Zinc in PDB 3iui: ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Enzymatic activity of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
All present enzymatic activity of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase:
5.3.1.14;
Protein crystallography data
The structure of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3iui
was solved by
H.Yoshida,
M.Yamaji,
T.Ishii,
K.Izumori,
S.Kamitori,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.81 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.692,
104.826,
101.768,
90.00,
102.98,
90.00
|
R / Rfree (%)
|
18.2 /
23
|
Zinc Binding Sites:
The binding sites of Zinc atom in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
(pdb code 3iui). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3iui:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 3iui
Go back to
Zinc Binding Sites List in 3iui
Zinc binding site 1 out
of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:61.8
occ:1.00
|
OE2
|
A:GLU219
|
2.3
|
28.2
|
1.0
|
OD2
|
A:ASP254
|
2.4
|
29.4
|
1.0
|
ND1
|
A:HIS281
|
2.4
|
23.8
|
1.0
|
OD2
|
A:ASP327
|
2.7
|
36.1
|
1.0
|
CD
|
A:GLU219
|
2.9
|
28.7
|
1.0
|
OE1
|
A:GLU219
|
3.0
|
31.8
|
1.0
|
CG
|
A:HIS281
|
3.4
|
25.2
|
1.0
|
CE1
|
A:HIS281
|
3.4
|
28.4
|
1.0
|
CG
|
A:ASP254
|
3.4
|
29.0
|
1.0
|
CG
|
A:ASP327
|
3.4
|
34.2
|
1.0
|
CB
|
A:HIS281
|
3.6
|
24.7
|
1.0
|
CB
|
A:ASP327
|
3.6
|
31.4
|
1.0
|
CB
|
A:ASP254
|
3.7
|
25.4
|
1.0
|
CE1
|
A:HIS257
|
4.1
|
29.3
|
1.0
|
CG
|
A:GLU219
|
4.3
|
26.0
|
1.0
|
OD1
|
A:ASP327
|
4.5
|
34.8
|
1.0
|
NE2
|
A:HIS281
|
4.5
|
26.4
|
1.0
|
CD2
|
A:HIS281
|
4.5
|
25.8
|
1.0
|
OD1
|
A:ASP254
|
4.5
|
30.5
|
1.0
|
NE2
|
A:HIS257
|
4.6
|
30.7
|
1.0
|
ZN
|
A:ZN502
|
4.7
|
46.5
|
0.5
|
CE
|
A:MET325
|
4.8
|
35.9
|
1.0
|
CA
|
A:ASP254
|
4.9
|
25.5
|
1.0
|
ND1
|
A:HIS257
|
4.9
|
28.4
|
1.0
|
|
Zinc binding site 2 out
of 8 in 3iui
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Zinc Binding Sites List in 3iui
Zinc binding site 2 out
of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:46.5
occ:0.50
|
NE2
|
A:HIS257
|
2.3
|
30.7
|
1.0
|
OD2
|
A:ASP289
|
2.4
|
39.2
|
1.0
|
O
|
A:HOH533
|
2.7
|
31.0
|
1.0
|
OD1
|
A:ASP289
|
3.1
|
40.3
|
1.0
|
CG
|
A:ASP289
|
3.1
|
38.9
|
1.0
|
OD1
|
A:ASP291
|
3.2
|
32.2
|
1.0
|
CE1
|
A:HIS257
|
3.2
|
29.3
|
1.0
|
CD2
|
A:HIS257
|
3.3
|
28.4
|
1.0
|
OD2
|
A:ASP291
|
3.6
|
31.9
|
1.0
|
CG
|
A:ASP291
|
3.8
|
30.8
|
1.0
|
OD2
|
A:ASP254
|
3.9
|
29.4
|
1.0
|
NZ
|
A:LYS221
|
4.2
