Nickel in PDB 5nhd: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose:
5.3.1.5;
Protein crystallography data
The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose, PDB code: 5nhd
was solved by
H.J.Rozeboom,
D.B.Janssen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.40 /
1.80
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.719,
79.040,
92.010,
115.14,
90.36,
117.01
|
|
R / Rfree (%)
|
15.3 /
17.5
|
Nickel Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Nickel atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
(pdb code 5nhd). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the
Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose, PDB code: 5nhd:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Nickel binding site 1 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 1 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni501
b:17.6
occ:0.80
|
O2
|
A:XLS503
|
2.0
|
28.4
|
1.0
|
|
OD2
|
A:ASP297
|
2.1
|
18.5
|
1.0
|
|
OE2
|
A:GLU233
|
2.1
|
20.3
|
1.0
|
|
OE1
|
A:GLU269
|
2.1
|
18.9
|
1.0
|
|
OD2
|
A:ASP340
|
2.2
|
16.3
|
1.0
|
|
O4
|
A:XLS503
|
2.2
|
29.9
|
1.0
|
|
CD
|
A:GLU233
|
2.9
|
18.0
|
1.0
|
|
OE1
|
A:GLU233
|
3.0
|
21.1
|
1.0
|
|
C4
|
A:XLS503
|
3.1
|
33.5
|
1.0
|
|
C2
|
A:XLS503
|
3.2
|
35.5
|
1.0
|
|
CG
|
A:ASP297
|
3.2
|
17.2
|
1.0
|
|
CG
|
A:ASP340
|
3.3
|
15.1
|
1.0
|
|
CD
|
A:GLU269
|
3.4
|
16.8
|
1.0
|
|
C3
|
A:XLS503
|
3.4
|
34.6
|
1.0
|
|
O3
|
A:XLS503
|
3.6
|
38.4
|
1.0
|
|
NI
|
A:NI502
|
3.6
|
13.1
|
0.5
|
|
CB
|
A:ASP340
|
3.8
|
14.5
|
1.0
|
|
CB
|
A:ASP297
|
3.8
|
15.8
|
1.0
|
|
O
|
A:HOH611
|
4.0
|
19.6
|
1.0
|
|
CE1
|
A:HIS272
|
4.0
|
15.8
|
1.0
|
|
OE2
|
A:GLU269
|
4.2
|
18.9
|
1.0
|
|
CG
|
A:GLU269
|
4.2
|
14.8
|
1.0
|
|
CB
|
A:GLU269
|
4.3
|
14.0
|
1.0
|
|
OD1
|
A:ASP297
|
4.3
|
16.9
|
1.0
|
|
CG
|
A:GLU233
|
4.3
|
17.5
|
1.0
|
|
OD1
|
A:ASP340
|
4.3
|
16.0
|
1.0
|
|
C1
|
A:XLS503
|
4.4
|
37.0
|
1.0
|
|
NE2
|
A:HIS272
|
4.5
|
15.9
|
1.0
|
|
C5
|
A:XLS503
|
4.5
|
32.4
|
1.0
|
|
ND2
|
A:ASN267
|
4.7
|
16.0
|
1.0
|
|
O1
|
A:XLS503
|
4.8
|
37.6
|
1.0
|
|
ND1
|
A:HIS272
|
4.9
|
15.2
|
1.0
|
|
Nickel binding site 2 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 2 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni502
