Sodium in PDB 8hcc: Crystal Structure of MTREX1-Rna Product Complex (Amp)
Enzymatic activity of Crystal Structure of MTREX1-Rna Product Complex (Amp)
All present enzymatic activity of Crystal Structure of MTREX1-Rna Product Complex (Amp):
3.1.11.2;
Protein crystallography data
The structure of Crystal Structure of MTREX1-Rna Product Complex (Amp), PDB code: 8hcc
was solved by
Y.Y.Hsiao,
K.W.Huang,
C.Y.Wu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
27.16 /
2.00
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.197,
86.433,
75.218,
90,
97.6,
90
|
|
R / Rfree (%)
|
16.7 /
21
|
Other elements in 8hcc:
The structure of Crystal Structure of MTREX1-Rna Product Complex (Amp) also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
(pdb code 8hcc). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Crystal Structure of MTREX1-Rna Product Complex (Amp), PDB code: 8hcc:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 8hcc
Go back to
Sodium Binding Sites List in 8hcc
Sodium binding site 1 out
of 5 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na304
b:26.1
occ:1.00
|
H
|
A:ALA214
|
2.5
|
23.9
|
1.0
|
|
H
|
A:GLN213
|
2.6
|
31.7
|
1.0
|
|
HB3
|
A:LYS211
|
2.9
|
35.4
|
1.0
|
|
HB2
|
A:GLN213
|
3.0
|
46.7
|
1.0
|
|
HG2
|
A:GLN213
|
3.0
|
56.6
|
1.0
|
|
HA
|
A:LYS211
|
3.2
|
31.8
|
1.0
|
|
HD2
|
A:PRO212
|
3.2
|
30.9
|
1.0
|
|
N
|
A:GLN213
|
3.3
|
26.4
|
1.0
|
|
C
|
A:LYS211
|
3.3
|
24.1
|
1.0
|
|
N
|
A:ALA214
|
3.4
|
19.9
|
1.0
|
|
CA
|
A:LYS211
|
3.5
|
26.5
|
1.0
|
|
HG12
|
A:ILE49
|
3.5
|
91.2
|
1.0
|
|
N
|
A:PRO212
|
3.6
|
25.5
|
1.0
|
|
CB
|
A:GLN213
|
3.6
|
39.0
|
1.0
|
|
CB
|
A:LYS211
|
3.6
|
29.5
|
1.0
|
|
O
|
A:LYS211
|
3.7
|
21.7
|
1.0
|
|
CG
|
A:GLN213
|
3.7
|
47.2
|
1.0
|
|
HB2
|
A:ALA214
|
3.7
|
28.2
|
1.0
|
|
HB3
|
A:ALA214
|
3.8
|
28.2
|
1.0
|
|
CD
|
A:PRO212
|
3.8
|
25.7
|
1.0
|
|
CA
|
A:GLN213
|
3.8
|
29.1
|
1.0
|
|
HG3
|
A:GLN213
|
4.1
|
56.6
|
1.0
|
|
C
|
A:GLN213
|
4.1
|
24.5
|
1.0
|
|
CB
|
A:ALA214
|
4.1
|
23.5
|
1.0
|
|
C
|
A:PRO212
|
4.2
|
26.1
|
1.0
|
|
HD3
|
A:LYS211
|
4.3
|
46.5
|
1.0
|
|
HB2
|
A:LYS211
|
4.3