|
22.1
|
1.0
|
CE
|
A:LYS221
|
4.3
|
23.3
|
1.0
|
ND1
|
A:HIS257
|
4.4
|
28.4
|
1.0
|
CG
|
A:ASP254
|
4.4
|
29.0
|
1.0
|
NH2
|
B:ARG65
|
4.4
|
23.2
|
1.0
|
CG
|
A:HIS257
|
4.4
|
28.9
|
1.0
|
OD1
|
A:ASP254
|
4.5
|
30.5
|
1.0
|
CB
|
A:ASP289
|
4.6
|
35.1
|
1.0
|
ZN
|
A:ZN501
|
4.7
|
61.8
|
1.0
|
CD
|
A:LYS221
|
4.8
|
25.5
|
1.0
|
OE2
|
A:GLU219
|
4.8
|
28.2
|
1.0
|
OD1
|
A:ASP327
|
4.9
|
34.8
|
1.0
|
OD2
|
A:ASP327
|
4.9
|
36.1
|
1.0
|
CG
|
A:ASP327
|
5.0
|
34.2
|
1.0
|
|
Zinc binding site 3 out
of 8 in 3iui
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Zinc Binding Sites List in 3iui
Zinc binding site 3 out
of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn503
b:53.8
occ:1.00
|
ND1
|
B:HIS281
|
2.2
|
39.3
|
1.0
|
OD2
|
B:ASP254
|
2.4
|
26.9
|
1.0
|
OE2
|
B:GLU219
|
2.5
|
31.7
|
1.0
|
OD2
|
B:ASP327
|
2.5
|
34.3
|
1.0
|
CD
|
B:GLU219
|
3.1
|
29.7
|
1.0
|
OE1
|
B:GLU219
|
3.1
|
33.4
|
1.0
|
CE1
|
B:HIS281
|
3.2
|
39.7
|
1.0
|
CG
|
B:HIS281
|
3.2
|
38.1
|
1.0
|
CG
|
B:ASP254
|
3.4
|
22.2
|
1.0
|
CG
|
B:ASP327
|
3.4
|
32.0
|
1.0
|
CB
|
B:HIS281
|
3.5
|
34.2
|
1.0
|
CB
|
B:ASP327
|
3.6
|
29.6
|
1.0
|
CB
|
B:ASP254
|
3.7
|
22.3
|
1.0
|
CE1
|
B:HIS257
|
3.9
|
27.7
|
1.0
|
ZN
|
B:ZN504
|
4.2
|
51.5
|
0.5
|
NE2
|
B:HIS281
|
4.3
|
39.8
|
1.0
|
CD2
|
B:HIS281
|
4.3
|
39.4
|
1.0
|
NE2
|
B:HIS257
|
4.3
|
26.4
|
1.0
|
CG
|
B:GLU219
|
4.4
|
28.4
|
1.0
|
OD1
|
B:ASP254
|
4.5
|
22.1
|
1.0
|
OD1
|
B:ASP327
|
4.5
|
29.8
|
1.0
|
ND1
|
B:HIS257
|
4.7
|
27.6
|
1.0
|
CD2
|
B:LEU252
|
4.8
|
39.5
|
1.0
|
CA
|
B:ASP254
|
4.9
|
22.9
|
1.0
|
CA
|
B:HIS281
|
5.0
|
33.3
|
1.0
|
|
Zinc binding site 4 out
of 8 in 3iui
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Zinc Binding Sites List in 3iui
Zinc binding site 4 out
of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn504
b:51.5
occ:0.50
|
NE2
|
B:HIS257
|
2.1
|
26.4
|
1.0
|
OD2
|
B:ASP289
|
2.4
|
39.7
|
1.0
|
O
|
B:HOH516
|
2.9
|
34.3
|
1.0
|
CE1
|
B:HIS257
|
3.0
|
27.7
|
1.0
|
CG
|
B:ASP289
|
3.1
|
38.8
|
1.0
|
OD1
|
B:ASP289
|
3.1
|
40.4
|
1.0
|
CD2
|
B:HIS257
|
3.2
|
27.4
|
1.0
|
OD1
|
B:ASP291
|
3.3
|
30.1
|
1.0
|
OD2
|
B:ASP254
|
3.7
|
26.9
|
1.0
|
OD2
|
B:ASP291
|
3.8
|
30.5
|
1.0
|
CG
|
B:ASP291
|
4.0
|
29.5
|
1.0
|
CG
|
B:ASP254
|
4.1
|
22.2
|
1.0
|
ND1
|
B:HIS257
|
4.1
|
27.6
|
1.0
|
ZN
|
B:ZN503
|
4.2
|
53.8
|
1.0
|
OD1
|
B:ASP254
|
4.2
|
22.1
|
1.0
|
CG
|
B:HIS257
|
4.3
|
26.1
|
1.0
|
NZ
|
B:LYS221
|
4.4
|
32.3
|
1.0
|
OD2
|
B:ASP327
|
4.4
|
34.3
|
1.0
|
CE
|
