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Manganese in PDB 1xlf: 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: 1xlf 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 (°) 106.000, 106.000, 153.800, 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 1xlf). 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: 1xlf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1xlf

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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:32.4
occ:1.00
 OE2 A:GLU216 2.1 13.9 1.0
OD2 A:ASP254 2.3 19.8 1.0
O A:HOH1043A 2.4 18.6 1.0
OD1 A:ASP256 2.5 16.1 1.0
NE2 A:HIS219 2.6 8.3 1.0
OD1 A:ASP254 2.6 16.8 1.0
CG A:ASP254 2.8 14.7 1.0
CD A:GLU216 3.0 15.5 1.0
CD2 A:HIS219 3.0 6.8 1.0
OE1 A:GLU216 3.1 18.9 1.0
CG A:ASP256 3.5 15.9 1.0
OD2 A:ASP256 3.7 17.8 1.0
O A:HOH1005A 3.7 25.9 1.0
CE1 A:HIS219 3.8 8.1 1.0
ND2 A:ASN246 3.9 11.6 1.0
O4 A:GCO400 4.2 23.3 1.0
CG A:HIS219 4.2 8.1 1.0
CB A:ASP254 4.2 11.9 1.0
CG A:GLU216 4.2 13.7 1.0
OD2 A:ASP292 4.6 17.0 1.0
O A:HOH645A 4.6 18.6 1.0
ND1 A:HIS219 4.6 8.4 1.0
MN A:MN399 4.7 19.8 1.0
O A:HOH1044A 4.8 31.7 1.0
CE A:LYS182 4.9 4.8 1.0
CB A:ASP256 4.9 14.5 1.0
NZ A:LYS182 5.0 2.1 1.0

Manganese binding site 2 out of 4 in 1xlf

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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:19.8
occ:1.00
 OE1 A:GLU216 2.0 18.9 1.0
O5 A:GCO400 2.1 27.9 1.0
OD2 A:ASP244 2.1 19.3 1.0
OD2 A:ASP292 2.2 17.0 1.0
OE2 A:GLU180 2.4 16.3 1.0
O4 A:GCO400 2.7 23.3 1.0
CD A:GLU216 3.1 15.5 1.0
CD A:GLU180 3.1 15.2 1.0
OE1 A:GLU180 3.2 15.4 1.0
C5 A:GCO400 3.2 24.7 1.0
CG A:ASP292 3.3 16.7 1.0
CG A:ASP244 3.4 17.9 1.0
C4 A:GCO400 3.5 24.7 1.0
O A:HOH1045A 3.8 25.3 1.0
CB A:ASP292 3.9 15.3 1.0
CG A:GLU216 4.0 13.7 1.0
O3 A:GCO400 4.0 24.1 1.0
O A:HOH1043A 4.0 18.6 1.0
OE2 A:GLU216 4.1 13.9 1.0
CB A:ASP244 4.1 15.3 1.0
CB A:GLU216 4.1 12.3 1.0
CE1 A:HIS219 4.2 8.1 1.0
OD1 A:ASP244 4.3 18.0 1.0
OD1 A:ASP292 4.3 17.7 1.0
C6 A:GCO400 4.4 23.1 1.0
C3 A:GCO400 4.4 25.1 1.0
CG A:GLU180 4.5 12.2 1.0
NE2 A:HIS219 4.5 8.3 1.0
MN A:MN398 4.7 32.4 1.0
ND2 A:ASN214 4.9 9.6 1.0
ND1 A:HIS219 4.9 8.4 1.0

Manganese binding site 3 out of 4 in 1xlf

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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:35.4
occ:1.00
 OE2 B:GLU216 2.4 14.3 1.0
OD1 B:ASP254 2.4 16.5 1.0
O B:HOH1033B 2.5 19.5 1.0
OD2 B:ASP254 2.5 22.5 1.0
OD1 B:ASP256 2.7 19.7 1.0
CG B:ASP254 2.7 17.8 1.0
NE2 B:HIS219 2.8 8.4 1.0
CD B:GLU216 3.1 12.6 1.0
OE1 B:GLU216 3.3 13.9 1.0
CD2 B:HIS219 3.3 6.6 1.0
OD2 B:ASP256 3.3 19.0 1.0
CG B:ASP256 3.4 17.2 1.0
O B:HOH1048B 3.5 12.8 1.0
CE1 B:HIS219 3.8 8.5 1.0
ND2 B:ASN246 4.2 9.6 1.0
CB B:ASP254 4.2 13.3 1.0
O4 B:GCO400 4.3 18.7 1.0
CG B:GLU216 4.4 8.1 1.0
CG B:HIS219 4.5 8.3 1.0
O B:HOH880B 4.6 16.1 1.0
O2 B:GCO400 4.7 29.6 1.0
OD2 B:ASP292 4.7 16.2 1.0
MN B:MN399 4.7 15.8 1.0
ND1 B:HIS219 4.7 8.3 1.0
NZ B:LYS182 4.8 9.6 1.0
CB B:ASP256 4.9 15.2 1.0

Manganese binding site 4 out of 4 in 1xlf

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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:15.8
occ:1.00
 OE1 B:GLU216 2.0 13.9 1.0
OD2 B:ASP292 2.1 16.2 1.0
OD2 B:ASP244 2.3 18.7 1.0
OE2 B:GLU180 2.3 20.4 1.0
O5 B:GCO400 2.5 25.5 1.0
O4 B:GCO400 2.7 18.7 1.0
CD B:GLU180 3.0 17.3 1.0
OE1 B:GLU180 3.1 18.2 1.0
CG B:ASP292 3.2 15.3 1.0
CD B:GLU216 3.2 12.6 1.0
C5 B:GCO400 3.4 22.4 1.0
CG B:ASP244 3.5 16.0 1.0
C4 B:GCO400 3.6 22.6 1.0
CB B:ASP292 3.8 13.5 1.0
O B:HOH1033B 3.8 19.5 1.0
O3 B:GCO400 3.9 25.7 1.0
CB B:ASP244 4.0 13.4 1.0
CG B:GLU216 4.1 8.1 1.0
O B:HOH1035B 4.1 25.6 1.0
CE1 B:HIS219 4.2 8.5 1.0
OD1 B:ASP292 4.2 14.8 1.0
CB B:GLU216 4.2 8.7 1.0
OE2 B:GLU216 4.3 14.3 1.0
C3 B:GCO400 4.3 25.5 1.0
CG B:GLU180 4.4 13.9 1.0
OD1 B:ASP244 4.4 14.9 1.0
C6 B:GCO400 4.5 21.2 1.0
NE2 B:HIS219 4.6 8.4 1.0
MN B:MN398 4.7 35.4 1.0
ND2 B:ASN214 4.8 9.0 1.0
ND1 B:HIS219 4.9 8.3 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 13:06:45 2024

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