|
35.4
|
1.0
|
|
CA
|
A:ALA214
|
4.3
|
21.3
|
1.0
|
|
HG2
|
A:LYS211
|
4.4
|
39.9
|
1.0
|
|
HG2
|
A:PRO212
|
4.4
|
33.6
|
1.0
|
|
HG23
|
A:ILE49
|
4.4
|
87.8
|
1.0
|
|
CG1
|
A:ILE49
|
4.5
|
76.0
|
1.0
|
|
CA
|
A:PRO212
|
4.5
|
25.8
|
1.0
|
|
HD3
|
A:PRO212
|
4.5
|
30.9
|
1.0
|
|
HB3
|
A:GLN213
|
4.5
|
46.7
|
1.0
|
|
CG
|
A:LYS211
|
4.5
|
33.2
|
1.0
|
|
CG
|
A:PRO212
|
4.7
|
28.0
|
1.0
|
|
H
|
A:LEU215
|
4.7
|
26.8
|
1.0
|
|
HD11
|
A:ILE49
|
4.7
|
91.7
|
1.0
|
|
HA
|
A:GLN213
|
4.8
|
35.0
|
1.0
|
|
HG21
|
A:ILE49
|
4.8
|
87.8
|
1.0
|
|
HG13
|
A:ILE49
|
4.8
|
91.2
|
1.0
|
|
CD
|
A:LYS211
|
4.9
|
38.7
|
1.0
|
|
HA
|
A:ALA214
|
4.9
|
25.5
|
1.0
|
|
N
|
A:LYS211
|
5.0
|
24.8
|
1.0
|
|
CD
|
A:GLN213
|
5.0
|
52.4
|
1.0
|
|
HD13
|
A:ILE49
|
5.0
|
91.7
|
1.0
|
|
Sodium binding site 2 out
of 5 in 8hcc
Go back to
Sodium Binding Sites List in 8hcc
Sodium binding site 2 out
of 5 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na304
b:31.9
occ:1.00
|
H
|
B:ALA214
|
2.5
|
29.7
|
1.0
|
|
H
|
B:GLN213
|
2.8
|
32.8
|
1.0
|
|
HB3
|
B:LYS211
|
2.8
|
33.1
|
1.0
|
|
HB2
|
B:GLN213
|
3.1
|
45.4
|
1.0
|
|
HA
|
B:LYS211
|
3.1
|
31.8
|
1.0
|
|
N
|
B:ALA214
|
3.3
|
24.8
|
1.0
|
|
C
|
B:LYS211
|
3.3
|
25.1
|
1.0
|
|
HD2
|
B:PRO212
|
3.4
|
30.1
|
1.0
|
|
N
|
B:GLN213
|
3.4
|
27.3
|
1.0
|
|
HB2
|
B:ALA214
|
3.4
|
28.2
|
1.0
|
|
CA
|
B:LYS211
|
3.5
|
26.5
|
1.0
|
|
CB
|
B:LYS211
|
3.5
|
27.6
|
1.0
|
|
O
|
B:LYS211
|
3.6
|
26.1
|
1.0
|
|
HB3
|
B:ALA214
|
3.6
|
28.2
|
1.0
|
|
N
|
B:PRO212
|
3.7
|
26.1
|
1.0
|
|
HD12
|
B:ILE49
|
3.9
|
73.5
|
1.0
|
|
CB
|
B:GLN213
|
3.9
|
37.8
|
1.0
|
|
CB
|
B:ALA214
|
3.9
|
23.5
|
1.0
|
|
HG2
|
B:LYS211
|
3.9
|
36.7
|
1.0
|
|
CD
|
B:PRO212
|
4.0
|
25.1
|
1.0
|
|
CA
|
B:GLN213
|
4.0
|
29.2
|
1.0
|
|
C
|
B:GLN213
|
4.1
|
24.8
|
1.0
|
|
CA
|
B:ALA214
|
4.2
|
23.9
|
1.0
|
|
CG
|
B:LYS211
|
4.3
|
30.6
|
1.0
|
|
HB2
|
B:LYS211
|
4.3
|
33.1
|
1.0
|
|
C
|
B:PRO212
|
4.3
|
27.7
|
1.0
|
|
HD3
|
B:LYS211
|
4.4
|
44.1
|
1.0
|
|
HG2
|
B:PRO212
|
4.4
|
31.0
|
1.0
|
|
HB3
|
B:GLN213
|
4.5
|
45.4
|
1.0
|
|
CD1
|
B:ILE49
|
4.5
|
61.3
|
1.0
|
|
HD11
|
B:ILE49
