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Magnesium in PDB 1die: Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase

Enzymatic activity of Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase

All present enzymatic activity of Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase:
5.3.1.5;

Protein crystallography data

The structure of Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase, PDB code: 1die was solved by C.A.Collyer, H.Viehmann, J.D.Goldberg, D.M.Blow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.600, 105.600, 153.400, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase (pdb code 1die). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase, PDB code: 1die:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1die

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Magnesium binding site 1 out of 4 in the Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg398

b:14.9
occ:1.00
 O A:HOH671 1.9 26.5 1.0
OE2 A:GLU216 1.9 21.0 1.0
OD2 A:ASP254 2.0 22.4 1.0
OD1 A:ASP256 2.2 20.9 1.0
OD1 A:ASP254 2.5 20.9 1.0
CG A:ASP254 2.7 19.6 1.0
CD A:GLU216 3.0 20.8 1.0
NE2 A:HIS219 3.0 9.8 1.0
CG A:ASP256 3.1 21.7 1.0
OE1 A:GLU216 3.3 25.3 1.0
OD2 A:ASP256 3.4 25.2 1.0
CD2 A:HIS219 3.4 8.7 1.0
ND2 A:ASN246 3.6 16.7 1.0
O A:HOH482 3.9 41.3 1.0
O3 A:NOJ400 4.0 43.8 1.0
O A:HOH512 4.1 16.1 1.0
CE1 A:HIS219 4.1 8.8 1.0
CB A:ASP254 4.2 16.6 1.0
CG A:GLU216 4.3 16.6 1.0
OD2 A:ASP292 4.5 20.6 1.0
O A:HOH687 4.6 39.2 1.0
CB A:ASP256 4.6 17.3 1.0
CG A:HIS219 4.6 9.9 1.0
O A:ASP292 4.8 19.1 1.0
CG A:ASN246 4.9 13.1 1.0
MG A:MG399 4.9 22.4 1.0
ND1 A:HIS219 5.0 9.9 1.0

Magnesium binding site 2 out of 4 in 1die

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Magnesium binding site 2 out of 4 in the Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg399

b:22.4
occ:1.00
 OD2 A:ASP292 2.0 20.6 1.0
OD2 A:ASP244 2.0 21.0 1.0
O4 A:NOJ400 2.1 45.0 1.0
OE1 A:GLU216 2.1 25.3 1.0
OE2 A:GLU180 2.4 26.3 1.0
O3 A:NOJ400 2.5 43.8 1.0
C3 A:NOJ400 2.8 44.7 1.0
C4 A:NOJ400 2.9 44.3 1.0
CD A:GLU180 3.0 25.4 1.0
OE1 A:GLU180 3.1 26.7 1.0
CG A:ASP292 3.2 19.9 1.0
CG A:ASP244 3.3 20.9 1.0
CD A:GLU216 3.3 20.8 1.0
O A:HOH514 3.5 24.6 1.0
CB A:ASP292 3.8 20.4 1.0
O A:HOH671 4.0 26.5 1.0
CB A:ASP244 4.1 18.4 1.0
OD1 A:ASP244 4.1 21.8 1.0
CG A:GLU216 4.1 16.6 1.0
C5 A:NOJ400 4.2 44.2 1.0
OD1 A:ASP292 4.2 19.2 1.0
OE2 A:GLU216 4.2 21.0 1.0
CE1 A:HIS219 4.3 8.8 1.0
C2 A:NOJ400 4.3 44.9 1.0
CB A:GLU216 4.4 14.0 1.0
CG A:GLU180 4.4 22.1 1.0
ND2 A:ASN214 4.7 11.2 1.0
NE2 A:HIS219 4.7 9.8 1.0
MG A:MG398 4.9 14.9 1.0
C6 A:NOJ400 5.0 43.9 1.0
O2 A:NOJ400 5.0 46.4 1.0

