Phosphorus in PDB 1ady: Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate
Enzymatic activity of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate
All present enzymatic activity of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate:
6.1.1.21;
Protein crystallography data
The structure of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate, PDB code: 1ady
was solved by
S.Cusack,
A.Aberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.80
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
171.300,
214.700,
49.300,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26 /
30
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate
(pdb code 1ady). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 4 binding sites of Phosphorus where determined in the
Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate, PDB code: 1ady:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
Phosphorus binding site 1 out
of 4 in 1ady
Go back to
Phosphorus Binding Sites List in 1ady
Phosphorus binding site 1 out
of 4 in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P423
b:28.1
occ:1.00
|
P
|
A:HAM423
|
0.0
|
28.1
|
1.0
|
O1P
|
A:HAM423
|
1.5
|
29.8
|
1.0
|
O2P
|
A:HAM423
|
1.5
|
30.4
|
1.0
|
O5'
|
A:HAM423
|
1.6
|
32.0
|
1.0
|
O3P
|
A:HAM423
|
1.6
|
23.0
|
1.0
|
C5'
|
A:HAM423
|
2.6
|
35.3
|
1.0
|
C
|
A:HAM423
|
2.8
|
20.9
|
1.0
|
O
|
A:HAM423
|
3.2
|
27.6
|
1.0
|
NH2
|
A:ARG259
|
3.6
|
44.2
|
1.0
|
C4'
|
A:HAM423
|
3.9
|
37.2
|
1.0
|
NH2
|
A:ARG112
|
4.0
|
40.0
|
1.0
|
CD1
|
A:LEU261
|
4.1
|
25.5
|
1.0
|
CA
|
A:HAM423
|
4.1
|
21.1
|
1.0
|
CZ
|
A:ARG259
|
4.3
|
41.2
|
1.0
|
O4'
|
A:HAM423
|
4.3
|
37.2
|
1.0
|
C3'
|
A:HAM423
|
4.4
|
37.1
|
1.0
|
NH1
|
A:ARG259
|
4.4
|
38.5
|
1.0
|
C8
|
A:HAM423
|
4.7
|
35.7
|
1.0
|
CB
|
A:HAM423
|
4.8
|
22.4
|
1.0
|
NH1
|
A:ARG112
|
4.8
|
39.8
|
1.0
|
CZ
|
A:ARG112
|
4.9
|
41.3
|
1.0
|
|
Phosphorus binding site 2 out
of 4 in 1ady
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Phosphorus Binding Sites List in 1ady
Phosphorus binding site 2 out
of 4 in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P423
b:28.4
occ:1.00
|
P
|
B:HAM423
|
0.0
|
28.4
|
1.0
|
O2P
|
B:HAM423
|
1.5
|
31.2
|
1.0
|
O1P
|
B:HAM423
|
1.5
|
30.2
|
1.0
|
O5'
|
B:HAM423
|
1.6
|
29.6
|
1.0
|
O3P
|
B:HAM423
|
1.6
|
21.6
|
1.0
|
C5'
|
B:HAM423
|
2.6
|
28.6
|
1.0
|
C
|
B:HAM423
|
2.8
|
22.6
|
1.0
|
O
|
B:HAM423
|
3.2
|
25.0
|
1.0
|
C4'
|
B:HAM423
|
3.9
|
26.9
|
1.0
|
CA
|
B:HAM423
|
4.1
|
24.6
|
1.0
|
NH2
|
B:ARG112
|
4.2
|
35.2
|
1.0
|