b:13.2
occ:0.50
|
NI
|
A:NI502
|
0.0
|
13.2
|
0.5
|
|
NI
|
A:NI502
|
1.9
|
13.1
|
0.5
|
|
OD2
|
A:ASP308
|
1.9
|
27.7
|
1.0
|
|
OE2
|
A:GLU269
|
2.0
|
18.9
|
1.0
|
|
OD1
|
A:ASP308
|
2.2
|
24.3
|
1.0
|
|
OD1
|
A:ASP310
|
2.2
|
17.3
|
1.0
|
|
CG
|
A:ASP308
|
2.4
|
25.2
|
1.0
|
|
O
|
A:HOH611
|
2.5
|
19.6
|
1.0
|
|
NE2
|
A:HIS272
|
2.8
|
15.9
|
1.0
|
|
CD
|
A:GLU269
|
3.1
|
16.8
|
1.0
|
|
CG
|
A:ASP310
|
3.2
|
17.4
|
1.0
|
|
CD2
|
A:HIS272
|
3.2
|
14.8
|
1.0
|
|
OD2
|
A:ASP310
|
3.3
|
19.8
|
1.0
|
|
O1
|
A:XLS503
|
3.6
|
37.6
|
1.0
|
|
OE1
|
A:GLU269
|
3.6
|
18.9
|
1.0
|
|
CB
|
A:ASP308
|
3.9
|
21.6
|
1.0
|
|
CE1
|
A:HIS272
|
4.0
|
15.8
|
1.0
|
|
ND2
|
A:ASN299
|
4.0
|
12.5
|
1.0
|
|
O2
|
A:XLS503
|
4.1
|
28.4
|
1.0
|
|
CB
|
A:ASN271
|
4.2
|
13.3
|
1.0
|
|
O
|
A:HOH892
|
4.3
|
41.4
|
1.0
|
|
CG
|
A:GLU269
|
4.4
|
14.8
|
1.0
|
|
C1
|
A:XLS503
|
4.4
|
37.0
|
1.0
|
|
CG
|
A:HIS272
|
4.5
|
14.1
|
1.0
|
|
CB
|
A:ASP310
|
4.6
|
16.1
|
1.0
|
|
OD1
|
A:ASN271
|
4.6
|
14.0
|
1.0
|
|
CG
|
A:ASN271
|
4.7
|
13.6
|
1.0
|
|
NZ
|
A:LYS235
|
4.7
|
17.0
|
1.0
|
|
CE
|
A:LYS235
|
4.8
|
15.4
|
1.0
|
|
CA
|
A:ASP308
|
4.8
|
19.2
|
1.0
|
|
ND1
|
A:HIS272
|
4.8
|
15.2
|
1.0
|
|
C2
|
A:XLS503
|
4.9
|
35.5
|
1.0
|
|
OD2
|
A:ASP340
|
5.0
|
16.3
|
1.0
|
|
Nickel binding site 3 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 3 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni502
b:13.1
occ:0.50
|
NI
|
A:NI502
|
0.0
|
13.1
|
0.5
|
|
O
|
A:HOH611
|
1.8
|
19.6
|
1.0
|
|
NI
|
A:NI502
|
1.9
|
13.2
|
0.5
|
|
NE2
|
A:HIS272
|
2.1
|
15.9
|
1.0
|
|
O2
|
A:XLS503
|
2.3
|
28.4
|
1.0
|
|
O1
|
A:XLS503
|
2.4
|
37.6
|
1.0
|
|
OE2
|
A:GLU269
|
2.4
|
18.9
|
1.0
|
|
OE1
|
A:GLU269
|
2.7
|
18.9
|
1.0
|
|
CE1
|
A:HIS272
|
2.8
|
15.8
|
1.0
|
|
CD
|
A:GLU269
|
2.8
|
16.8
|
1.0
|
|
C1
|
A:XLS503
|
2.9
|
37.0
|
1.0
|
|
OD2
|
A:ASP308
|
3.0
|
27.7
|
1.0
|
|
C2
|
A:XLS503
|
3.1
|
35.5
|
1.0
|
|
CD2
|
A:HIS272
|
3.2
|
14.8
|
1.0
|
|
NI
|
A:NI501
|
3.6
|
17.6
|
0.8
|
|
OD1
|
A:ASP310
|
3.7
|
17.3
|
1.0
|
|
OD2
|
A:ASP340
|
3.7
|
16.3
|
1.0
|
|
CG
|
A:ASP308
|
3.9
|
25.2
|
1.0
|
|
OD1
|
A:ASP308
|
4.0
|
