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Manganese in PDB 1xli: Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift

Enzymatic activity of Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift

All present enzymatic activity of Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift:
5.3.1.5;

Protein crystallography data

The structure of Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift, PDB code: 1xli was solved by C.A.Collyer, K.Henrick, 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 (°) 105.800, 105.800, 153.200, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Manganese Binding Sites:

The binding sites of Manganese atom in the Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift (pdb code 1xli). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift, PDB code: 1xli:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1xli

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Manganese binding site 1 out of 4 in the Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn398

b:12.1
occ:1.00
 OD2 A:ASP254 2.2 11.9 1.0
OE2 A:GLU216 2.2 13.6 1.0
OD1 A:ASP256 2.2 12.5 1.0
O A:HOH908A 2.3 10.8 1.0
OD1 A:ASP254 2.5 11.7 1.0
NE2 A:HIS219 2.5 9.0 1.0
CG A:ASP254 2.6 10.2 1.0
OE1 A:GLU216 2.9 18.7 1.0
CD A:GLU216 2.9 14.7 1.0
CD2 A:HIS219 3.0 7.9 1.0
CG A:ASP256 3.2 11.6 1.0
OD2 A:ASP256 3.3 12.8 1.0
CE1 A:HIS219 3.5 8.4 1.0
O3 A:GLT400 3.8 23.0 1.0
ND2 A:ASN246 3.9 11.8 1.0
O A:HOH911A 4.0 22.9 1.0
O A:HOH501A 4.0 10.0 1.0
CB A:ASP254 4.1 9.8 1.0
CG A:HIS219 4.2 8.8 1.0
OD2 A:ASP292 4.3 12.7 1.0
CG A:GLU216 4.4 13.2 1.0
ND1 A:HIS219 4.4 8.2 1.0
O A:HOH570A 4.5 23.6 1.0
CB A:ASP256 4.6 9.5 1.0
MN A:MN399 4.6 13.4 1.0
CE A:LYS182 4.9 4.2 1.0
N A:ASP256 4.9 7.8 1.0
CA A:ASP256 5.0 8.2 1.0
CG A:ASP292 5.0 11.8 1.0

Manganese binding site 2 out of 4 in 1xli

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Manganese binding site 2 out of 4 in the Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn399

b:13.4
occ:1.00
 O4 A:GLT400 1.9 24.3 1.0
OD2 A:ASP292 2.0 12.7 1.0
OD2 A:ASP244 2.0 15.3 1.0
OE1 A:GLU216 2.2 18.7 1.0
OE2 A:GLU180 2.4 15.3 1.0
O3 A:GLT400 2.5 23.0 1.0
C4 A:GLT400 3.0 25.0 1.0
CG A:ASP292 3.1 11.8 1.0
CD A:GLU180 3.2 13.5 1.0
CG A:ASP244 3.2 16.6 1.0
OE1 A:GLU180 3.3 16.5 1.0
CD A:GLU216 3.3 14.7 1.0
C3 A:GLT400 3.3 24.6 1.0
CB A:ASP292 3.6 11.7 1.0
O A:HOH908A 3.8 10.8 1.0
CG A:GLU216 3.8 13.2 1.0
CB A:ASP244 3.9 15.0 1.0
O A:HOH912A 4.0 19.6 1.0
CE1 A:HIS219 4.0 8.4 1.0
CB A:GLU216 4.1 11.1 1.0
OD1 A:ASP292 4.1 10.6 1.0
OD1 A:ASP244 4.2 17.2 1.0
C5 A:GLT400 4.2 26.6 1.0
OE2 A:GLU216 4.3 13.6 1.0
CG A:GLU180 4.6 11.1 1.0
NE2 A:HIS219 4.6 9.0 1.0
MN A:MN398 4.6 12.1 1.0
ND1 A:HIS219 4.7 8.2 1.0
C6 A:GLT400 4.7 28.2 1.0
C2 A:GLT400 4.7 25.6 1.0
ND2 A:ASN214 4.8 8.5 1.0

