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Manganese in PDB 1xlk: 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: 1xlk 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, 154.300, 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 1xlk). 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: 1xlk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1xlk

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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:31.1
occ:1.00
 O A:HOH503A 2.0 29.2 1.0
OE2 A:GLU216 2.1 19.1 1.0
OD2 A:ASP254 2.3 24.2 1.0
OD1 A:ASP256 2.5 22.8 1.0
OD1 A:ASP254 2.5 23.1 1.0
NE2 A:HIS219 2.5 14.3 1.0
CG A:ASP254 2.8 20.8 1.0
CD2 A:HIS219 3.0 12.3 1.0
CD A:GLU216 3.1 20.2 1.0
CG A:ASP256 3.3 22.4 1.0
OD2 A:ASP256 3.4 25.0 1.0
OE1 A:GLU216 3.5 23.2 1.0
CE1 A:HIS219 3.6 12.8 1.0
O A:HOH473A 3.8 35.3 1.0
ND2 A:ASN246 4.0 15.2 1.0
CG A:HIS219 4.2 12.6 1.0
CB A:ASP254 4.2 18.6 1.0
OD2 A:ASP292 4.4 23.9 1.0
CG A:GLU216 4.4 17.6 1.0
ND1 A:HIS219 4.4 13.5 1.0
O A:HOH646B 4.5 37.2 1.0
NZ A:LYS182 4.6 10.1 1.0
O A:HOH502A 4.7 23.8 1.0
CB A:ASP256 4.7 18.4 1.0
CE A:LYS182 4.7 10.5 1.0
MN A:MN399 4.8 34.5 1.0
O A:HOH575A 5.0 41.5 1.0

Manganese binding site 2 out of 4 in 1xlk

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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:34.5
occ:1.00
 OD2 A:ASP292 2.0 23.9 1.0
OE1 A:GLU216 2.0 23.2 1.0
OD2 A:ASP244 2.2 27.5 1.0
OE2 A:GLU180 2.4 24.9 1.0
O A:HOH646B 3.0 37.2 1.0
CD A:GLU180 3.1 24.6 1.0
OE1 A:GLU180 3.1 27.1 1.0
CG A:ASP292 3.1 21.8 1.0
CD A:GLU216 3.3 20.2 1.0
CG A:ASP244 3.4 25.2 1.0
O A:HOH503A 3.5 29.2 1.0
O A:HOH505A 3.5 33.8 1.0
CB A:ASP292 3.8 21.1 1.0
OD1 A:ASP292 4.0 23.3 1.0
OE2 A:GLU216 4.1 19.1 1.0
CB A:ASP244 4.1 21.1 1.0
CE1 A:HIS219 4.1 12.8 1.0
CG A:GLU216 4.2 17.6 1.0
CB A:GLU216 4.2 14.7 1.0
OD1 A:ASP244 4.4 26.0 1.0
CG A:GLU180 4.4 20.6 1.0
O A:HOH545A 4.4 50.5 1.0
NE2 A:HIS219 4.6 14.3 1.0
ND2 A:ASN214 4.7 14.5 1.0
ND1 A:HIS219 4.8 13.5 1.0
MN A:MN398 4.8 31.1 1.0

Manganese binding site 3 out of 4 in 1xlk

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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:32.4
occ:1.00
 O B:HOH508B 2.1 35.1 1.0
OE2 B:GLU216 2.3 16.6 1.0
OD1 B:ASP254 2.5 23.3 1.0
OD1 B:ASP256 2.5 26.1 1.0
OD2 B:ASP254 2.6 24.8 1.0
NE2 B:HIS219 2.6 12.3 1.0
CG B:ASP254 2.8 22.1 1.0
CD B:GLU216 3.2 15.8 1.0
CD2 B:HIS219 3.2 11.8 1.0
OE1 B:GLU216 3.4 17.8 1.0
CG B:ASP256 3.5 24.0 1.0
O B:HOH478B 3.6 29.6 1.0
CE1 B:HIS219 3.6 12.7 1.0
OD2 B:ASP256 3.6 27.0 1.0
O B:HOH664A 4.1 39.0 1.0
ND2 B:ASN246 4.2 11.5 1.0
CB B:ASP254 4.3 17.5 1.0
CG B:GLU216 4.4 13.6 1.0
CG B:HIS219 4.4 13.2 1.0
O B:HOH507B 4.5 24.2 1.0
NZ B:LYS182 4.5 14.5 1.0
OD2 B:ASP292 4.6 26.3 1.0
ND1 B:HIS219 4.6 13.6 1.0
MN B:MN399 4.6 31.6 1.0
CE B:LYS182 4.7 13.8 1.0
O B:HOH474B 4.7 34.8 1.0
CB B:ASP256 4.9 19.5 1.0

Manganese binding site 4 out of 4 in 1xlk

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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:31.6
occ:1.00
 OE1 B:GLU216 2.0 17.8 1.0
OD2 B:ASP292 2.1 26.3 1.0
OE2 B:GLU180 2.2 25.7 1.0
OD2 B:ASP244 2.3 30.4 1.0
O B:HOH474B 2.6 34.8 1.0
CD B:GLU180 3.0 24.0 1.0
O B:HOH510B 3.1 42.6 1.0
OE1 B:GLU180 3.1 26.3 1.0
CG B:ASP292 3.2 25.7 1.0
CD B:GLU216 3.2 15.8 1.0
CG B:ASP244 3.5 28.1 1.0
O B:HOH508B 3.6 35.1 1.0
CB B:ASP292 3.7 25.2 1.0
O B:HOH414B 4.0 32.4 1.0
OE2 B:GLU216 4.1 16.6 1.0
CE1 B:HIS219 4.1 12.7 1.0
CG B:GLU216 4.2 13.6 1.0
CB B:ASP244 4.2 24.8 1.0
OD1 B:ASP292 4.2 26.0 1.0
CG B:GLU180 4.3 21.0 1.0
CB B:GLU216 4.4 12.5 1.0
OD1 B:ASP244 4.4 29.4 1.0
O B:HOH641B 4.4 66.0 1.0
MN B:MN398 4.6 32.4 1.0
NE2 B:HIS219 4.6 12.3 1.0
O B:HOH478B 4.8 29.6 1.0
ND2 B:ASN214 4.8 15.8 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 13:07:29 2024

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