Potassium in PDB 1tz3: Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside
Enzymatic activity of Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside
All present enzymatic activity of Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside:
2.7.1.4;
Protein crystallography data
The structure of Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside, PDB code: 1tz3
was solved by
Y.Zhang,
M.Dougherty,
D.M.Downs,
S.E.Ealick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.77 /
2.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.851,
54.098,
89.796,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.5 /
27.5
|
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside
(pdb code 1tz3). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside, PDB code: 1tz3:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 1tz3
Go back to
Potassium Binding Sites List in 1tz3
Potassium binding site 1 out
of 4 in the Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K404
b:52.8
occ:1.00
|
O
|
A:ASP246
|
2.6
|
85.1
|
1.0
|
O
|
A:ALA287
|
2.8
|
39.6
|
1.0
|
O
|
A:THR248
|
2.9
|
57.0
|
1.0
|
OD2
|
A:ASP246
|
3.0
|
67.6
|
1.0
|
O
|
A:GLY292
|
3.0
|
56.8
|
1.0
|
C
|
A:GLY292
|
3.5
|
56.8
|
1.0
|
N
|
A:GLY292
|
3.5
|
56.8
|
1.0
|
CG
|
A:ASP246
|
3.5
|
67.6
|
1.0
|
O
|
A:ALA290
|
3.6
|
57.5
|
1.0
|
CB
|
A:ASP246
|
3.6
|
67.6
|
1.0
|
C
|
A:ASP246
|
3.7
|
85.1
|
1.0
|
C
|
A:THR248
|
3.9
|
57.0
|
1.0
|
C
|
A:ALA287
|
4.0
|
39.6
|
1.0
|
CA
|
A:GLY292
|
4.1
|
56.8
|
1.0
|
CA
|
A:VAL288
|
4.1
|
56.4
|
1.0
|
N
|
A:ALA293
|
4.1
|
47.7
|
1.0
|
C
|
A:ALA290
|
4.2
|
57.5
|
1.0
|
CA
|
A:ASP246
|
4.3
|
85.1
|
1.0
|
N
|
A:THR248
|
4.4
|
57.0
|
1.0
|
CA
|
A:ALA293
|
4.4
|
47.7
|
1.0
|
C
|
A:THR247
|
4.5
|
57.8
|
1.0
|
CA
|
A:THR248
|
4.5
|
57.0
|
1.0
|
N
|
A:VAL288
|
4.5
|
56.4
|
1.0
|
OD1
|
A:ASP246
|
4.6
|
67.6
|
1.0
|
C
|
A:VAL288
|
4.6
|
56.4
|
1.0
|
C
|
A:LYS291
|
4.6
|
74.1
|
1.0
|
N
|
A:LYS291
|
4.7
|
74.1
|
1.0
|
CB
|
A:THR248
|
4.7
|
78.0
|
1.0
|
N
|
A:ALA290
|
4.7
|
57.5
|
1.0
|
O
|
A:THR247
|
4.7
|
57.8
|
1.0
|
CA
|
A:LYS291
|
4.8
|
74.1
|
1.0
|
N
|
A:THR247
|
4.8
|
57.8
|
1.0
|
C
|
A:ALA293
|
4.8
|
47.7
|
1.0
|
O
|
A:VAL288
|
4.9
|
56.4
|
1.0
|
