Sodium in PDB 4d1q: Hermes Transposase Bound to Its Terminal Inverted Repeat
Protein crystallography data
The structure of Hermes Transposase Bound to Its Terminal Inverted Repeat, PDB code: 4d1q
was solved by
A.B.Hickman,
H.Ewis,
X.Li,
J.Knapp,
T.Laver,
A.L.Doss,
G.Tolun,
A.Steven,
A.Grishaev,
A.Bax,
P.Atkinson,
N.L.Craig,
F.Dyda,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.0 /
3.40
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
265.150,
265.150,
157.640,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.18 /
25.43
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Hermes Transposase Bound to Its Terminal Inverted Repeat
(pdb code 4d1q). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Hermes Transposase Bound to Its Terminal Inverted Repeat, PDB code: 4d1q:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 4d1q
Go back to
Sodium Binding Sites List in 4d1q
Sodium binding site 1 out
of 4 in the Hermes Transposase Bound to Its Terminal Inverted Repeat
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Hermes Transposase Bound to Its Terminal Inverted Repeat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1610
b:44.1
occ:1.00
|
O
|
A:LEU141
|
2.4
|
98.4
|
1.0
|
OP2
|
F:DG6
|
2.6
|
96.7
|
1.0
|
O
|
A:GLU139
|
2.7
|
88.3
|
1.0
|
O
|
A:GLU138
|
3.1
|
82.4
|
1.0
|
C
|
A:LEU141
|
3.4
|
93.6
|
1.0
|
C
|
A:GLU139
|
3.5
|
90.3
|
1.0
|
O5'
|
F:DG6
|
3.6
|
0.7
|
1.0
|
P
|
F:DG6
|
3.6
|
0.7
|
1.0
|
CA
|
A:GLU139
|
3.9
|
91.3
|
1.0
|
C5'
|
F:DG6
|
4.0
|
99.5
|
1.0
|
CA
|
A:PRO142
|
4.0
|
86.3
|
1.0
|
NZ
|
B:LYS91
|
4.0
|
0.1
|
1.0
|
N
|
A:PRO142
|
4.1
|
88.3
|
1.0
|
C
|
A:GLU138
|
4.1
|
89.1
|
1.0
|
C
|
A:PRO142
|
4.2
|
86.7
|
1.0
|
N
|
A:LEU141
|
4.3
|
95.2
|
1.0
|
CA
|
A:LEU141
|
4.4
|
90.6
|
1.0
|
N
|
A:SER143
|
4.4
|
87.3
|
1.0
|
C
|
A:LEU140
|
4.5
|
95.0
|
1.0
|
N
|
A:GLU139
|
4.5
|
88.6
|
1.0
|
OP1
|
F:DG6
|
4.5
|
0.8
|
1.0
|
N
|
A:LEU140
|
4.6
|
89.8
|
1.0
|
O
|
A:PRO142
|
4.7
|
89.8
|
1.0
|
CE
|
B:LYS91
|
4.7
|
0.9
|
1.0
|
O
|
A:LEU140
|
4.8
|
94.1
|
1.0
|
O3'
|
F:DT5
|
4.9
|
96.0
|
1.0
|
|
Sodium binding site 2 out
of 4 in 4d1q
Go back to
Sodium Binding Sites List in 4d1q
Sodium binding site 2 out
of 4 in the Hermes Transposase Bound to Its Terminal Inverted Repeat
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Hermes Transposase Bound to Its Terminal Inverted Repeat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1610
b:57.3
occ:1.00
|
OP2
|
D:DG6
|
2.4
|
0.8
|
1.0
|
O
|
B:LEU141
|
2.5
|
95.4
|
1.0
|
O
|
B:GLU139
|
2.6
|
94.0
|
1.0
|
O
|
B:GLU138
|
2.8
|
90.6
|
1.0
|
C
|
B:GLU139
|
3.4
|
96.1
|
1.0
|
C
|
B:LEU141
|
3.4
|
91.2
|
1.0
|
P
|
D:DG6
|
3.7
|
0.9
|
1.0
|
CA
|
B:GLU139
|
3.9
|
98.7
|
1.0
|
C
|
B:GLU138
|
3.9
|
91.1
|
1.0
|
O5'
|
D:DG6
|
3.9
|
0.6
|
1.0
|
CA
|
B:PRO142
|
4.0
|
83.2
|
1.0
|
N
|
B:PRO142
|
4.1
|
86.0
|
1.0
|
NZ
|
A:LYS91
|
4.1
|
93.8
|
1.0
|
CE
|
A:LYS91
|
4.2
|
0.3
|
1.0
|
N
|
B:LEU141
|
4.3
|
91.8
|
1.0
|
C
|
B:LEU140
|
4.3
|
92.6
|
1.0
|
N
|
B:GLU139
|
4.4
|
95.2
|
1.0
|
N
|
B:LEU140
|
4.4
|
92.7
|
1.0
|
C
|
B:PRO142
|