24.3
|
1.0
|
|
ND1
|
A:HIS272
|
4.0
|
15.2
|
1.0
|
|
OD2
|
A:ASP310
|
4.0
|
19.8
|
1.0
|
|
CG
|
A:HIS272
|
4.2
|
14.1
|
1.0
|
|
OE2
|
A:GLU233
|
4.2
|
20.3
|
1.0
|
|
CG
|
A:GLU269
|
4.3
|
14.8
|
1.0
|
|
CG
|
A:ASP310
|
4.3
|
17.4
|
1.0
|
|
C3
|
A:XLS503
|
4.4
|
34.6
|
1.0
|
|
CG
|
A:ASP340
|
4.4
|
15.1
|
1.0
|
|
O3
|
A:XLS503
|
4.5
|
38.4
|
1.0
|
|
O
|
A:HOH892
|
4.6
|
41.4
|
1.0
|
|
NZ
|
A:LYS235
|
4.8
|
17.0
|
1.0
|
|
OD1
|
A:ASP340
|
4.8
|
16.0
|
1.0
|
|
CE
|
A:LYS235
|
4.8
|
15.4
|
1.0
|
|
ND2
|
A:ASN299
|
4.9
|
12.5
|
1.0
|
|
CB
|
A:GLU269
|
4.9
|
14.0
|
1.0
|
|
CD
|
A:LYS235
|
4.9
|
14.5
|
1.0
|
|
Nickel binding site 4 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 4 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni501
b:15.1
occ:0.80
|
O2
|
B:XLS503
|
2.1
|
23.3
|
1.0
|
|
OD2
|
B:ASP297
|
2.1
|
18.0
|
1.0
|
|
OE1
|
B:GLU269
|
2.1
|
15.8
|
1.0
|
|
OD2
|
B:ASP340
|
2.2
|
15.8
|
1.0
|
|
OE2
|
B:GLU233
|
2.2
|
18.5
|
1.0
|
|
O4
|
B:XLS503
|
2.2
|
22.4
|
1.0
|
|
CD
|
B:GLU233
|
2.9
|
17.3
|
1.0
|
|
OE1
|
B:GLU233
|
3.1
|
19.0
|
1.0
|
|
C4
|
B:XLS503
|
3.1
|
27.2
|
1.0
|
|
C2
|
B:XLS503
|
3.2
|
27.7
|
1.0
|
|
CG
|
B:ASP340
|
3.2
|
14.6
|
1.0
|
|
CG
|
B:ASP297
|
3.3
|
16.1
|
1.0
|
|
CD
|
B:GLU269
|
3.4
|
16.4
|
1.0
|
|
C3
|
B:XLS503
|
3.5
|
28.8
|
1.0
|
|
NI
|
B:NI502
|
3.6
|
11.8
|
0.5
|
|
O3
|
B:XLS503
|
3.6
|
32.1
|
1.0
|
|
CB
|
B:ASP340
|
3.8
|
13.9
|
1.0
|
|
CB
|
B:ASP297
|
3.9
|
14.8
|
1.0
|
|
O
|
B:HOH619
|
4.0
|
15.4
|
1.0
|
|
CE1
|
B:HIS272
|
4.1
|
14.1
|
1.0
|
|
OE2
|
B:GLU269
|
4.2
|
17.9
|
1.0
|
|
CG
|
B:GLU269
|
4.2
|
14.7
|
1.0
|
|
OD1
|
B:ASP297
|
4.3
|
17.4
|
1.0
|
|
CB
|
B:GLU269
|
4.3
|
13.6
|
1.0
|
|
OD1
|
B:ASP340
|
4.3
|
15.3
|
1.0
|
|
CG
|
B:GLU233
|
4.4
|
16.1
|
1.0
|
|
NE2
|
B:HIS272
|
4.5
|
14.3
|
1.0
|
|
C1
|
B:XLS503
|
4.5
|
30.7
|
1.0
|
|
C5
|
B:XLS503
|
4.5
|
27.5
|
1.0
|
|
ND2
|
B:ASN267
|
4.8
|
16.9
|
1.0
|
|
ND1
|
B:HIS272
|
4.9
|
14.2
|
1.0
|
|
O1
|
B:XLS503
|
4.9
|
28.5
|
1.0
|
|
Nickel binding site 5 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 5 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni502
b:12.3
occ:0.50
|
NI
|
B:NI502
|
0.0
|
12.3
|
0.5
|
|
OD2
|
B:ASP308