|
4.5
|
73.5
|
1.0
|
|
CA
|
B:PRO212
|
4.6
|
25.7
|
1.0
|
|
HG3
|
B:GLN213
|
4.6
|
56.6
|
1.0
|
|
HD13
|
B:ILE49
|
4.6
|
73.5
|
1.0
|
|
HD3
|
B:PRO212
|
4.7
|
30.1
|
1.0
|
|
H
|
B:LEU215
|
4.7
|
29.6
|
1.0
|
|
HA
|
B:ALA214
|
4.7
|
28.7
|
1.0
|
|
CG
|
B:PRO212
|
4.8
|
25.9
|
1.0
|
|
CG
|
B:GLN213
|
4.8
|
47.2
|
1.0
|
|
HB1
|
B:ALA214
|
4.8
|
28.2
|
1.0
|
|
OE1
|
B:GLN213
|
4.9
|
57.7
|
1.0
|
|
CD
|
B:LYS211
|
4.9
|
36.8
|
1.0
|
|
N
|
B:LYS211
|
4.9
|
26.6
|
1.0
|
|
HA
|
B:GLN213
|
4.9
|
35.0
|
1.0
|
|
HG23
|
B:ILE49
|
5.0
|
74.5
|
1.0
|
|
Sodium binding site 3 out
of 5 in 8hcc
Go back to
Sodium Binding Sites List in 8hcc
Sodium binding site 3 out
of 5 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na305
b:40.6
occ:1.00
|
HG2
|
B:ARG140
|
2.5
|
54.1
|
1.0
|
|
HE
|
B:ARG140
|
2.7
|
69.7
|
1.0
|
|
OE1
|
B:GLU137
|
2.7
|
27.9
|
1.0
|
|
O
|
B:GLU137
|
2.8
|
24.9
|
1.0
|
|
HA
|
B:GLU137
|
2.9
|
22.3
|
1.0
|
|
HB3
|
B:PHE100
|
2.9
|
27.1
|
1.0
|
|
HD2
|
B:ARG140
|
3.1
|
61.3
|
1.0
|
|
NE
|
B:ARG140
|
3.1
|
58.1
|
1.0
|
|
HB3
|
B:GLU137
|
3.2
|
23.5
|
1.0
|
|
CG
|
B:ARG140
|
3.2
|
45.1
|
1.0
|
|
CD
|
B:ARG140
|
3.3
|
51.1
|
1.0
|
|
HG3
|
B:ARG140
|
3.4
|
54.1
|
1.0
|
|
O
|
B:HOH465
|
3.4
|
53.4
|
1.0
|
|
O
|
B:HOH409
|
3.5
|
27.7
|
1.0
|
|
HD21
|
B:LEU141
|
3.5
|
33.8
|
1.0
|
|
HD1
|
B:PHE100
|
3.5
|
31.2
|
1.0
|
|
C
|
B:GLU137
|
3.5
|
20.9
|
1.0
|
|
CA
|
B:GLU137
|
3.5
|
18.6
|
1.0
|
|
O
|
B:PHE100
|
3.7
|
24.0
|
1.0
|
|
CB
|
B:GLU137
|
3.8
|
19.6
|
1.0
|
|
HD23
|
B:LEU141
|
3.8
|
33.8
|
1.0
|
|
CB
|
B:PHE100
|
3.8
|
22.6
|
1.0
|
|
CD1
|
B:PHE100
|
3.8
|
26.0
|
1.0
|
|
CD
|
B:GLU137
|
3.8
|
27.0
|
1.0
|
|
HG
|
B:LEU141
|
3.9
|
36.0
|
1.0
|
|
CG
|
B:PHE100
|
4.0
|
23.7
|
1.0
|
|
CD2
|
B:LEU141
|
4.0
|
28.1
|
1.0
|
|
CZ
|
B:ARG140
|
4.2
|
60.8
|
1.0
|
|
HD3
|
B:ARG140
|
4.2
|
61.3
|
1.0
|
|
HH11
|
B:ARG140
|
4.3
|
71.7
|
1.0
|
|
HB2
|
B:PHE100
|
4.3
|
27.1
|
1.0
|
|
CG
|
B:GLU137
|
4.4
|
24.6
|
1.0
|
|
C
|
B:PHE100
|
4.4
|
23.9
|
1.0
|
|
CG
|
B:LEU141
|
4.5
|
30.0
|
1.0
|
|
CB
|
B:ARG140
|
4.5
|
40.7
|
1.0
|
|
HB2
|
B:GLU137
|
4.6
|
23.5
|
1.0
