.1 36.7 1.0
ND1 B:HIS69 4.1 28.5 1.0
CG B:HIS32 4.2 30.8 1.0
CG B:HIS25 4.2 27.0 1.0
CG B:HIS69 4.2 23.9 1.0
CG B:GLU114 4.2 28.3 1.0
OE1 B:GLU116 4.3 40.7 1.0
C12 B:BHI302 4.5 27.9 0.6
C13 B:BHI302 4.6 31.3 0.6
O B:HOH523 4.6 38.1 1.0
CG1 B:VAL6 4.7 32.0 1.0
O1 B:BHI302 4.9 27.7 0.6
CB B:GLU114 5.0 29.1 1.0

Reference:

J.Wouters, Y.Oudjama, S.Ghosh, V.Stalon, L.Droogmans, E.Oldfield. Structure and Mechanism of Action of Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase. J.Am.Chem.Soc. V. 125 3198 2003.
ISSN: ISSN 0002-7863
PubMed: 12630859
DOI: 10.1021/JA029171P
Page generated: Sat Oct 5 12:09:15 2024

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