B:LYS221
|
4.5
|
29.6
|
1.0
|
CB
|
B:ASP289
|
4.6
|
34.2
|
1.0
|
OE2
|
B:GLU219
|
4.6
|
31.7
|
1.0
|
CG
|
B:ASP327
|
4.8
|
32.0
|
1.0
|
NH2
|
A:ARG65
|
4.8
|
24.9
|
1.0
|
CD
|
B:LYS221
|
4.9
|
28.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 3iui
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Zinc Binding Sites List in 3iui
Zinc binding site 5 out
of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn505
b:58.1
occ:1.00
|
ND1
|
C:HIS281
|
2.3
|
27.8
|
1.0
|
OD2
|
C:ASP254
|
2.5
|
26.4
|
1.0
|
OE2
|
C:GLU219
|
2.5
|
33.9
|
1.0
|
OD2
|
C:ASP327
|
2.6
|
24.5
|
1.0
|
CD
|
C:GLU219
|
3.1
|
31.2
|
1.0
|
OE1
|
C:GLU219
|
3.1
|
30.4
|
1.0
|
CG
|
C:HIS281
|
3.3
|
27.8
|
1.0
|
CE1
|
C:HIS281
|
3.3
|
27.7
|
1.0
|
CB
|
C:HIS281
|
3.5
|
23.4
|
1.0
|
CG
|
C:ASP254
|
3.5
|
25.4
|
1.0
|
CG
|
C:ASP327
|
3.5
|
25.1
|
1.0
|
CB
|
C:ASP327
|
3.7
|
22.0
|
1.0
|
CB
|
C:ASP254
|
3.8
|
23.0
|
1.0
|
CE1
|
C:HIS257
|
4.3
|
19.1
|
1.0
|
CG
|
C:GLU219
|
4.4
|
27.2
|
1.0
|
CD2
|
C:HIS281
|
4.4
|
27.6
|
1.0
|
NE2
|
C:HIS281
|
4.4
|
29.4
|
1.0
|
NE2
|
C:HIS257
|
4.5
|
21.9
|
1.0
|
OD1
|
C:ASP254
|
4.6
|
24.8
|
1.0
|
OD1
|
C:ASP327
|
4.7
|
26.8
|
1.0
|
ZN
|
C:ZN506
|
4.7
|
51.4
|
0.5
|
CA
|
C:ASP254
|
4.9
|
23.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 3iui
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Zinc Binding Sites List in 3iui
Zinc binding site 6 out
of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn506
b:51.4
occ:0.50
|
NE2
|
C:HIS257
|
2.2
|
21.9
|
1.0
|
OD2
|
C:ASP289
|
2.3
|
35.6
|
1.0
|
OD1
|
C:ASP289
|
2.7
|
35.5
|
1.0
|
CG
|
C:ASP289
|
2.9
|
32.3
|
1.0
|
O
|
C:HOH469
|
3.0
|
23.9
|
1.0
|
OD1
|
C:ASP291
|
3.0
|
26.0
|
1.0
|
CD2
|
C:HIS257
|
3.1
|
22.8
|
1.0
|
CE1
|
C:HIS257
|
3.2
|
19.1
|
1.0
|
OD2
|
C:ASP291
|
3.6
|
25.9
|
1.0
|
OD2
|
C:ASP254
|
3.7
|
26.4
|
1.0
|
CG
|
C:ASP291
|
3.7
|
24.9
|
1.0
|
OD1
|
C:ASP254
|
4.1
|
24.8
|
1.0
|
CG
|
C:ASP254
|
4.1
|
25.4
|
1.0
|
CG
|
C:HIS257
|
4.3
|
22.7
|
1.0
|
ND1
|
C:HIS257
|
4.3
|
23.1
|
1.0
|
CB
|
C:ASP289
|
4.4
|
26.8
|
1.0
|
NZ
|
C:LYS221
|
4.4
|
24.2
|
1.0
|
CE
|
C:LYS221
|
4.4
|
22.2
|
1.0
|
NH2
|
D:ARG65
|
4.7
|
19.3
|
1.0
|
OD2
|
C:ASP327
|
4.7
|
24.5
|
1.0
|
ZN
|
C:ZN505
|
4.7
|
58.1
|
1.0
|
ND2
|
C:ASN283
|
4.9
|
22.6
|
1.0
|
OE2
|
C:GLU219
|
4.9
|
33.9
|
1.0
|
CD
|
C:LYS221
|
5.0
|
22.9
|
1.0
|
O
|
C:HOH539
|
5.0
|
32.5
|
1.0
|
CG
|
C:ASP327
|
5.0
|
25.1
|
1.0
|
|
Zinc binding site 7 out
of 8 in 3iui
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Zinc Binding Sites List in 3iui