N
|
A:ASP246
|
4.9
|
85.1
|
1.0
|
N
|
A:GLY249
|
4.9
|
41.7
|
1.0
|
CA
|
A:ALA290
|
4.9
|
57.5
|
1.0
|
O
|
A:ALA293
|
4.9
|
47.7
|
1.0
|
|
Potassium binding site 2 out
of 4 in 1tz3
Go back to
Potassium Binding Sites List in 1tz3
Potassium binding site 2 out
of 4 in the Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K405
b:69.8
occ:1.00
|
O
|
A:ALA183
|
2.6
|
41.2
|
1.0
|
O
|
A:ALA180
|
2.7
|
50.9
|
1.0
|
O
|
A:GLY213
|
2.8
|
45.0
|
1.0
|
O
|
A:ALA181
|
2.8
|
53.0
|
1.0
|
C
|
A:ALA181
|
3.4
|
53.0
|
1.0
|
O
|
A:HOH602
|
3.6
|
54.2
|
1.0
|
C
|
A:GLY213
|
3.6
|
45.0
|
1.0
|
C
|
A:ALA183
|
3.7
|
41.2
|
1.0
|
CA
|
A:CYS214
|
3.8
|
51.9
|
1.0
|
C
|
A:ALA180
|
3.8
|
50.9
|
1.0
|
CA
|
A:ALA181
|
3.9
|
53.0
|
1.0
|
N
|
A:ALA183
|
4.0
|
41.2
|
1.0
|
N
|
A:CYS214
|
4.0
|
51.9
|
1.0
|
CA
|
A:ALA183
|
4.3
|
41.2
|
1.0
|
N
|
A:ALA181
|
4.4
|
53.0
|
1.0
|
N
|
A:LEU182
|
4.4
|
44.2
|
1.0
|
C
|
A:LEU182
|
4.4
|
44.2
|
1.0
|
CB
|
A:CYS214
|
4.5
|
76.0
|
1.0
|
N
|
A:ASP215
|
4.7
|
53.8
|
1.0
|
SG
|
A:CYS214
|
4.7
|
76.0
|
1.0
|
CA
|
A:GLY213
|
4.7
|
45.0
|
1.0
|
CB
|
A:ALA183
|
4.8
|
49.8
|
1.0
|
N
|
A:SER184
|
4.8
|
49.5
|
1.0
|
NH2
|
A:ARG149
|
4.8
|
46.5
|
1.0
|
C
|
A:CYS214
|
4.8
|
51.9
|
1.0
|
CA
|
A:LEU182
|
4.9
|
44.2
|
1.0
|
O
|
A:LEU182
|
4.9
|
44.2
|
1.0
|
|
Potassium binding site 3 out
of 4 in 1tz3
Go back to
Potassium Binding Sites List in 1tz3
Potassium binding site 3 out
of 4 in the Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K406
b:64.3
occ:1.00
|
O
|
B:ALA181
|
2.3
|
60.7
|
1.0
|
O
|
B:GLY213
|
2.8
|
48.9
|
1.0
|
O
|
B:ALA180
|
2.9
|
53.0
|
1.0
|
O
|
B:ALA183
|
2.9
|
54.9
|
1.0
|
O
|
B:HOH603
|
3.1
|
54.2
|
1.0
|
C
|
B:ALA181
|
3.1
|
60.7
|
1.0
|
O
|
B:HOH623
|
3.2
|
54.2
|
1.0
|
O
|
B:HOH624
|
3.5
|
54.2
|
1.0
|
CA
|
B:ALA181
|
3.7
|
60.7
|
1.0
|
C
|
B:ALA180
|
3.9
|
53.0
|
1.0
|
C
|
B:GLY213
|
3.9
|
48.9
|
1.0
|
N
|
B:LEU182
|
4.0
|
38.5
|
1.0
|
C
|
B:LEU182
|
4.1
|
38.5
|
1.0
|
C
|
B:ALA183
|
4.1
|
54.9
|
1.0
|
O
|
B:LEU182
|
4.2
|
38.5
|
1.0
|
N
|
B:ALA181
|
4.3
|
60.7
|
1.0
|
N
|
B:ALA183
|
4.3
|
54.9
|
1.0
|
CA
|
B:LEU182
|
4.4
|
38.5
|
1.0
|
NH2
|
B:ARG149
|
4.5
|
57.4
|
1.0
|
CA
|
B:CYS214
|
4.7
|
64.0
|
1.0
|
CA
|
B:ALA183