Manganese binding site 3 out of 4 in 1xli

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Manganese binding site 3 out of 4 in the Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn398

b:12.6
occ:1.00
 OE2 B:GLU216 2.1 6.6 1.0
OD1 B:ASP256 2.2 8.2 1.0
OD2 B:ASP254 2.3 12.5 1.0
OD1 B:ASP254 2.4 9.4 1.0
O B:HOH916B 2.4 21.4 1.0
NE2 B:HIS219 2.6 9.4 1.0
CG B:ASP254 2.6 9.6 1.0
CD B:GLU216 3.0 6.6 1.0
CG B:ASP256 3.1 7.9 1.0
CD2 B:HIS219 3.1 7.8 1.0
OE1 B:GLU216 3.2 7.5 1.0
OD2 B:ASP256 3.3 8.7 1.0
CE1 B:HIS219 3.6 10.2 1.0
O3 B:GLT400 3.8 25.6 1.0
O B:HOH917B 3.9 26.6 1.0
ND2 B:ASN246 4.0 7.5 1.0
CB B:ASP254 4.1 8.4 1.0
CG B:GLU216 4.2 5.6 1.0
OD2 B:ASP292 4.3 12.8 1.0
O B:HOH763B 4.3 6.7 1.0
CG B:HIS219 4.3 8.0 1.0
CB B:ASP256 4.5 7.4 1.0
O B:HOH918B 4.5 28.2 1.0
ND1 B:HIS219 4.5 8.9 1.0
MN B:MN399 4.6 12.4 1.0
CE B:LYS182 4.9 8.1 1.0
C3 B:GLT400 5.0 28.5 1.0
O2 B:GLT400 5.0 28.7 1.0
CA B:ASP256 5.0 7.8 1.0

Manganese binding site 4 out of 4 in 1xli

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Manganese binding site 4 out of 4 in the Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn399

b:12.4
occ:1.00
 OE1 B:GLU216 2.0 7.5 1.0
OD2 B:ASP244 2.0 13.6 1.0
OD2 B:ASP292 2.1 12.8 1.0
O4 B:GLT400 2.1 30.1 1.0
OE2 B:GLU180 2.3 15.4 1.0
O3 B:GLT400 2.6 25.6 1.0
CG B:ASP292 3.0 12.9 1.0
C4 B:GLT400 3.0 28.8 1.0
CD B:GLU180 3.0 13.1 1.0
OE1 B:GLU180 3.1 13.6 1.0
CD B:GLU216 3.2 6.6 1.0
C3 B:GLT400 3.2 28.5 1.0
CG B:ASP244 3.2 13.1 1.0
CB B:ASP292 3.6 13.3 1.0
CB B:ASP244 3.9 12.9 1.0
O B:HOH916B 3.9 21.4 1.0
O B:HOH915B 4.0 18.3 1.0
CE1 B:HIS219 4.1 10.2 1.0
CB B:GLU216 4.1 6.9 1.0
CG B:GLU216 4.1 5.6 1.0
OD1 B:ASP292 4.1 13.8 1.0
OE2 B:GLU216 4.1 6.6 1.0
OD1 B:ASP244 4.2 12.7 1.0
C5 B:GLT400 4.3 29.5 1.0
CG B:GLU180 4.4 10.5 1.0
NE2 B:HIS219 4.6 9.4 1.0
MN B:MN398 4.6 12.6 1.0
C2 B:GLT400 4.7 28.9 1.0
ND1 B:HIS219 4.8 8.9 1.0
C6 B:GLT400 4.8 30.7 1.0
ND2 B:ASN214 4.9 6.9 1.0

Reference:

C.A.Collyer, K.Henrick, D.M.Blow. Mechanism For Aldose-Ketose Interconversion By D-Xylose Isomerase Involving Ring Opening Followed By A 1,2-Hydride Shift. J.Mol.Biol. V. 212 211 1990.
ISSN: ISSN 0022-2836
PubMed: 2319597
DOI: 10.1016/0022-2836(90)90316-E
Page generated: Sat Oct 5 13:07:22 2024

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