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Manganese in PDB 1pvf: E.Coli Ipp Isomerase in Complex with Diphosphate

Enzymatic activity of E.Coli Ipp Isomerase in Complex with Diphosphate

All present enzymatic activity of E.Coli Ipp Isomerase in Complex with Diphosphate:
5.3.3.2;

Protein crystallography data

The structure of E.Coli Ipp Isomerase in Complex with Diphosphate, PDB code: 1pvf was solved by J.Wouters, V.Durisotti, Y.Oudjama, V.Stalon, L.Droogmans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.090, 71.880, 91.730, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.6

Other elements in 1pvf:

The structure of E.Coli Ipp Isomerase in Complex with Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the E.Coli Ipp Isomerase in Complex with Diphosphate (pdb code 1pvf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the E.Coli Ipp Isomerase in Complex with Diphosphate, PDB code: 1pvf:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 1pvf

Go back to Manganese Binding Sites List in 1pvf
Manganese binding site 1 out of 2 in the E.Coli Ipp Isomerase in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of E.Coli Ipp Isomerase in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:13.8
occ:1.00
OE2 A:GLU116 1.9 19.2 1.0
NE2 A:HIS32 2.1 14.5 1.0
NE2 A:HIS25 2.1 17.3 1.0
NE2 A:HIS69 2.1 21.2 1.0
OE2 A:GLU114 2.2 19.5 1.0
OE1 A:GLU114 2.3 17.6 1.0
CD A:GLU114 2.6 21.2 1.0
CE1 A:HIS32 2.9 22.9 1.0
CD A:GLU116 3.0 20.9 1.0
CD2 A:HIS25 3.0 18.2 1.0
CE1 A:HIS69 3.1 16.4 1.0
CD2 A:HIS69 3.1 19.6 1.0
CE1 A:HIS25 3.1 13.5 1.0
CD2 A:HIS32 3.3 26.7 1.0
CG A:GLU116 3.6 21.3 1.0
OE1 A:GLU116 4.0 22.3 1.0
CG A:GLU114 4.1 20.7 1.0
ND1 A:HIS32 4.1 23.4 1.0
ND1 A:HIS69 4.2 16.1 1.0
CG A:HIS25 4.2 16.2 1.0
ND1 A:HIS25 4.2 17.5 1.0
CG A:HIS69 4.3 18.0 1.0
CG A:HIS32 4.3 19.6 1.0
O A:HOH1503 4.3 18.4 1.0
CB A:GLU114 4.9 20.6 1.0
CG1 A:VAL6 4.9 15.4 1.0
O A:HOH1511 4.9 46.7 1.0
CB A:ALA34 4.9 16.5 1.0

Manganese binding site 2 out of 2 in 1pvf

Go back to Manganese Binding Sites List in 1pvf
Manganese binding site 2 out of 2 in the E.Coli Ipp Isomerase in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of E.Coli Ipp Isomerase in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:18.4
occ:1.00
NE2 B:HIS25 2.0 31.6 1.0
OE2 B:GLU116 2.1 27.3 1.0
NE2 B:HIS32 2.1 28.9 1.0
NE2 B:HIS69 2.2 22.6 1.0
OE2 B:GLU114 2.3 26.9 1.0
OE1 B:GLU114 2.4 22.9 1.0
CD B:GLU114 2.7 31.9 1.0
CE1 B:HIS25 2.9 33.0 1.0
CD2 B:HIS69 3.1 21.8 1.0
CE1 B:HIS32 3.1 33.9 1.0
CD2 B:HIS25 3.1 23.5 1.0
CD2 B:HIS32 3.1 34.0 1.0
CD B:GLU116 3.2 33.5 1.0
CE1 B:HIS69 3.2 19.3 1.0
CG B:GLU116 3.7 28.7 1.0
ND1 B:HIS25 4.1 29.2 1.0
CG B:HIS25 4.2 25.4 1.0
ND1 B:HIS32 4.2 32.0 1.0
CG B:GLU114 4.2 32.7 1.0
OE1 B:GLU116 4.2 37.6 1.0
CG B:HIS69 4.3 17.9 1.0
CG B:HIS32 4.3 28.9 1.0
ND1 B:HIS69 4.3 18.9 1.0
O B:HOH1505 4.4 39.0 1.0
CB B:ALA34 4.9 13.6 1.0
CG1 B:VAL6 4.9 24.7 1.0

Reference:

J.Wouters, V.Durisotti, Y.Oudjama, V.Stalon, L.Droogmans. E.Coli Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase in Complex with Diphosphate To Be Published.
Page generated: Tue Dec 15 03:54:27 2020

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