|
4.7
|
54.9
|
1.0
|
CA
|
B:GLY213
|
4.8
|
48.9
|
1.0
|
N
|
B:CYS214
|
4.8
|
64.0
|
1.0
|
CB
|
B:ALA181
|
5.0
|
21.1
|
1.0
|
|
Potassium binding site 4 out
of 4 in 1tz3
Go back to
Potassium Binding Sites List in 1tz3
Potassium binding site 4 out
of 4 in the Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of Aminoimidazole Riboside Kinase Complexed with Aminoimidazole Riboside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K407
b:52.9
occ:1.00
|
O
|
B:ASP246
|
2.4
|
81.7
|
1.0
|
O
|
B:ALA287
|
2.7
|
54.6
|
1.0
|
O
|
B:THR248
|
2.7
|
45.2
|
1.0
|
OD2
|
B:ASP246
|
2.9
|
66.8
|
1.0
|
O
|
B:ALA290
|
3.2
|
72.2
|
1.0
|
N
|
B:THR248
|
3.3
|
45.2
|
1.0
|
C
|
B:ASP246
|
3.4
|
81.7
|
1.0
|
CG
|
B:ASP246
|
3.5
|
66.8
|
1.0
|
C
|
B:THR248
|
3.6
|
45.2
|
1.0
|
O
|
B:GLY292
|
3.6
|
82.1
|
1.0
|
C
|
B:ALA287
|
3.6
|
54.6
|
1.0
|
CA
|
B:THR248
|
3.7
|
45.2
|
1.0
|
CB
|
B:ASP246
|
3.8
|
66.8
|
1.0
|
CB
|
B:THR248
|
3.9
|
50.4
|
1.0
|
C
|
B:THR247
|
4.1
|
61.1
|
1.0
|
CA
|
B:ASP246
|
4.2
|
81.7
|
1.0
|
O
|
B:VAL288
|
4.2
|
74.7
|
1.0
|
CA
|
B:VAL288
|
4.2
|
74.7
|
1.0
|
N
|
B:THR247
|
4.2
|
61.1
|
1.0
|
C
|
B:ALA290
|
4.2
|
72.2
|
1.0
|
C
|
B:GLY292
|
4.3
|
82.1
|
1.0
|
OD1
|
B:ASP246
|
4.3
|
66.8
|
1.0
|
N
|
B:VAL288
|
4.3
|
74.7
|
1.0
|
CA
|
B:THR247
|
4.4
|
61.1
|
1.0
|
O
|
B:LYS291
|
4.5
|
78.6
|
1.0
|
C
|
B:LYS291
|
4.5
|
78.6
|
1.0
|
CB
|
B:ALA296
|
4.5
|
79.2
|
1.0
|
CA
|
B:ALA293
|
4.5
|
73.2
|
1.0
|
C
|
B:VAL288
|
4.6
|
74.7
|
1.0
|
CA
|
B:ALA287
|
4.7
|
54.6
|
1.0
|
CA
|
B:LYS291
|
4.7
|
78.6
|
1.0
|
N
|
B:ALA293
|
4.7
|
73.2
|
1.0
|
OG1
|
B:THR248
|
4.7
|
50.4
|
1.0
|
N
|
B:GLY292
|
4.8
|
82.1
|
1.0
|
N
|
B:GLY249
|
4.8
|
51.1
|
1.0
|
O
|
B:ALA293
|
4.8
|
73.2
|
1.0
|
N
|
B:ASP246
|
4.9
|
81.7
|
1.0
|
N
|
B:LYS291
|
4.9
|
78.6
|
1.0
|
O
|
B:THR247
|
4.9
|
61.1
|
1.0
|
CB
|
B:ALA287
|
4.9
|
70.5
|
1.0
|
|
Reference:
Y.Zhang,
M.Dougherty,
D.M.Downs,
S.E.Ealick.
Crystal Structure of An Aminoimidazole Riboside Kinase From Salmonella Enterica; Implications For the Evolution of the Ribokinase Superfamily Structure V. 12 1809 2004.
ISSN: ISSN 0969-2126
PubMed: 15458630
DOI: 10.1016/J.STR.2004.07.020
Page generated: Mon Aug 12 05:30:48 2024
|