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
Go back to
Zinc Binding Sites List in 1xll
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
Go back to
Zinc Binding Sites List in 1xll
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
Go back to
Zinc Binding Sites List in 1xll
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
Go back to
Zinc Binding Sites List in 1xll
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
|