CD1
|
B:LEU261
|
4.2
|
45.0
|
1.0
|
NH2
|
B:ARG259
|
4.3
|
36.3
|
1.0
|
C3'
|
B:HAM423
|
4.3
|
26.9
|
1.0
|
O4'
|
B:HAM423
|
4.3
|
25.8
|
1.0
|
NH1
|
B:ARG259
|
4.3
|
32.8
|
1.0
|
CB
|
B:HAM423
|
4.6
|
27.9
|
1.0
|
C8
|
B:HAM423
|
4.7
|
28.0
|
1.0
|
CZ
|
B:ARG259
|
4.8
|
38.9
|
1.0
|
|
Phosphorus binding site 3 out
of 4 in 1ady
Go back to
Phosphorus Binding Sites List in 1ady
Phosphorus binding site 3 out
of 4 in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P423
b:34.3
occ:1.00
|
P
|
C:HAM423
|
0.0
|
34.3
|
1.0
|
O1P
|
C:HAM423
|
1.5
|
26.9
|
1.0
|
O2P
|
C:HAM423
|
1.5
|
34.2
|
1.0
|
O3P
|
C:HAM423
|
1.6
|
27.2
|
1.0
|
O5'
|
C:HAM423
|
1.6
|
39.0
|
1.0
|
C5'
|
C:HAM423
|
2.6
|
38.7
|
1.0
|
C
|
C:HAM423
|
2.8
|
28.1
|
1.0
|
O
|
C:HAM423
|
3.3
|
30.7
|
1.0
|
C4'
|
C:HAM423
|
3.9
|
37.5
|
1.0
|
CA
|
C:HAM423
|
4.0
|
24.0
|
1.0
|
NH2
|
C:ARG112
|
4.2
|
38.4
|
1.0
|
O4'
|
C:HAM423
|
4.2
|
38.3
|
1.0
|
NH2
|
C:ARG259
|
4.3
|
76.0
|
1.0
|
C3'
|
C:HAM423
|
4.3
|
36.7
|
1.0
|
NH1
|
C:ARG259
|
4.3
|
72.9
|
1.0
|
CD1
|
C:LEU261
|
4.5
|
37.3
|
1.0
|
CB
|
C:HAM423
|
4.6
|
20.3
|
1.0
|
C8
|
C:HAM423
|
4.7
|
37.7
|
1.0
|
CZ
|
C:ARG259
|
4.8
|
74.5
|
1.0
|
OE1
|
C:GLN126
|
4.9
|
20.9
|
1.0
|
NH1
|
C:ARG112
|
4.9
|
39.5
|
1.0
|
|
Phosphorus binding site 4 out
of 4 in 1ady
Go back to
Phosphorus Binding Sites List in 1ady
Phosphorus binding site 4 out
of 4 in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:P423
b:39.4
occ:1.00
|
P
|
D:HAM423
|
0.0
|
39.4
|
1.0
|
O2P
|
D:HAM423
|
1.5
|
40.8
|
1.0
|
O1P
|
D:HAM423
|
1.5
|
42.5
|
1.0
|
O5'
|
D:HAM423
|
1.6
|
37.8
|
1.0
|
O3P
|
D:HAM423
|
1.6
|
39.4
|
1.0
|
C5'
|
D:HAM423
|
2.6
|
36.3
|
1.0
|
C
|
D:HAM423
|
2.8
|
43.3
|
1.0
|
O
|
D:HAM423
|
3.2
|
49.4
|
1.0
|
NH2
|
D:ARG259
|
3.8
|
35.2
|
1.0
|
C4'
|
D:HAM423
|
3.9
|
39.4
|
1.0
|
NH2
|
D:ARG112
|
4.1
|
35.7
|
1.0
|
CD1
|
D:LEU261
|
4.2
|
54.6
|
1.0
|
CA
|
D:HAM423
|
4.2
|
44.5
|
1.0
|
C3'
|
D:HAM423
|
4.2
|
39.3
|
1.0
|
O4'
|
D:HAM423
|
4.3
|
38.4
|
1.0
|
CB
|
D:HAM423
|
4.6
|
45.6
|
1.0
|
C8
|
D:HAM423
|
4.7
|
45.8
|
1.0
|
NH1
|
D:ARG112
|
4.8
|
37.5
|
1.0
|
O3'
|
D:HAM423
|
4.9
|
36.4
|
1.0
|
CZ
|
D:ARG259
|
4.9
|
38.2
|
1.0
|
CZ
|
D:ARG112
|
5.0
|
36.8
|
1.0
|
|
Reference:
A.Aberg,
A.Yaremchuk,
M.Tukalo,
B.Rasmussen,
S.Cusack.
Crystal Structure Analysis of the Activation of Histidine By Thermus Thermophilus Histidyl-Trna Synthetase. Biochemistry V. 36 3084 1997.
ISSN: ISSN 0006-2960
PubMed: 9115984
DOI: 10.1021/BI9618373
Page generated: Fri Sep 25 12:46:26 2020
|