|
1.9
|
27.3
|
1.0
|
|
NI
|
B:NI502
|
1.9
|
11.8
|
0.5
|
|
OE2
|
B:GLU269
|
2.0
|
17.9
|
1.0
|
|
OD1
|
B:ASP308
|
2.2
|
26.9
|
1.0
|
|
OD1
|
B:ASP310
|
2.3
|
15.7
|
1.0
|
|
CG
|
B:ASP308
|
2.4
|
25.1
|
1.0
|
|
O
|
B:HOH619
|
2.4
|
15.4
|
1.0
|
|
NE2
|
B:HIS272
|
2.7
|
14.3
|
1.0
|
|
CD
|
B:GLU269
|
3.1
|
16.4
|
1.0
|
|
CD2
|
B:HIS272
|
3.2
|
13.7
|
1.0
|
|
CG
|
B:ASP310
|
3.2
|
15.7
|
1.0
|
|
OD2
|
B:ASP310
|
3.4
|
18.8
|
1.0
|
|
O1
|
B:XLS503
|
3.5
|
28.5
|
1.0
|
|
OE1
|
B:GLU269
|
3.6
|
15.8
|
1.0
|
|
CB
|
B:ASP308
|
3.8
|
21.2
|
1.0
|
|
CE1
|
B:HIS272
|
3.9
|
14.1
|
1.0
|
|
O2
|
B:XLS503
|
4.0
|
23.3
|
1.0
|
|
ND2
|
B:ASN299
|
4.0
|
14.3
|
1.0
|
|
CB
|
B:ASN271
|
4.2
|
12.5
|
1.0
|
|
C1
|
B:XLS503
|
4.3
|
30.7
|
1.0
|
|
CG
|
B:GLU269
|
4.4
|
14.7
|
1.0
|
|
CG
|
B:HIS272
|
4.5
|
13.7
|
1.0
|
|
NZ
|
B:LYS235
|
4.7
|
16.7
|
1.0
|
|
CB
|
B:ASP310
|
4.7
|
14.7
|
1.0
|
|
OD1
|
B:ASN271
|
4.7
|
12.7
|
1.0
|
|
CG
|
B:ASN271
|
4.7
|
12.6
|
1.0
|
|
CE
|
B:LYS235
|
4.7
|
15.8
|
1.0
|
|
CA
|
B:ASP308
|
4.8
|
18.1
|
1.0
|
|
ND1
|
B:HIS272
|
4.8
|
14.2
|
1.0
|
|
C2
|
B:XLS503
|
4.8
|
27.7
|
1.0
|
|
OD2
|
B:ASP340
|
4.9
|
15.8
|
1.0
|
|
Nickel binding site 6 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 6 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni502
b:11.8
occ:0.50
|
NI
|
B:NI502
|
0.0
|
11.8
|
0.5
|
|
O
|
B:HOH619
|
1.8
|
15.4
|
1.0
|
|
NI
|
B:NI502
|
1.9
|
12.3
|
0.5
|
|
NE2
|
B:HIS272
|
2.1
|
14.3
|
1.0
|
|
O2
|
B:XLS503
|
2.1
|
23.3
|
1.0
|
|
O1
|
B:XLS503
|
2.4
|
28.5
|
1.0
|
|
OE2
|
B:GLU269
|
2.4
|
17.9
|
1.0
|
|
OE1
|
B:GLU269
|
2.6
|
15.8
|
1.0
|
|
CD
|
B:GLU269
|
2.8
|
16.4
|
1.0
|
|
CE1
|
B:HIS272
|
2.8
|
14.1
|
1.0
|
|
C1
|
B:XLS503
|
2.9
|
30.7
|
1.0
|
|
C2
|
B:XLS503
|
3.0
|
27.7
|
1.0
|
|
OD2
|
B:ASP308
|
3.0
|
27.3
|
1.0
|
|
CD2
|
B:HIS272
|
3.3
|
13.7
|
1.0
|
|
NI
|
B:NI501
|
3.6
|
15.1
|
0.8
|
|
OD2
|
B:ASP340
|
3.7
|
15.8
|
1.0
|
|
OD1
|
B:ASP310
|
3.8
|
15.7
|
1.0
|
|
CG
|
B:ASP308
|
3.9
|
25.1
|
1.0
|
|
ND1
|
B:HIS272
|
4.0
|
14.2
|
1.0
|
|
OD1
|
B:ASP308
|
4.0
|
26.9
|
1.0
|
|
OD2
|
B:ASP310
|
4.0
|
18.8
|
1.0
|
|
OE2
|
B:GLU233
|
4.2
|
18.5
|
1.0
|
|
CG
|
B:HIS272
|
4.2
|
13.7
|
1.0
|
|
CG
|
