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Manganese in PDB 1did: 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: 1did was solved by C.A.Collyer, 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 (°) 106.100, 106.100, 153.300, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 1did

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Manganese 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 Manganese with other atoms in the Mn 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:Mn398

b:12.9
occ:1.00
 OE2 A:GLU216 2.1 12.9 1.0
O A:HOH498 2.1 18.6 1.0
OD1 A:ASP256 2.2 13.1 1.0
OD2 A:ASP254 2.2 14.4 1.0
OD1 A:ASP254 2.4 14.6 1.0
NE2 A:HIS219 2.6 9.1 1.0
CG A:ASP254 2.7 13.4 1.0
CD A:GLU216 3.0 13.5 1.0
CG A:ASP256 3.1 12.3 1.0
CD2 A:HIS219 3.2 8.1 1.0
OE1 A:GLU216 3.3 15.2 1.0
OD2 A:ASP256 3.4 12.6 1.0
CE1 A:HIS219 3.6 9.4 1.0
O A:HOH651 3.9 23.2 1.0
ND2 A:ASN246 4.0 13.7 1.0
O A:HOH653 4.1 33.7 1.0
CB A:ASP254 4.1 12.9 1.0
O A:HOH496 4.2 13.1 1.0
O6 A:DIG400 4.3 22.0 1.0
CG A:HIS219 4.3 9.2 1.0
CG A:GLU216 4.4 10.9 1.0
O A:HOH654 4.4 38.3 1.0
CB A:ASP256 4.5 11.6 1.0
ND1 A:HIS219 4.5 9.7 1.0
OD2 A:ASP292 4.7 13.7 1.0
CE A:LYS182 4.8 9.8 1.0
NZ A:LYS182 4.8 9.3 1.0
CA A:ASP256 5.0 10.7 1.0

Manganese binding site 2 out of 4 in 1did

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Manganese 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 Manganese with other atoms in the Mn 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:Mn399

b:12.2
occ:1.00
 OD2 A:ASP292 2.0 13.7 1.0
OD2 A:ASP244 2.1 16.1 1.0
OE1 A:GLU180 2.2 15.5 1.0
OE1 A:GLU216 2.3 15.2 1.0
O6 A:DIG400 2.3 22.0 1.0
N5 A:DIG400 2.5 24.1 1.0
CD A:GLU180 3.1 16.0 1.0
CG A:ASP292 3.1 11.7 1.0
C6 A:DIG400 3.2 23.8 1.0
CG A:ASP244 3.3 16.7 1.0
OE2 A:GLU180 3.3 16.9 1.0
CD A:GLU216 3.4 13.5 1.0
C5 A:DIG400 3.4 23.9 1.0
C2 A:DIG400 3.6 24.0 1.0
CB A:ASP292 3.7 12.5 1.0
C1 A:DIG400 3.8 23.2 1.0
O A:HOH498 3.8 18.6 1.0
O1 A:DIG400 3.9 21.2 1.0
CB A:ASP244 3.9 16.0 1.0
O3 A:DIG400 4.1 24.8 1.0
CG A:GLU216 4.1 10.9 1.0
OD1 A:ASP292 4.1 10.9 1.0
C3 A:DIG400 4.2 24.4 1.0
C4 A:DIG400 4.2 24.5 1.0
OD1 A:ASP244 4.2 18.9 1.0
OE2 A:GLU216 4.2 12.9 1.0
CB A:GLU216 4.4 11.2 1.0
CG A:GLU180 4.4 14.3 1.0
CE1 A:HIS219 4.5 9.4 1.0
ND2 A:ASN214 4.6 17.8 1.0

Manganese binding site 3 out of 4 in 1did

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Manganese 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 Manganese with other atoms in the Mn 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:Mn398

b:14.1
occ:1.00
 OE2 B:GLU216 2.1 12.3 1.0
OD1 B:ASP256 2.2 14.5 1.0
OD2 B:ASP254 2.3 13.0 1.0
O B:HOH519 2.3 14.0 1.0
OD1 B:ASP254 2.4 14.3 1.0
NE2 B:HIS219 2.5 8.3 1.0
CG B:ASP254 2.6 12.5 1.0
CG B:ASP256 3.1 13.9 1.0
CD2 B:HIS219 3.2 7.4 1.0
CD B:GLU216 3.2 12.4 1.0
OD2 B:ASP256 3.2 16.8 1.0
CE1 B:HIS219 3.6 9.2 1.0
OE1 B:GLU216 3.7 15.6 1.0
O B:HOH645 3.9 24.2 1.0
ND2 B:ASN246 4.1 9.8 1.0
CB B:ASP254 4.1 11.9 1.0
CG B:GLU216 4.3 11.3 1.0
O B:HOH517 4.3 5.3 1.0
CG B:HIS219 4.4 8.9 1.0
O6 B:DIG400 4.5 20.3 1.0
CB B:ASP256 4.5 12.9 1.0
O B:HOH647 4.6 36.1 1.0
ND1 B:HIS219 4.6 9.5 1.0
NZ B:LYS182 4.6 11.5 1.0
OD2 B:ASP292 4.6 15.6 1.0
CE B:LYS182 4.7 10.6 1.0

Manganese binding site 4 out of 4 in 1did

Go back to Manganese Binding Sites List in 1did
Manganese 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 Manganese with other atoms in the Mn 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:Mn399

b:13.5
occ:1.00
 OD2 B:ASP292 2.0 15.6 1.0
OD2 B:ASP244 2.1 15.6 1.0
OE1 B:GLU180 2.1 15.9 1.0
OE1 B:GLU216 2.1 15.6 1.0
O6 B:DIG400 2.5 20.3 1.0
N5 B:DIG400 2.6 24.2 1.0
C6 B:DIG400 3.0 23.7 1.0
CD B:GLU180 3.0 16.9 1.0
CG B:ASP292 3.2 14.2 1.0
C5 B:DIG400 3.2 24.0 1.0
CG B:ASP244 3.3 15.2 1.0
CD B:GLU216 3.3 12.4 1.0
OE2 B:GLU180 3.3 16.4 1.0
C2 B:DIG400 3.6 24.4 1.0
C1 B:DIG400 3.6 25.2 1.0
CB B:ASP292 3.8 15.1 1.0
O B:HOH519 3.9 14.0 1.0
CB B:ASP244 4.0 15.6 1.0
O1 B:DIG400 4.0 26.5 1.0
C4 B:DIG400 4.0 24.8 1.0
OE2 B:GLU216 4.1 12.3 1.0
OD1 B:ASP292 4.1 12.2 1.0
O3 B:DIG400 4.1 26.6 1.0
C3 B:DIG400 4.1 25.1 1.0
OD1 B:ASP244 4.2 14.8 1.0
CG B:GLU216 4.3 11.3 1.0
CG B:GLU180 4.3 14.1 1.0
CB B:GLU216 4.3 10.1 1.0
CE1 B:HIS219 4.6 9.2 1.0
ND2 B:ASN214 4.6 13.2 1.0
NE2 B:HIS219 5.0 8.3 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: Sat Oct 5 10:07:03 2024

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