Magnesium binding site 3 out of 4 in 1die

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Magnesium binding site 3 out of 4 in the Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg398

b:18.6
occ:1.00
 O B:HOH688 1.9 26.7 1.0
OE2 B:GLU216 2.0 23.1 1.0
OD2 B:ASP254 2.3 25.5 1.0
OD1 B:ASP256 2.3 17.4 1.0
OD1 B:ASP254 2.6 21.6 1.0
CG B:ASP254 2.8 22.1 1.0
NE2 B:HIS219 3.0 6.5 1.0
CD B:GLU216 3.1 21.5 1.0
CG B:ASP256 3.3 17.9 1.0
OE1 B:GLU216 3.3 21.9 1.0
CD2 B:HIS219 3.4 3.8 1.0
OD2 B:ASP256 3.6 21.0 1.0
ND2 B:ASN246 3.7 15.1 1.0
O B:HOH686 3.7 42.4 1.0
O3 B:NOJ400 4.1 41.2 1.0
CE1 B:HIS219 4.1 6.6 1.0
CG B:GLU216 4.3 17.2 1.0
O B:HOH673 4.3 22.9 1.0
CB B:ASP254 4.3 19.2 1.0
OD2 B:ASP292 4.5 25.3 1.0
CG B:HIS219 4.6 5.3 1.0
CB B:ASP256 4.6 15.4 1.0
O B:ASP292 4.7 20.0 1.0
C3 B:NOJ400 4.9 42.4 1.0
O2 B:NOJ400 4.9 44.6 1.0
MG B:MG399 4.9 17.4 1.0
ND1 B:HIS219 4.9 6.2 1.0
CA B:ASP256 4.9 14.7 1.0
CG B:ASN246 5.0 14.0 1.0
CG B:ASP292 5.0 22.7 1.0

Magnesium binding site 4 out of 4 in 1die

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Magnesium binding site 4 out of 4 in the Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Observations of Reaction Intermediates and the Mechanism of Aldose- Ketose Interconversion By D-Xylose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg399

b:17.4
occ:1.00
 O4 B:NOJ400 1.9 43.4 1.0
OE1 B:GLU216 2.0 21.9 1.0
OD2 B:ASP244 2.2 21.3 1.0
OD2 B:ASP292 2.2 25.3 1.0
OE2 B:GLU180 2.3 20.8 1.0
O3 B:NOJ400 2.7 41.2 1.0
C4 B:NOJ400 2.9 43.0 1.0
C3 B:NOJ400 2.9 42.4 1.0
CD B:GLU180 3.1 19.1 1.0
CG B:ASP292 3.2 22.7 1.0
CD B:GLU216 3.2 21.5 1.0
CG B:ASP244 3.3 17.7 1.0
OE1 B:GLU180 3.4 21.2 1.0
CB B:ASP292 3.5 21.8 1.0
CB B:ASP244 3.7 15.6 1.0
O B:HOH685 3.9 33.6 1.0
O B:HOH688 4.1 26.7 1.0
CG B:GLU216 4.1 17.2 1.0
OE2 B:GLU216 4.1 23.1 1.0
C5 B:NOJ400 4.1 43.7 1.0
CB B:GLU216 4.2 15.0 1.0
CE1 B:HIS219 4.2 6.6 1.0
OD1 B:ASP292 4.3 21.8 1.0
CG B:GLU180 4.3 17.7 1.0
OD1 B:ASP244 4.3 17.3 1.0
C2 B:NOJ400 4.4 43.4 1.0
NE2 B:HIS219 4.6 6.5 1.0
ND2 B:ASN214 4.7 16.7 1.0
C6 B:NOJ400 4.9 44.0 1.0
MG B:MG398 4.9 18.6 1.0
ND1 B:HIS219 5.0 6.2 1.0

Reference:

C.A.Collyer, D.M.Blow. Observations of Reaction Intermediates and the Mechanism of Aldose-Ketose Interconversion By D-Xylose Isomerase. Proc.Natl.Acad.Sci.Usa V. 87 1362 1990.
ISSN: ISSN 0027-8424
PubMed: 2304904
DOI: 10.1073/PNAS.87.4.1362
Page generated: Tue Aug 13 02:39:54 2024

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