|
|
NH1
|
B:ARG140
|
4.6
|
59.8
|
1.0
|
|
HB3
|
B:ARG140
|
4.7
|
48.8
|
1.0
|
|
CE1
|
B:PHE100
|
4.7
|
25.4
|
1.0
|
|
H
|
B:ARG140
|
4.7
|
42.5
|
1.0
|
|
CA
|
B:PHE100
|
4.7
|
22.4
|
1.0
|
|
N
|
B:LEU138
|
4.8
|
20.9
|
1.0
|
|
HD11
|
B:LEU141
|
4.8
|
37.8
|
1.0
|
|
OE2
|
B:GLU137
|
4.8
|
25.9
|
1.0
|
|
N
|
B:GLU137
|
4.8
|
19.9
|
1.0
|
|
HD22
|
B:LEU141
|
4.9
|
33.8
|
1.0
|
|
HG2
|
B:GLU137
|
4.9
|
29.5
|
1.0
|
|
O
|
B:THR136
|
4.9
|
25.8
|
1.0
|
|
HE1
|
B:PHE100
|
4.9
|
30.4
|
1.0
|
|
CD2
|
B:PHE100
|
5.0
|
21.9
|
1.0
|
|
Sodium binding site 4 out
of 5 in 8hcc
Go back to
Sodium Binding Sites List in 8hcc
Sodium binding site 4 out
of 5 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na304
b:35.4
occ:1.00
|
H
|
C:ALA214
|
2.4
|
40.1
|
1.0
|
|
HB2
|
C:GLN213
|
2.7
|
58.5
|
1.0
|
|
H
|
C:GLN213
|
2.8
|
42.1
|
1.0
|
|
HB3
|
C:LYS211
|
2.8
|
49.5
|
1.0
|
|
HZ2
|
C:LYS211
|
3.2
|
74.0
|
1.0
|
|
N
|
C:ALA214
|
3.2
|
33.4
|
1.0
|
|
HA
|
C:LYS211
|
3.3
|
42.0
|
1.0
|
|
N
|
C:GLN213
|
3.3
|
35.1
|
1.0
|
|
HD2
|
C:PRO212
|
3.4
|
41.7
|
1.0
|
|
C
|
C:LYS211
|
3.5
|
33.1
|
1.0
|
|
HB2
|
C:ALA214
|
3.5
|
40.0
|
1.0
|
|
CB
|
C:GLN213
|
3.6
|
48.8
|
1.0
|
|
CB
|
C:LYS211
|
3.6
|
41.3
|
1.0
|
|
CA
|
C:LYS211
|
3.6
|
35.0
|
1.0
|
|
HB3
|
C:ALA214
|
3.7
|
40.0
|
1.0
|
|
N
|
C:PRO212
|
3.7
|
34.6
|
1.0
|
|
O
|
C:LYS211
|
3.8
|
34.4
|
1.0
|
|
CA
|
C:GLN213
|
3.8
|
39.4
|
1.0
|
|
NZ
|
C:LYS211
|
3.9
|
61.7
|
1.0
|
|
HZ1
|
C:LYS211
|
3.9
|
74.0
|
1.0
|
|
HE3
|
C:LYS211
|
3.9
|
73.1
|
1.0
|
|
CB
|
C:ALA214
|
4.0
|
33.4
|
1.0
|
|
HG2
|
C:LYS211
|
4.0
|
58.7
|
1.0
|
|
C
|
C:GLN213
|
4.0
|
33.5
|
1.0
|
|
CD
|
C:PRO212
|
4.0
|
34.7
|
1.0
|
|
HB3
|
C:GLN213
|
4.2
|
58.5
|
1.0
|
|
CA
|
C:ALA214
|
4.2
|
32.0
|
1.0
|
|
C
|
C:PRO212
|
4.2
|
34.7
|
1.0
|
|
HG2
|
C:GLN213
|
4.3
|
67.9
|
1.0
|
|
HB2
|
C:LYS211
|
4.3
|
49.5
|
1.0
|
|
CG
|
C:LYS211
|
4.3
|
48.9
|
1.0
|
|
HD3
|
C:PRO212
|
4.4
|
41.7
|
1.0
|
|
CE
|
C:LYS211
|
4.4
|
60.9
|
1.0
|
|
CG
|
C:GLN213
|
4.4
|
56.6
|
1.0
|
|
CA
|
C:PRO212
|
4.6
|
34.6
|
1.0
|
|
HG3
|
C:GLN213
|
4.6
|
67.9
|
1.0
|
|
HZ3
|
C:LYS211
|
4.6
|