4.4
|
83.5
|
1.0
|
C5'
|
D:DG6
|
4.4
|
0.2
|
1.0
|
CA
|
B:LEU141
|
4.5
|
89.9
|
1.0
|
O
|
B:LEU140
|
4.5
|
91.2
|
1.0
|
OP1
|
D:DG6
|
4.5
|
0.6
|
1.0
|
N
|
B:SER143
|
4.5
|
87.4
|
1.0
|
O3'
|
D:DT5
|
4.8
|
93.9
|
1.0
|
CA
|
B:LEU140
|
4.9
|
92.0
|
1.0
|
|
Sodium binding site 3 out
of 4 in 4d1q
Go back to
Sodium Binding Sites List in 4d1q
Sodium binding site 3 out
of 4 in the Hermes Transposase Bound to Its Terminal Inverted Repeat
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Hermes Transposase Bound to Its Terminal Inverted Repeat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na1610
b:77.5
occ:1.00
|
OP2
|
L:DG6
|
2.6
|
0.4
|
1.0
|
O
|
G:LEU141
|
2.6
|
0.5
|
1.0
|
O
|
G:GLU138
|
2.7
|
0.5
|
1.0
|
O5'
|
L:DG6
|
3.7
|
0.2
|
1.0
|
C
|
G:GLU139
|
3.7
|
0.1
|
1.0
|
P
|
L:DG6
|
3.7
|
0.0
|
1.0
|
C
|
G:LEU141
|
3.7
|
0.8
|
1.0
|
C5'
|
L:DG6
|
3.8
|
0.4
|
1.0
|
C
|
G:GLU138
|
3.8
|
0.6
|
1.0
|
O
|
G:GLU139
|
3.8
|
0.5
|
1.0
|
CA
|
G:GLU139
|
3.9
|
0.4
|
1.0
|
O
|
G:LEU140
|
3.9
|
1.0
|
1.0
|
NZ
|
H:LYS91
|
4.0
|
87.1
|
1.0
|
CE
|
H:LYS91
|
4.1
|
0.8
|
1.0
|
C
|
G:LEU140
|
4.2
|
0.3
|
1.0
|
N
|
G:LEU140
|
4.2
|
0.1
|
1.0
|
N
|
G:GLU139
|
4.3
|
0.8
|
1.0
|
CA
|
G:PRO142
|
4.3
|
0.1
|
1.0
|
N
|
G:PRO142
|
4.5
|
0.4
|
1.0
|
OE1
|
G:GLU139
|
4.5
|
0.6
|
1.0
|
N
|
G:LEU141
|
4.5
|
0.7
|
1.0
|
O3'
|
L:DT5
|
4.7
|
0.9
|
1.0
|
CA
|
G:LEU140
|
4.8
|
0.1
|
1.0
|
CA
|
G:LEU141
|
4.8
|
0.4
|
1.0
|
OP1
|
L:DG6
|
4.8
|
0.9
|
1.0
|
C
|
G:PRO142
|
4.9
|
0.9
|
1.0
|
|
Sodium binding site 4 out
of 4 in 4d1q
Go back to
Sodium Binding Sites List in 4d1q
Sodium binding site 4 out
of 4 in the Hermes Transposase Bound to Its Terminal Inverted Repeat
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Hermes Transposase Bound to Its Terminal Inverted Repeat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na1610
b:59.0
occ:1.00
|
OP2
|
J:DG6
|
2.6
|
0.5
|
1.0
|
O
|
H:GLU138
|
2.6
|
0.6
|
1.0
|
O
|
H:GLU139
|
2.9
|
1.0
|
1.0
|
O
|
H:LEU141
|
2.9
|
0.0
|
1.0
|
C
|
H:GLU139
|
3.4
|
0.3
|
1.0
|
CA
|
H:GLU139
|
3.6
|
0.4
|
1.0
|
O5'
|
J:DG6
|
3.7
|
0.1
|
1.0
|
C
|
H:GLU138
|
3.7
|
1.0
|
1.0
|
P
|
J:DG6
|
3.7
|
0.4
|
1.0
|
C5'
|
J:DG6
|
3.9
|
0.7
|
1.0
|
C
|
H:LEU141
|
4.0
|
1.0
|
1.0
|
N
|
H:GLU139
|
4.1
|
0.2
|
1.0
|
NZ
|
G:LYS91
|
4.2
|
0.3
|
1.0
|
N
|
H:LEU140
|
4.5
|
0.7
|
1.0
|
CA
|
H:PRO142
|
4.6
|
0.5
|
1.0
|
OP1
|
J:DG6
|
4.7
|
0.5
|
1.0
|
C
|
H:LEU140
|
4.7
|
0.7
|
1.0
|
N
|
H:LEU141
|
4.8
|
0.9
|
1.0
|
N
|
H:PRO142
|
4.8
|
0.5
|
1.0
|
O
|
H:LEU140
|
4.8
|
0.2
|
1.0
|
C
|
H:PRO142
|
4.9
|
0.1
|
1.0
|
O3'
|
J:DT5
|
4.9
|
1.0
|
1.0
|
CE
|
G:LYS91
|
5.0
|
0.2
|
1.0
|
N
|
H:SER143
|
5.0
|
0.5
|
1.0
|
|
Reference:
A.B.Hickman,
H.E.Ewis,
X.Li,
J.A.Knapp,
T.Laver,
A.Doss,
G.Tolun,
A.C.Steven,
A.Grishaev,
A.Bax,
P.W.Atkinson,
N.L.Craig,
F.Dyda.
Structural Basis of Hat Transposon End Recognition By Hermes, An Octameric Dna Transposase From Musca Domestica. Cell(Cambridge,Mass.) V. 158 353 2014.
ISSN: ISSN 0092-8674
PubMed: 25036632
DOI: 10.1016/J.CELL.2014.05.037
Page generated: Mon Oct 7 14:49:46 2024
|