B:GLU269
|
4.3
|
14.7
|
1.0
|
|
C3
|
B:XLS503
|
4.3
|
28.8
|
1.0
|
|
CG
|
B:ASP310
|
4.3
|
15.7
|
1.0
|
|
CG
|
B:ASP340
|
4.4
|
14.6
|
1.0
|
|
O3
|
B:XLS503
|
4.4
|
32.1
|
1.0
|
|
OD1
|
B:ASP340
|
4.7
|
15.3
|
1.0
|
|
NZ
|
B:LYS235
|
4.8
|
16.7
|
1.0
|
|
CE
|
B:LYS235
|
4.9
|
15.8
|
1.0
|
|
ND2
|
B:ASN299
|
4.9
|
14.3
|
1.0
|
|
CB
|
B:GLU269
|
4.9
|
13.6
|
1.0
|
|
CD
|
B:LYS235
|
5.0
|
14.8
|
1.0
|
|
Nickel binding site 7 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 7 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni501
b:16.2
occ:0.80
|
O2
|
C:XLS503
|
2.1
|
27.3
|
1.0
|
|
OD2
|
C:ASP297
|
2.1
|
20.4
|
1.0
|
|
OE2
|
C:GLU233
|
2.1
|
23.6
|
1.0
|
|
OD2
|
C:ASP340
|
2.1
|
16.3
|
1.0
|
|
OE1
|
C:GLU269
|
2.2
|
17.9
|
1.0
|
|
O4
|
C:XLS503
|
2.3
|
26.2
|
1.0
|
|
CD
|
C:GLU233
|
2.9
|
20.5
|
1.0
|
|
OE1
|
C:GLU233
|
3.0
|
22.2
|
1.0
|
|
C4
|
C:XLS503
|
3.1
|
30.4
|
1.0
|
|
C2
|
C:XLS503
|
3.3
|
32.3
|
1.0
|
|
CG
|
C:ASP340
|
3.3
|
14.5
|
1.0
|
|
CG
|
C:ASP297
|
3.3
|
16.8
|
1.0
|
|
CD
|
C:GLU269
|
3.4
|
16.2
|
1.0
|
|
C3
|
C:XLS503
|
3.5
|
32.0
|
1.0
|
|
O3
|
C:XLS503
|
3.6
|
36.1
|
1.0
|
|
NI
|
C:NI502
|
3.6
|
14.9
|
0.5
|
|
CB
|
C:ASP340
|
3.8
|
14.3
|
1.0
|
|
CB
|
C:ASP297
|
3.9
|
15.4
|
1.0
|
|
O
|
C:HOH620
|
4.0
|
17.4
|
1.0
|
|
CE1
|
C:HIS272
|
4.1
|
16.1
|
1.0
|
|
OE2
|
C:GLU269
|
4.2
|
18.7
|
1.0
|
|
CG
|
C:GLU269
|
4.3
|
14.3
|
1.0
|
|
OD1
|
C:ASP297
|
4.3
|
16.6
|
1.0
|
|
CB
|
C:GLU269
|
4.3
|
13.7
|
1.0
|
|
OD1
|
C:ASP340
|
4.3
|
15.9
|
1.0
|
|
CG
|
C:GLU233
|
4.3
|
17.9
|
1.0
|
|
NE2
|
C:HIS272
|
4.5
|
16.8
|
1.0
|
|
C5
|
C:XLS503
|
4.5
|
29.6
|
1.0
|
|
C1
|
C:XLS503
|
4.5
|
35.2
|
1.0
|
|
ND2
|
C:ASN267
|
4.8
|
15.0
|
1.0
|
|
ND1
|
C:HIS272
|
4.9
|
15.8
|
1.0
|
|
O1
|
C:XLS503
|
5.0
|
32.2
|
1.0
|
|
Nickel binding site 8 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 8 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni502
b:14.3
occ:0.50
|
NI
|
C:NI502
|
0.0
|
14.3
|
0.5
|
|
OD2
|
C:ASP308
|
1.9
|
31.6
|
1.0
|
|
NI
|
C:NI502
|
1.9
|
14.9
|
0.5
|
|
OE2
|
C:GLU269
|
2.0
|
18.7
|
1.0
|
|
OD1
|
C:ASP308
|
2.2
|
30.6
|
1.0
|
|
OD1
|
C:ASP310
|
2.2
|
16.7
|
1.0
|
|
CG
|
C:ASP308
|
2.3
|
30.4
|
1.0
|
|