74.0
|
1.0
|
|
H
|
C:LEU215
|
4.6
|
39.2
|
1.0
|
|
HA
|
C:GLN213
|
4.7
|
47.2
|
1.0
|
|
HA
|
C:ALA214
|
4.8
|
38.4
|
1.0
|
|
HB1
|
C:ALA214
|
4.9
|
40.0
|
1.0
|
|
Sodium binding site 5 out
of 5 in 8hcc
Go back to
Sodium Binding Sites List in 8hcc
Sodium binding site 5 out
of 5 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na304
b:42.3
occ:1.00
|
H
|
D:ALA214
|
2.4
|
36.6
|
1.0
|
|
HB3
|
D:LYS211
|
2.7
|
38.9
|
1.0
|
|
H
|
D:GLN213
|
3.0
|
41.2
|
1.0
|
|
HB3
|
D:GLN213
|
3.0
|
52.1
|
1.0
|
|
HA
|
D:LYS211
|
3.2
|
35.3
|
1.0
|
|
N
|
D:ALA214
|
3.2
|
30.5
|
1.0
|
|
HB2
|
D:ALA214
|
3.3
|
33.8
|
1.0
|
|
C
|
D:LYS211
|
3.4
|
27.6
|
1.0
|
|
CB
|
D:LYS211
|
3.5
|
32.4
|
1.0
|
|
HB3
|
D:ALA214
|
3.5
|
33.8
|
1.0
|
|
N
|
D:GLN213
|
3.5
|
34.3
|
1.0
|
|
CA
|
D:LYS211
|
3.5
|
29.4
|
1.0
|
|
HD2
|
D:PRO212
|
3.6
|
39.0
|
1.0
|
|
HG2
|
D:LYS211
|
3.6
|
42.7
|
1.0
|
|
O
|
D:LYS211
|
3.7
|
24.9
|
1.0
|
|
N
|
D:PRO212
|
3.8
|
31.0
|
1.0
|
|
CB
|
D:GLN213
|
3.8
|
43.5
|
1.0
|
|
CB
|
D:ALA214
|
3.8
|
28.2
|
1.0
|
|
HB2
|
D:GLN213
|
4.0
|
52.1
|
1.0
|
|
CA
|
D:GLN213
|
4.0
|
35.7
|
1.0
|
|
C
|
D:GLN213
|
4.1
|
29.4
|
1.0
|
|
CG
|
D:LYS211
|
4.1
|
35.6
|
1.0
|
|
CD
|
D:PRO212
|
4.1
|
32.5
|
1.0
|
|
CA
|
D:ALA214
|
4.1
|
28.1
|
1.0
|
|
HB2
|
D:LYS211
|
4.3
|
38.9
|
1.0
|
|
HG23
|
D:ILE49
|
4.3
|
83.3
|
1.0
|
|
C
|
D:PRO212
|
4.3
|
34.0
|
1.0
|
|
HE3
|
D:LYS211
|
4.3
|
56.6
|
1.0
|
|
HE2
|
D:LYS211
|
4.4
|
56.6
|
1.0
|
|
HD3
|
D:PRO212
|
4.5
|
39.0
|
1.0
|
|
CA
|
D:PRO212
|
4.6
|
32.0
|
1.0
|
|
HA
|
D:ALA214
|
4.7
|
33.7
|
1.0
|
|
H
|
D:LEU215
|
4.7
|
32.8
|
1.0
|
|
HB1
|
D:ALA214
|
4.7
|
33.8
|
1.0
|
|
CE
|
D:LYS211
|
4.7
|
47.1
|
1.0
|
|
HG3
|
D:LYS211
|
4.8
|
42.7
|
1.0
|
|
HD12
|
D:ILE49
|
4.9
|
80.8
|
1.0
|
|
HA
|
D:GLN213
|
4.9
|
42.8
|
1.0
|
|
N
|
D:LYS211
|
5.0
|
28.2
|
1.0
|
|
Reference:
Y.Y.Hsiao,
K.W.Huang,
C.Y.Wu.
Molecular Insight Into the Specific Enzymatic Properties of TREX1 Revealing the Diverse Functions in Processing Rna and Dna/Rna Hybrids. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAD910
Page generated: Wed Oct 9 12:14:32 2024
|