Zinc binding site 7 out
of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn507
b:66.1
occ:1.00
|
ND1
|
D:HIS281
|
2.4
|
24.8
|
1.0
|
OD2
|
D:ASP254
|
2.4
|
23.1
|
1.0
|
OE2
|
D:GLU219
|
2.6
|
34.9
|
1.0
|
OD2
|
D:ASP327
|
3.0
|
24.4
|
1.0
|
OE1
|
D:GLU219
|
3.0
|
29.8
|
1.0
|
CD
|
D:GLU219
|
3.0
|
30.4
|
1.0
|
CG
|
D:HIS281
|
3.2
|
23.6
|
1.0
|
CG
|
D:ASP254
|
3.4
|
22.9
|
1.0
|
CE1
|
D:HIS281
|
3.4
|
24.8
|
1.0
|
CB
|
D:HIS281
|
3.4
|
21.4
|
1.0
|
CB
|
D:ASP254
|
3.6
|
23.6
|
1.0
|
CG
|
D:ASP327
|
3.7
|
25.8
|
1.0
|
CB
|
D:ASP327
|
3.7
|
24.5
|
1.0
|
CE1
|
D:HIS257
|
4.1
|
18.8
|
1.0
|
CG
|
D:GLU219
|
4.3
|
28.8
|
1.0
|
CD2
|
D:HIS281
|
4.4
|
23.6
|
1.0
|
NE2
|
D:HIS281
|
4.5
|
23.6
|
1.0
|
NE2
|
D:HIS257
|
4.5
|
18.6
|
1.0
|
OD1
|
D:ASP254
|
4.5
|
24.8
|
1.0
|
ZN
|
D:ZN508
|
4.6
|
58.0
|
0.5
|
CA
|
D:ASP254
|
4.8
|
25.4
|
1.0
|
CE
|
D:MET325
|
4.8
|
24.6
|
1.0
|
ND1
|
D:HIS257
|
4.9
|
19.9
|
1.0
|
OD1
|
D:ASP327
|
4.9
|
26.6
|
1.0
|
CA
|
D:HIS281
|
4.9
|
22.3
|
1.0
|
|
Zinc binding site 8 out
of 8 in 3iui
Go back to
Zinc Binding Sites List in 3iui
Zinc binding site 8 out
of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn508
b:58.0
occ:0.50
|
NE2
|
D:HIS257
|
2.2
|
18.6
|
1.0
|
OD2
|
D:ASP289
|
2.4
|
33.4
|
1.0
|
O
|
D:HOH546
|
3.0
|
26.0
|
1.0
|
CG
|
D:ASP289
|
3.0
|
32.8
|
1.0
|
OD1
|
D:ASP289
|
3.1
|
34.6
|
1.0
|
CE1
|
D:HIS257
|
3.1
|
18.8
|
1.0
|
OD1
|
D:ASP291
|
3.2
|
26.7
|
1.0
|
CD2
|
D:HIS257
|
3.3
|
17.3
|
1.0
|
OD2
|
D:ASP254
|
3.7
|
23.1
|
1.0
|
OD2
|
D:ASP291
|
3.9
|
29.2
|
1.0
|
CG
|
D:ASP291
|
3.9
|
28.5
|
1.0
|
CG
|
D:ASP254
|
4.1
|
22.9
|
1.0
|
OD1
|
D:ASP254
|
4.2
|
24.8
|
1.0
|
ND1
|
D:HIS257
|
4.3
|
19.9
|
1.0
|
CG
|
D:HIS257
|
4.4
|
18.4
|
1.0
|
NZ
|
D:LYS221
|
4.5
|
14.3
|
1.0
|
CB
|
D:ASP289
|
4.5
|
27.7
|
1.0
|
OD2
|
D:ASP327
|
4.5
|
24.4
|
1.0
|
ZN
|
D:ZN507
|
4.6
|
66.1
|
1.0
|
CE
|
D:LYS221
|
4.7
|
14.4
|
1.0
|
CG
|
D:ASP327
|
4.7
|
25.8
|
1.0
|
OE2
|
D:GLU219
|
4.8
|
34.9
|
1.0
|
NH2
|
C:ARG65
|
4.9
|
24.3
|
1.0
|
OD1
|
D:ASP327
|
4.9
|
26.6
|
1.0
|
OD1
|
D:ASN283
|
4.9
|
23.0
|
1.0
|
|
Reference:
H.Yoshida,
M.Yamaji,
T.Ishii,
K.Izumori,
S.Kamitori.
Catalytic Reaction Mechanism of Pseudomonas Stutzeri L-Rhamnose Isomerase Deduced From X-Ray Structures Febs J. V. 277 1045 2010.
ISSN: ISSN 1742-464X
PubMed: 20088877
DOI: 10.1111/J.1742-4658.2009.07548.X
Page generated: Sat Oct 26 07:20:59 2024
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