O
|
C:HOH620
|
2.4
|
17.4
|
1.0
|
|
NE2
|
C:HIS272
|
2.8
|
16.8
|
1.0
|
|
CD
|
C:GLU269
|
3.2
|
16.2
|
1.0
|
|
CG
|
C:ASP310
|
3.2
|
16.6
|
1.0
|
|
CD2
|
C:HIS272
|
3.2
|
15.9
|
1.0
|
|
OD2
|
C:ASP310
|
3.4
|
17.7
|
1.0
|
|
O1
|
C:XLS503
|
3.5
|
32.2
|
1.0
|
|
OE1
|
C:GLU269
|
3.7
|
17.9
|
1.0
|
|
CB
|
C:ASP308
|
3.8
|
24.2
|
1.0
|
|
CE1
|
C:HIS272
|
4.0
|
16.1
|
1.0
|
|
ND2
|
C:ASN299
|
4.0
|
12.9
|
1.0
|
|
O2
|
C:XLS503
|
4.1
|
27.3
|
1.0
|
|
CB
|
C:ASN271
|
4.2
|
12.7
|
1.0
|
|
C1
|
C:XLS503
|
4.4
|
35.2
|
1.0
|
|
CG
|
C:GLU269
|
4.4
|
14.3
|
1.0
|
|
CG
|
C:HIS272
|
4.5
|
14.4
|
1.0
|
|
OD1
|
C:ASN271
|
4.6
|
12.9
|
1.0
|
|
CB
|
C:ASP310
|
4.6
|
15.9
|
1.0
|
|
CG
|
C:ASN271
|
4.7
|
12.9
|
1.0
|
|
NZ
|
C:LYS235
|
4.7
|
18.8
|
1.0
|
|
CE
|
C:LYS235
|
4.7
|
17.8
|
1.0
|
|
CA
|
C:ASP308
|
4.7
|
20.5
|
1.0
|
|
ND1
|
C:HIS272
|
4.8
|
15.8
|
1.0
|
|
C2
|
C:XLS503
|
4.9
|
32.3
|
1.0
|
|
OD2
|
C:ASP340
|
5.0
|
16.3
|
1.0
|
|
Nickel binding site 9 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 9 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 9 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni502
b:14.9
occ:0.50
|
NI
|
C:NI502
|
0.0
|
14.9
|
0.5
|
|
O
|
C:HOH620
|
1.8
|
17.4
|
1.0
|
|
NI
|
C:NI502
|
1.9
|
14.3
|
0.5
|
|
NE2
|
C:HIS272
|
2.1
|
16.8
|
1.0
|
|
O2
|
C:XLS503
|
2.2
|
27.3
|
1.0
|
|
O1
|
C:XLS503
|
2.4
|
32.2
|
1.0
|
|
OE2
|
C:GLU269
|
2.4
|
18.7
|
1.0
|
|
OE1
|
C:GLU269
|
2.7
|
17.9
|
1.0
|
|
CE1
|
C:HIS272
|
2.8
|
16.1
|
1.0
|
|
CD
|
C:GLU269
|
2.8
|
16.2
|
1.0
|
|
C1
|
C:XLS503
|
2.9
|
35.2
|
1.0
|
|
OD2
|
C:ASP308
|
3.0
|
31.6
|
1.0
|
|
C2
|
C:XLS503
|
3.0
|
32.3
|
1.0
|
|
CD2
|
C:HIS272
|
3.3
|
15.9
|
1.0
|
|
NI
|
C:NI501
|
3.6
|
16.2
|
0.8
|
|
OD2
|
C:ASP340
|
3.7
|
16.3
|
1.0
|
|
OD1
|
C:ASP310
|
3.7
|
16.7
|
1.0
|
|
CG
|
C:ASP308
|
3.9
|
30.4
|
1.0
|
|
OD1
|
C:ASP308
|
4.0
|
30.6
|
1.0
|
|
ND1
|
C:HIS272
|
4.0
|
15.8
|
1.0
|
|
OD2
|
C:ASP310
|
4.0
|
17.7
|
1.0
|
|
OE2
|
C:GLU233
|
4.2
|
23.6
|
1.0
|
|
CG
|
C:HIS272
|
4.2
|
14.4
|
1.0
|
|
CG
|
C:GLU269
|
4.3
|
14.3
|
1.0
|
|
C3
|
C:XLS503
|
4.3
|
32.0
|
1.0
|
|
CG
|
C:ASP310
|
4.3
|
16.6
|
1.0
|
|
CG
|
C:ASP340
|
4.4
|
14.5
|
1.0
|
|
O3
|
C:XLS503
