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Zinc in PDB 1xll: 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: 1xll 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, 154.100, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 1xll

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Zinc 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 Zinc with other atoms in the Zn 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:Zn398

b:14.8
occ:1.00
 OE2 A:GLU216 2.0 6.9 1.0
O A:HOH503A 2.0 15.7 1.0
OD2 A:ASP254 2.2 14.6 1.0
OD1 A:ASP256 2.3 16.6 1.0
NE2 A:HIS219 2.3 10.6 1.0
O A:HOH633A 2.5 64.1 1.0
OD1 A:ASP254 2.5 13.6 1.0
CG A:ASP254 2.7 11.3 1.0
CD2 A:HIS219 2.9 7.6 1.0
OD2 A:ASP256 3.0 18.1 1.0
CG A:ASP256 3.1 15.0 1.0
CD A:GLU216 3.1 11.3 1.0
CE1 A:HIS219 3.5 8.9 1.0
OE1 A:GLU216 3.7 13.3 1.0
O A:HOH473A 4.0 22.4 1.0
ND2 A:ASN246 4.0 12.0 1.0
CG A:HIS219 4.1 7.4 1.0
CB A:ASP254 4.2 10.9 1.0
CG A:GLU216 4.3 9.1 1.0
ND1 A:HIS219 4.3 8.4 1.0
O A:HOH502A 4.4 14.8 1.0
O A:HOH575A 4.4 30.6 1.0
CB A:ASP256 4.5 12.2 1.0
O A:HOH646B 4.7 34.2 1.0
OD2 A:ASP292 4.8 12.7 1.0
CE A:LYS182 4.8 6.8 1.0
NZ A:LYS182 4.8 6.3 1.0
ZN A:ZN399 4.9 18.9 1.0

Zinc binding site 2 out of 4 in 1xll

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Zinc 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 Zinc with other atoms in the Zn 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:Zn399

b:18.9
occ:1.00
 OE1 A:GLU216 1.6 13.3 1.0
OD2 A:ASP244 1.8 13.2 1.0
OD2 A:ASP292 2.0 12.7 1.0
OE2 A:GLU180 2.2 14.9 1.0
CD A:GLU216 2.9 11.3 1.0
CD A:GLU180 2.9 14.6 1.0
OE1 A:GLU180 3.0 15.5 1.0
CG A:ASP292 3.0 15.6 1.0
CG A:ASP244 3.0 13.5 1.0
CB A:ASP292 3.6 15.9 1.0
CB A:ASP244 3.6 11.8 1.0
CB A:GLU216 3.7 8.1 1.0
O A:HOH503A 3.7 15.7 1.0
CG A:GLU216 3.7 9.1 1.0
OE2 A:GLU216 3.8 6.9 1.0
O A:HOH505A 3.8 25.8 1.0
OD1 A:ASP244 4.0 15.1 1.0
CE1 A:HIS219 4.1 8.9 1.0
OD1 A:ASP292 4.1 15.3 1.0
CG A:GLU180 4.2 13.2 1.0
O A:HOH655B 4.2 16.1 1.0
O A:HOH646B 4.3 34.2 1.0
ND2 A:ASN214 4.6 13.4 1.0
NE2 A:HIS219 4.6 10.6 1.0
ND1 A:HIS219 4.6 8.4 1.0
ZN A:ZN398 4.9 14.8 1.0
CA A:GLU216 5.0 10.0 1.0

Zinc binding site 3 out of 4 in 1xll

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Zinc 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 Zinc with other atoms in the Zn 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:Zn398

b:18.8
occ:1.00
 OD1 B:ASP254 2.1 18.0 1.0
O B:HOH508B 2.1 14.4 1.0
OD1 B:ASP256 2.1 13.9 1.0
OE2 B:GLU216 2.2 13.7 1.0
OD2 B:ASP254 2.3 19.9 1.0
NE2 B:HIS219 2.5 7.2 1.0
CG B:ASP254 2.6 16.3 1.0
CG B:ASP256 3.1 13.5 1.0
CD2 B:HIS219 3.1 7.6 1.0
CD B:GLU216 3.2 14.2 1.0
OD2 B:ASP256 3.2 19.1 1.0
OE1 B:GLU216 3.5 14.1 1.0
CE1 B:HIS219 3.5 9.3 1.0
O B:HOH478B 3.6 28.7 1.0
CB B:ASP254 4.0 12.7 1.0
ND2 B:ASN246 4.1 10.4 1.0
O B:HOH664A 4.2 34.2 1.0
CG B:HIS219 4.3 8.7 1.0
CG B:GLU216 4.4 8.0 1.0
O B:HOH507B 4.4 12.6 1.0
ND1 B:HIS219 4.5 8.8 1.0
CB B:ASP256 4.5 11.8 1.0
NZ B:LYS182 4.8 10.2 1.0
OD2 B:ASP292 4.9 18.0 1.0
CE B:LYS182 4.9 6.7 1.0
ZN B:ZN399 4.9 19.3 1.0

Zinc binding site 4 out of 4 in 1xll

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Zinc 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 Zinc with other atoms in the Zn 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:Zn399

b:19.3
occ:1.00
 OD2 B:ASP244 1.8 19.5 1.0
OE1 B:GLU216 1.8 14.1 1.0
OD2 B:ASP292 2.1 18.0 1.0
OE2 B:GLU180 2.2 16.9 1.0
CD B:GLU180 2.9 16.1 1.0
CD B:GLU216 3.0 14.2 1.0
CG B:ASP292 3.0 16.6 1.0
CG B:ASP244 3.0 17.5 1.0
OE1 B:GLU180 3.1 17.8 1.0
CB B:ASP292 3.5 14.8 1.0
O B:HOH474B 3.6 41.0 1.0
O B:HOH510B 3.7 36.4 1.0
CB B:ASP244 3.7 14.2 1.0
CG B:GLU216 3.8 8.0 1.0
CB B:GLU216 3.9 9.9 1.0
O B:HOH508B 4.0 14.4 1.0
OD1 B:ASP244 4.0 18.9 1.0
OE2 B:GLU216 4.1 13.7 1.0
OD1 B:ASP292 4.1 15.1 1.0
CG B:GLU180 4.2 15.4 1.0
CE1 B:HIS219 4.2 9.3 1.0
O B:HOH414B 4.4 29.7 1.0
ND2 B:ASN214 4.6 13.3 1.0
NE2 B:HIS219 4.8 7.2 1.0
ND1 B:HIS219 4.9 8.8 1.0
CA B:ASP292 4.9 15.1 1.0
ZN B:ZN398 4.9 18.8 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: Wed Oct 16 20:28:56 2024

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