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Manganese in PDB 1xld: 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: 1xld 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 (°) 105.600, 105.600, 153.500, 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 1xld). 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: 1xld:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1xld

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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:9.3
occ:1.00
 O A:HOH519A 2.0 8.2 1.0
OE2 A:GLU216 2.1 14.8 1.0
OD1 A:ASP256 2.2 17.4 1.0
OD2 A:ASP254 2.2 16.3 1.0
OD1 A:ASP254 2.4 16.3 1.0
NE2 A:HIS219 2.5 12.5 1.0
CG A:ASP254 2.6 14.4 1.0
CD A:GLU216 2.9 16.0 1.0
OE1 A:GLU216 2.9 17.8 1.0
CD2 A:HIS219 3.0 10.7 1.0
CG A:ASP256 3.2 17.1 1.0
OD2 A:ASP256 3.4 19.0 1.0
CE1 A:HIS219 3.6 13.1 1.0
O2 A:XYL400 3.8 18.2 1.0
ND2 A:ASN246 3.9 15.3 1.0
O1 A:XYL400 4.0 21.2 1.0
CB A:ASP254 4.1 14.0 1.0
CG A:HIS219 4.2 11.9 1.0
O A:HOH517A 4.2 11.5 1.0
CG A:GLU216 4.3 14.0 1.0
ND1 A:HIS219 4.5 13.0 1.0
OD2 A:ASP292 4.5 15.8 1.0
C1 A:XYL400 4.6 20.1 1.0
CB A:ASP256 4.6 14.7 1.0
O A:HOH747B 4.7 34.3 1.0
MN A:MN399 4.7 16.9 1.0
NZ A:LYS182 4.7 8.8 1.0
CE A:LYS182 4.8 8.3 1.0
C2 A:XYL400 4.8 20.7 1.0

Manganese binding site 2 out of 4 in 1xld

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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:16.9
occ:1.00
 OD2 A:ASP244 2.0 19.8 1.0
OD2 A:ASP292 2.1 15.8 1.0
OE1 A:GLU216 2.2 17.8 1.0
OE2 A:GLU180 2.3 18.2 1.0
O2 A:XYL400 2.4 18.2 1.0
O4 A:XYL400 2.4 24.4 1.0
CD A:GLU180 3.1 17.5 1.0
OE1 A:GLU180 3.1 18.1 1.0
CG A:ASP292 3.2 15.9 1.0
CG A:ASP244 3.3 20.2 1.0
CD A:GLU216 3.3 16.0 1.0
C4 A:XYL400 3.6 22.7 1.0
C2 A:XYL400 3.6 20.7 1.0
CB A:ASP292 3.7 15.8 1.0
C3 A:XYL400 3.8 21.7 1.0
O3 A:XYL400 3.9 20.7 1.0
CB A:ASP244 4.0 17.8 1.0
CG A:GLU216 4.0 14.0 1.0
CE1 A:HIS219 4.0 13.1 1.0
O A:HOH521A 4.0 11.3 1.0
CB A:GLU216 4.1 13.6 1.0
O A:HOH519A 4.1 8.2 1.0
OD1 A:ASP244 4.2 22.0 1.0
OD1 A:ASP292 4.3 15.8 1.0
OE2 A:GLU216 4.3 14.8 1.0
CG A:GLU180 4.4 14.5 1.0
NE2 A:HIS219 4.5 12.5 1.0
MN A:MN398 4.7 9.3 1.0
C1 A:XYL400 4.8 20.1 1.0
ND1 A:HIS219 4.8 13.0 1.0
ND2 A:ASN214 4.8 15.8 1.0
C5 A:XYL400 4.8 22.8 1.0

Manganese binding site 3 out of 4 in 1xld

Go back to Manganese Binding Sites List in 1xld
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:10.3
occ:1.00
 O B:HOH519B 2.1 8.1 1.0
OD1 B:ASP256 2.1 16.5 1.0
OE2 B:GLU216 2.2 13.1 1.0
OD2 B:ASP254 2.3 13.9 1.0
OD1 B:ASP254 2.3 15.0 1.0
CG B:ASP254 2.6 13.4 1.0
NE2 B:HIS219 2.6 5.7 1.0
CD B:GLU216 3.1 14.4 1.0
CG B:ASP256 3.1 16.3 1.0
CD2 B:HIS219 3.2 5.9 1.0
OE1 B:GLU216 3.3 14.7 1.0
OD2 B:ASP256 3.4 20.1 1.0
O1 B:XYL400 3.7 21.2 1.0
CE1 B:HIS219 3.8 7.5 1.0
O2 B:XYL400 3.8 20.1 1.0
ND2 B:ASN246 4.1 12.2 1.0
CB B:ASP254 4.1 12.4 1.0
O B:HOH517B 4.3 15.8 1.0
CG B:GLU216 4.4 11.2 1.0
C1 B:XYL400 4.4 20.4 1.0
CG B:HIS219 4.4 7.4 1.0
NZ B:LYS182 4.5 13.1 1.0
CB B:ASP256 4.5 15.2 1.0
OD2 B:ASP292 4.5 18.0 1.0
CE B:LYS182 4.6 12.8 1.0
O B:HOH750B 4.7 38.1 1.0
ND1 B:HIS219 4.7 6.8 1.0
C2 B:XYL400 4.8 20.6 1.0
MN B:MN399 4.8 13.2 1.0

Manganese binding site 4 out of 4 in 1xld

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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:13.2
occ:1.00
 OD2 B:ASP244 2.0 17.7 1.0
OE1 B:GLU216 2.1 14.7 1.0
OD2 B:ASP292 2.1 18.0 1.0
OE2 B:GLU180 2.2 18.5 1.0
O2 B:XYL400 2.3 20.1 1.0
O4 B:XYL400 2.4 20.8 1.0
CD B:GLU180 3.0 17.7 1.0
CG B:ASP292 3.1 17.6 1.0
OE1 B:GLU180 3.1 17.5 1.0
CD B:GLU216 3.2 14.4 1.0
CG B:ASP244 3.2 16.9 1.0
C2 B:XYL400 3.5 20.6 1.0
C4 B:XYL400 3.5 19.7 1.0
CB B:ASP292 3.6 16.2 1.0
C3 B:XYL400 3.8 20.2 1.0
CB B:ASP244 3.8 15.6 1.0
O3 B:XYL400 3.9 21.7 1.0
CG B:GLU216 4.0 11.2 1.0
O B:HOH519B 4.1 8.1 1.0
O B:HOH521B 4.1 23.1 1.0
CB B:GLU216 4.1 11.3 1.0
CE1 B:HIS219 4.1 7.5 1.0
OD1 B:ASP244 4.2 18.3 1.0
OD1 B:ASP292 4.2 17.0 1.0
OE2 B:GLU216 4.2 13.1 1.0
CG B:GLU180 4.3 16.6 1.0
NE2 B:HIS219 4.6 5.7 1.0
C1 B:XYL400 4.6 20.4 1.0
C5 B:XYL400 4.7 19.4 1.0
ND2 B:ASN214 4.8 12.2 1.0
MN B:MN398 4.8 10.3 1.0
ND1 B:HIS219 4.9 6.8 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 13:06:01 2024

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