|
4.4
|
36.1
|
1.0
|
|
OD1
|
C:ASP340
|
4.7
|
15.9
|
1.0
|
|
NZ
|
C:LYS235
|
4.8
|
18.8
|
1.0
|
|
CE
|
C:LYS235
|
4.8
|
17.8
|
1.0
|
|
ND2
|
C:ASN299
|
4.9
|
12.9
|
1.0
|
|
CD
|
C:LYS235
|
4.9
|
16.3
|
1.0
|
|
CB
|
C:GLU269
|
4.9
|
13.7
|
1.0
|
|
Nickel binding site 10 out
of 12 in 5nhd
Go back to
Nickel Binding Sites List in 5nhd
Nickel binding site 10 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 10 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with 2 NI2+ Ions and Xylose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni501
b:15.9
occ:0.80
|
O2
|
D:XLS503
|
2.0
|
25.1
|
1.0
|
|
OD2
|
D:ASP297
|
2.1
|
17.4
|
1.0
|
|
OE2
|
D:GLU233
|
2.1
|
24.2
|
1.0
|
|
OE1
|
D:GLU269
|
2.2
|
16.6
|
1.0
|
|
OD2
|
D:ASP340
|
2.2
|
17.9
|
1.0
|
|
O4
|
D:XLS503
|
2.2
|
24.2
|
1.0
|
|
CD
|
D:GLU233
|
2.9
|
20.1
|
1.0
|
|
OE1
|
D:GLU233
|
3.0
|
22.5
|
1.0
|
|
C2
|
D:XLS503
|
3.2
|
30.2
|
1.0
|
|
CG
|
D:ASP297
|
3.2
|
16.0
|
1.0
|
|
C4
|
D:XLS503
|
3.2
|
29.8
|
1.0
|
|
CG
|
D:ASP340
|
3.3
|
15.9
|
1.0
|
|
CD
|
D:GLU269
|
3.4
|
15.8
|
1.0
|
|
C3
|
D:XLS503
|
3.5
|
30.9
|
1.0
|
|
NI
|
D:NI502
|
3.6
|
14.6
|
0.5
|
|
O3
|
D:XLS503
|
3.6
|
36.0
|
1.0
|
|
CB
|
D:ASP340
|
3.8
|
15.4
|
1.0
|
|
CB
|
D:ASP297
|
3.8
|
15.0
|
1.0
|
|
O
|
D:HOH634
|
3.9
|
18.2
|
1.0
|
|
CE1
|
D:HIS272
|
4.1
|
14.2
|
1.0
|
|
OD1
|
D:ASP297
|
4.2
|
16.9
|
1.0
|
|
OE2
|
D:GLU269
|
4.2
|
18.1
|
1.0
|
|
CG
|
D:GLU269
|
4.3
|
14.0
|
1.0
|
|
CB
|
D:GLU269
|
4.3
|
12.7
|
1.0
|
|
CG
|
D:GLU233
|
4.3
|
17.2
|
1.0
|
|
OD1
|
D:ASP340
|
4.4
|
17.2
|
1.0
|
|
C1
|
D:XLS503
|
4.4
|
31.9
|
1.0
|
|
NE2
|
D:HIS272
|
4.5
|
15.0
|
1.0
|
|
C5
|
D:XLS503
|
4.5
|
29.1
|
1.0
|
|
ND2
|
D:ASN267
|
4.7
|
15.5
|
1.0
|
|
ND1
|
D:HIS272
|
4.9
|
13.9
|
1.0
|
|
O1
|
D:XLS503
|
5.0
|
32.8
|
1.0
|
|
Reference:
M.Lee,
H.J.Rozeboom,
P.P.De Waal,
R.M.De Jong,
H.M.Dudek,
D.B.Janssen.
Metal Dependence of the Xylose Isomerase From Piromyces Sp. E2 Explored By Activity Profiling and Protein Crystallography. Biochemistry V. 56 5991 2017.
ISSN: ISSN 1520-4995
PubMed: 29045784
DOI: 10.1021/ACS.BIOCHEM.7B00777
Page generated: Thu Oct 10 06:40:57 2024
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