Atomistry » Manganese » PDB 1n0n-1o99 » 1nfs
Atomistry »
  Manganese »
    PDB 1n0n-1o99 »
      1nfs »

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: Sat Oct 5 11:50:53 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy