Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Crystal Structure of MTREX1-Rna Product Complex (Amp), PDB code: 8hcc:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 8hcc
Go back to
Magnesium Binding Sites List in 8hcc
Magnesium binding site 1 out
of 8 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg302
b:19.9
occ:1.00
|
OE1
|
A:GLU20
|
2.1
|
19.7
|
1.0
|
|
OD2
|
A:ASP18
|
2.1
|
20.6
|
1.0
|
|
O3P
|
A:AMP301
|
2.2
|
19.3
|
1.0
|
|
OD2
|
A:ASP200
|
2.2
|
17.5
|
1.0
|
|
O2P
|
A:AMP301
|
2.9
|
25.0
|
1.0
|
|
HB2
|
A:ASP200
|
3.0
|
20.9
|
1.0
|
|
CG
|
A:ASP18
|
3.0
|
22.1
|
1.0
|
|
CD
|
A:GLU20
|
3.1
|
19.8
|
1.0
|
|
P
|
A:AMP301
|
3.1
|
24.5
|
1.0
|
|
HA
|
A:HIS195
|
3.1
|
28.4
|
1.0
|
|
CG
|
A:ASP200
|
3.1
|
19.2
|
1.0
|
|
OD1
|
A:ASP18
|
3.3
|
20.3
|
1.0
|
|
CB
|
A:ASP200
|
3.4
|
17.4
|
1.0
|
|
OE2
|
A:GLU20
|
3.4
|
19.9
|
1.0
|
|
MG
|
A:MG303
|
3.5
|
23.0
|
1.0
|
|
HB3
|
A:ASP200
|
3.5
|
20.9
|
1.0
|
|
O
|
A:HOH535
|
3.7
|
21.2
|
1.0
|
|
HA
|
A:ALA197
|
3.8
|
20.9
|
1.0
|
|
O
|
A:LEU19
|
3.8
|
17.7
|
1.0
|
|
O1P
|
A:AMP301
|
4.0
|
23.0
|
1.0
|
|
O
|
A:THR196
|
4.0
|
20.2
|
1.0
|
|
CA
|
A:HIS195
|
4.0
|
23.7
|
1.0
|
|
H5'2
|
A:AMP301
|
4.1
|
27.7
|
1.0
|
|
H
|
A:HIS195
|
4.2
|
28.5
|
1.0
|
|
C
|
A:HIS195
|
4.3
|
25.5
|
1.0
|
|
HG2
|
A:GLU20
|
4.3
|
24.3
|
1.0
|
|
C
|
A:THR196
|
4.3
|
18.9
|
1.0
|
|
OD1
|
A:ASP200
|
4.3
|
18.7
|
1.0
|
|
HD1
|
A:HIS195
|
4.3
|
28.9
|
1.0
|
|
CG
|
A:GLU20
|
4.3
|
20.2
|
1.0
|
|
O
|
A:HOH492
|
4.4
|
17.1
|
1.0
|
|
CB
|
A:ASP18
|
4.4
|
21.2
|
1.0
|
|
O5'
|
A:AMP301
|
4.4
|
24.1
|
1.0
|
|
N
|
A:THR196
|
4.4
|
21.2
|
1.0
|
|
O
|
A:HOH424
|
4.5
|
21.9
|
1.0
|
|
HB3
|
A:ASP18
|
4.5
|
25.4
|
1.0
|
|
N
|
A:HIS195
|
4.6
|
23.8
|
1.0
|
|
C
|
A:LEU19
|
4.6
|
17.7
|
1.0
|
|
H
|
A:THR196
|
4.6
|
25.4
|
1.0
|
|
CA
|
A:ALA197
|
4.7
|
17.4
|
1.0
|
|
N
|
A:ALA197
|
4.7
|
16.2
|
1.0
|
|
HA
|
A:GLU20
|
4.7
|
22.9
|
1.0
|
|
H
|
A:LEU19
|
4.7
|
22.9
|
1.0
|
|
C5'
|
A:AMP301
|
4.7
|
23.1
|
1.0
|
|
H
|
A:ASP200
|
4.8
|
19.2
|
1.0
|
|
O
|
A:HOH490
|
4.8
|
23.9
|
1.0
|
|
HB2
|
A:ASP18
|
4.8
|
25.4
|
1.0
|
|
O
|
A:HIS195
|
4.9
|
27.3
|
1.0
|
|
HG3
|
A:GLU20
|
4.9
|
24.3
|
1.0
|
|
CA
|
A:ASP200
|
4.9
|
16.5
|
1.0
|
|
CA
|
A:THR196
|
4.9
|
19.6
|
1.0
|
|
ND1
|
A:HIS195
|
5.0
|
24.1
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 8hcc
Go back to
Magnesium Binding Sites List in 8hcc
Magnesium binding site 2 out
of 8 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:23.0
occ:1.00
|
O
|
A:HOH492
|
2.0
|
17.1
|
1.0
|
|
OD1
|
A:ASP18
|
2.0
|
20.3
|
1.0
|
|
O3P
|
A:AMP301
|
2.1
|
19.3
|
1.0
|
|
O
|
A:HOH490
|
2.1
|
23.9
|
1.0
|
|
O
|
A:HOH433
|
2.2
|
21.8
|
1.0
|
|
O
|
A:HOH535
|
2.2
|
21.2
|
1.0
|
|
CG
|
A:ASP18
|
3.1
|
22.1
|
1.0
|
|
P
|
A:AMP301
|
3.4
|
24.5
|
1.0
|
|
MG
|
A:MG302
|
3.5
|
19.9
|
1.0
|
|
OD2
|
A:ASP18
|
3.6
|
20.6
|
1.0
|
|
O1P
|
A:AMP301
|
3.8
|
23.0
|
1.0
|
|
H
|
A:LEU19
|
3.8
|
22.9
|
1.0
|
|
H5'2
|
A:AMP301
|
3.9
|
27.7
|
1.0
|
|
OD2
|
A:ASP130
|
3.9
|
28.1
|
1.0
|
|
O
|
A:LEU19
|
3.9
|
17.7
|
1.0
|
|
O5'
|
A:AMP301
|
4.0
|
24.1
|
1.0
|
|
H5'1
|
A:AMP301
|
4.0
|
27.7
|
1.0
|
|
O
|
A:HOH441
|
4.0
|
16.6
|
1.0
|
|
O
|
A:HOH424
|
4.1
|
21.9
|
1.0
|
|
OD1
|
A:ASP130
|
4.1
|
30.9
|
1.0
|
|
O
|
A:HIS124
|
4.1
|
23.3
|
1.0
|
|
C5'
|
A:AMP301
|
4.2
|
23.1
|
1.0
|
|
HA
|
A:ASP18
|
4.2
|
24.7
|
1.0
|
|
O
|
A:HOH546
|
4.2
|
37.8
|
1.0
|
|
O
|
A:HOH531
|
4.3
|
21.6
|
1.0
|
|
CB
|
A:ASP18
|
4.4
|
21.2
|
1.0
|
|
CG
|
A:ASP130
|
4.4
|
27.9
|
1.0
|
|
HB3
|
A:HIS124
|
4.5
|
22.6
|
1.0
|
|
N
|
A:LEU19
|
4.5
|
19.0
|
1.0
|
|
HB2
|
A:ASP18
|
4.5
|
25.4
|
1.0
|
|
O2P
|
A:AMP301
|
4.5
|
25.0
|
1.0
|
|
HB3
|
A:ASP200
|
4.6
|
20.9
|
1.0
|
|
CA
|
A:ASP18
|
4.8
|
20.6
|
1.0
|
|
O
|
A:HOH560
|
4.8
|
44.0
|
1.0
|
|
OD2
|
A:ASP200
|
4.8
|
17.5
|
1.0
|
|
C
|
A:LEU19
|
5.0
|
17.7
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 8hcc
Go back to
Magnesium Binding Sites List in 8hcc
Magnesium binding site 3 out
of 8 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg302
b:23.4
occ:1.00
|
OE1
|
B:GLU20
|
2.0
|
24.4
|
1.0
|
|
OD2
|
B:ASP200
|
2.1
|
22.2
|
1.0
|
|
OD2
|
B:ASP18
|
2.2
|
21.3
|
1.0
|
|
O2P
|
B:AMP301
|
2.3
|
24.1
|
1.0
|
|
O1P
|
B:AMP301
|
2.8
|
33.0
|
1.0
|
|
CD
|
B:GLU20
|
3.0
|
25.2
|
1.0
|
|
P
|
B:AMP301
|
3.0
|
28.5
|
1.0
|
|
HA
|
B:HIS195
|
3.0
|
36.2
|
1.0
|
|
CG
|
B:ASP18
|
3.1
|
20.1
|
1.0
|
|
HB2
|
B:ASP200
|
3.1
|
26.1
|
1.0
|
|
CG
|
B:ASP200
|
3.1
|
23.0
|
1.0
|
|
OE2
|
B:GLU20
|
3.3
|
23.6
|
1.0
|
|
OD1
|
B:ASP18
|
3.4
|
19.5
|
1.0
|
|
CB
|
B:ASP200
|
3.5
|
21.8
|
1.0
|
|
MG
|
B:MG303
|
3.5
|
21.5
|
1.0
|
|
HB3
|
B:ASP200
|
3.6
|
26.1
|
1.0
|
|
O
|
B:HOH509
|
3.8
|
19.1
|
1.0
|
|
HA
|
B:ALA197
|
3.9
|
22.9
|
1.0
|
|
H5'2
|
B:AMP301
|
3.9
|
31.8
|
1.0
|
|
CA
|
B:HIS195
|
3.9
|
30.2
|
1.0
|
|
O3P
|
B:AMP301
|
4.0
|
24.1
|
1.0
|
|
O
|
B:LEU19
|
4.0
|
17.4
|
1.0
|
|
O
|
B:THR196
|
4.0
|
20.1
|
1.0
|
|
H
|
B:HIS195
|
4.1
|
35.9
|
1.0
|
|
C
|
B:HIS195
|
4.2
|
28.7
|
1.0
|
|
HD1
|
B:HIS195
|
4.2
|
43.8
|
1.0
|
|
O5'
|
B:AMP301
|
4.3
|
27.8
|
1.0
|
|
OD1
|
B:ASP200
|
4.3
|
23.5
|
1.0
|
|
HG2
|
B:GLU20
|
4.3
|
27.5
|
1.0
|
|
CG
|
B:GLU20
|
4.3
|
22.9
|
1.0
|
|
C
|
B:THR196
|
4.3
|
21.7
|
1.0
|
|
O
|
B:HOH466
|
4.5
|
17.7
|
1.0
|
|
N
|
B:THR196
|
4.5
|
25.8
|
1.0
|
|
CB
|
B:ASP18
|
4.5
|
20.6
|
1.0
|
|
N
|
B:HIS195
|
4.5
|
29.9
|
1.0
|
|
C5'
|
B:AMP301
|
4.6
|
26.5
|
1.0
|
|
O
|
B:HOH411
|
4.6
|
26.3
|
1.0
|
|
HB3
|
B:ASP18
|
4.6
|
24.8
|
1.0
|
|
CA
|
B:ALA197
|
4.7
|
19.1
|
1.0
|
|
N
|
B:ALA197
|
4.7
|
20.4
|
1.0
|
|
C
|
B:LEU19
|
4.7
|
17.2
|
1.0
|
|
H
|
B:THR196
|
4.7
|
31.0
|
1.0
|
|
HG3
|
B:GLU20
|
4.8
|
27.5
|
1.0
|
|
O
|
B:HIS195
|
4.8
|
29.1
|
1.0
|
|
O
|
B:HOH462
|
4.8
|
24.3
|
1.0
|
|
HA
|
B:GLU20
|
4.8
|
20.8
|
1.0
|
|
H
|
B:ASP200
|
4.9
|
19.9
|
1.0
|
|
H
|
B:LEU19
|
4.9
|
24.6
|
1.0
|
|
ND1
|
B:HIS195
|
4.9
|
36.5
|
1.0
|
|
HB2
|
B:ASP18
|
4.9
|
24.8
|
1.0
|
|
HB3
|
B:HIS195
|
4.9
|
39.0
|
1.0
|
|
CA
|
B:THR196
|
5.0
|
24.8
|
1.0
|
|
CB
|
B:HIS195
|
5.0
|
32.5
|
1.0
|
|
CA
|
B:ASP200
|
5.0
|
18.7
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 8hcc
Go back to
Magnesium Binding Sites List in 8hcc
Magnesium binding site 4 out
of 8 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:21.5
occ:1.00
|
O2P
|
B:AMP301
|
2.0
|
24.1
|
1.0
|
|
O
|
B:HOH509
|
2.0
|
19.1
|
1.0
|
|
OD1
|
B:ASP18
|
2.0
|
19.5
|
1.0
|
|
O
|
B:HOH466
|
2.1
|
17.7
|
1.0
|
|
O
|
B:HOH462
|
2.1
|
24.3
|
1.0
|
|
O
|
B:HOH423
|
2.1
|
21.8
|
1.0
|
|
CG
|
B:ASP18
|
3.1
|
20.1
|
1.0
|
|
P
|
B:AMP301
|
3.3
|
28.5
|
1.0
|
|
MG
|
B:MG302
|
3.5
|
23.4
|
1.0
|
|
OD2
|
B:ASP18
|
3.6
|
21.3
|
1.0
|
|
O3P
|
B:AMP301
|
3.8
|
24.1
|
1.0
|
|
H
|
B:LEU19
|
3.9
|
24.6
|
1.0
|
|
H5'1
|
B:AMP301
|
3.9
|
31.8
|
1.0
|
|
H5'2
|
B:AMP301
|
3.9
|
31.8
|
1.0
|
|
OD2
|
B:ASP130
|
4.0
|
25.9
|
1.0
|
|
O
|
B:LEU19
|
4.0
|
17.4
|
1.0
|
|
O5'
|
B:AMP301
|
4.1
|
27.8
|
1.0
|
|
O
|
B:HOH411
|
4.1
|
26.3
|
1.0
|
|
O
|
B:HOH425
|
4.1
|
17.4
|
1.0
|
|
C5'
|
B:AMP301
|
4.2
|
26.5
|
1.0
|
|
O
|
B:HIS124
|
4.2
|
24.5
|
1.0
|
|
OD1
|
B:ASP130
|
4.2
|
26.8
|
1.0
|
|
HA
|
B:ASP18
|
4.2
|
23.3
|
1.0
|
|
O
|
B:HOH534
|
4.3
|
21.1
|
1.0
|
|
O
|
B:HOH499
|
4.3
|
33.0
|
1.0
|
|
CB
|
B:ASP18
|
4.4
|
20.6
|
1.0
|
|
CG
|
B:ASP130
|
4.5
|
25.9
|
1.0
|
|
HB3
|
B:HIS124
|
4.5
|
26.3
|
1.0
|
|
HB2
|
B:ASP18
|
4.5
|
24.8
|
1.0
|
|
HB3
|
B:ASP200
|
4.6
|
26.1
|
1.0
|
|
O1P
|
B:AMP301
|
4.6
|
33.0
|
1.0
|
|
N
|
B:LEU19
|
4.6
|
20.5
|
1.0
|
|
OD2
|
B:ASP200
|
4.7
|
22.2
|
1.0
|
|
CA
|
B:ASP18
|
4.8
|
19.4
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 8hcc
Go back to
Magnesium Binding Sites List in 8hcc
Magnesium binding site 5 out
of 8 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg302
b:28.6
occ:1.00
|
O3P
|
C:AMP301
|
1.9
|
29.0
|
1.0
|
|
OD2
|
C:ASP200
|
2.0
|
27.4
|
1.0
|
|
OD2
|
C:ASP18
|
2.1
|
28.9
|
1.0
|
|
OE2
|
C:GLU20
|
2.1
|
29.8
|
1.0
|
|
O
|
C:HOH429
|
2.9
|
47.2
|
1.0
|
|
CG
|
C:ASP18
|
3.0
|
28.2
|
1.0
|
|
CG
|
C:ASP200
|
3.0
|
26.3
|
1.0
|
|
CD
|
C:GLU20
|
3.1
|
30.8
|
1.0
|
|
HB2
|
C:ASP200
|
3.2
|
29.8
|
1.0
|
|
HA
|
C:HIS195
|
3.3
|
48.1
|
1.0
|
|
P
|
C:AMP301
|
3.3
|
34.1
|
1.0
|
|
OD1
|
C:ASP18
|
3.4
|
27.6
|
1.0
|
|
OE1
|
C:GLU20
|
3.4
|
30.9
|
1.0
|
|
CB
|
C:ASP200
|
3.5
|
24.8
|
1.0
|
|
MG
|
C:MG303
|
3.5
|
32.3
|
1.0
|
|
HB3
|
C:ASP200
|
3.6
|
29.8
|
1.0
|
|
O2P
|
C:AMP301
|
3.8
|
33.5
|
1.0
|
|
O
|
C:HOH488
|
3.8
|
25.5
|
1.0
|
|
HA
|
C:ALA197
|
3.9
|
26.9
|
1.0
|
|
O
|
C:LEU19
|
4.0
|
31.7
|
1.0
|
|
O
|
C:THR196
|
4.0
|
27.5
|
1.0
|
|
O5'
|
C:AMP301
|
4.0
|
31.6
|
1.0
|
|
CA
|
C:HIS195
|
4.1
|
40.1
|
1.0
|
|
H5'2
|
C:AMP301
|
4.1
|
39.1
|
1.0
|
|
OD1
|
C:ASP200
|
4.2
|
26.7
|
1.0
|
|
O
|
C:HOH428
|
4.3
|
23.2
|
1.0
|
|
O
|
C:HOH404
|
4.3
|
38.4
|
1.0
|
|
C
|
C:HIS195
|
4.3
|
34.0
|
1.0
|
|
HG2
|
C:GLU20
|
4.3
|
35.9
|
1.0
|
|
C
|
C:THR196
|
4.3
|
24.6
|
1.0
|
|
CG
|
C:GLU20
|
4.4
|
29.9
|
1.0
|
|
O1P
|
C:AMP301
|
4.4
|
34.5
|
1.0
|
|
CB
|
C:ASP18
|
4.4
|
26.3
|
1.0
|
|
H
|
C:HIS195
|
4.4
|
47.8
|
1.0
|
|
HB3
|
C:ASP18
|
4.5
|
31.6
|
1.0
|
|
N
|
C:THR196
|
4.5
|
28.7
|
1.0
|
|
C5'
|
C:AMP301
|
4.7
|
32.6
|
1.0
|
|
C
|
C:LEU19
|
4.7
|
27.9
|
1.0
|
|
CA
|
C:ALA197
|
4.7
|
22.4
|
1.0
|
|
N
|
C:ALA197
|
4.7
|
21.0
|
1.0
|
|
HA
|
C:GLU20
|
4.8
|
30.0
|
1.0
|
|
N
|
C:HIS195
|
4.8
|
39.8
|
1.0
|
|
H
|
C:THR196
|
4.8
|
34.4
|
1.0
|
|
O
|
C:HIS195
|
4.8
|
35.2
|
1.0
|
|
H
|
C:ASP200
|
4.8
|
27.0
|
1.0
|
|
HB2
|
C:ASP18
|
4.9
|
31.6
|
1.0
|
|
HO3'
|
C:AMP301
|
4.9
|
36.5
|
1.0
|
|
HG3
|
C:GLU20
|
4.9
|
35.9
|
1.0
|
|
H
|
C:LEU19
|
5.0
|
27.6
|
1.0
|
|
CA
|
C:THR196
|
5.0
|
26.6
|
1.0
|
|
CA
|
C:ASP200
|
5.0
|
23.9
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 8hcc
Go back to
Magnesium Binding Sites List in 8hcc
Magnesium binding site 6 out
of 8 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg303
b:32.3
occ:1.00
|
O
|
C:HOH427
|
2.0
|
29.9
|
1.0
|
|
OD1
|
C:ASP18
|
2.1
|
27.6
|
1.0
|
|
O
|
C:HOH488
|
2.1
|
25.5
|
1.0
|
|
O
|
C:HOH428
|
2.1
|
23.2
|
1.0
|
|
O3P
|
C:AMP301
|
2.2
|
29.0
|
1.0
|
|
O1P
|
C:AMP301
|
2.4
|
34.5
|
1.0
|
|
P
|
C:AMP301
|
2.8
|
34.1
|
1.0
|
|
CG
|
C:ASP18
|
3.1
|
28.2
|
1.0
|
|
MG
|
C:MG302
|
3.5
|
28.6
|
1.0
|
|
OD2
|
C:ASP18
|
3.6
|
28.9
|
1.0
|
|
H5'2
|
C:AMP301
|
3.7
|
39.1
|
1.0
|
|
O
|
C:HOH404
|
3.8
|
38.4
|
1.0
|
|
OD2
|
C:ASP130
|
3.9
|
30.9
|
1.0
|
|
H
|
C:LEU19
|
4.0
|
27.6
|
1.0
|
|
O2P
|
C:AMP301
|
4.0
|
33.5
|
1.0
|
|
O
|
C:HOH446
|
4.0
|
26.1
|
1.0
|
|
O5'
|
C:AMP301
|
4.0
|
31.6
|
1.0
|
|
H5'1
|
C:AMP301
|
4.0
|
39.1
|
1.0
|
|
O
|
C:LEU19
|
4.1
|
31.7
|
1.0
|
|
OD1
|
C:ASP130
|
4.1
|
32.2
|
1.0
|
|
C5'
|
C:AMP301
|
4.1
|
32.6
|
1.0
|
|
O
|
C:HIS124
|
4.1
|
25.5
|
1.0
|
|
O
|
C:HOH476
|
4.1
|
41.6
|
1.0
|
|
HA
|
C:ASP18
|
4.3
|
28.6
|
1.0
|
|
CG
|
C:ASP130
|
4.4
|
31.1
|
1.0
|
|
CB
|
C:ASP18
|
4.4
|
26.3
|
1.0
|
|
O
|
C:HOH509
|
4.5
|
28.9
|
1.0
|
|
HB2
|
C:ASP18
|
4.7
|
31.6
|
1.0
|
|
N
|
C:LEU19
|
4.7
|
23.0
|
1.0
|
|
HB3
|
C:ASP200
|
4.7
|
29.8
|
1.0
|
|
OD2
|
C:ASP200
|
4.7
|
27.4
|
1.0
|
|
HB3
|
C:HIS124
|
4.7
|
32.3
|
1.0
|
|
HD2
|
C:TYR129
|
4.8
|
42.0
|
1.0
|
|
CA
|
C:ASP18
|
4.8
|
23.8
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 8hcc
Go back to
Magnesium Binding Sites List in 8hcc
Magnesium binding site 7 out
of 8 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:41.9
occ:1.00
|
O2P
|
D:AMP301
|
2.2
|
44.5
|
1.0
|
|
OD2
|
D:ASP18
|
2.2
|
29.4
|
1.0
|
|
OE1
|
D:GLU20
|
2.3
|
44.4
|
1.0
|
|
OD2
|
D:ASP200
|
2.4
|
27.1
|
1.0
|
|
O1P
|
D:AMP301
|
2.9
|
57.3
|
1.0
|
|
CG
|
D:ASP18
|
3.0
|
28.1
|
1.0
|
|
P
|
D:AMP301
|
3.0
|
55.4
|
1.0
|
|
OD1
|
D:ASP18
|
3.0
|
29.2
|
1.0
|
|
HB2
|
D:ASP200
|
3.2
|
27.4
|
1.0
|
|
CD
|
D:GLU20
|
3.2
|
42.9
|
1.0
|
|
HA
|
D:HIS195
|
3.3
|
60.4
|
1.0
|
|
MG
|
D:MG303
|
3.3
|
34.3
|
1.0
|
|
CG
|
D:ASP200
|
3.3
|
25.3
|
1.0
|
|
O
|
D:HOH461
|
3.5
|
25.7
|
1.0
|
|
OE2
|
D:GLU20
|
3.5
|
44.5
|
1.0
|
|
CB
|
D:ASP200
|
3.6
|
22.8
|
1.0
|
|
HB3
|
D:ASP200
|
3.7
|
27.4
|
1.0
|
|
O3P
|
D:AMP301
|
3.8
|
57.7
|
1.0
|
|
O
|
D:LEU19
|
4.0
|
26.2
|
1.0
|
|
HA
|
D:ALA197
|
4.0
|
28.4
|
1.0
|
|
O
|
D:HOH411
|
4.0
|
26.1
|
1.0
|
|
H5'2
|
D:AMP301
|
4.2
|
68.2
|
1.0
|
|
CA
|
D:HIS195
|
4.2
|
50.4
|
1.0
|
|
O5'
|
D:AMP301
|
4.4
|
56.9
|
1.0
|
|
O
|
D:THR196
|
4.4
|
30.1
|
1.0
|
|
CB
|
D:ASP18
|
4.4
|
25.7
|
1.0
|
|
C
|
D:HIS195
|
4.4
|
47.4
|
1.0
|
|
OD1
|
D:ASP200
|
4.5
|
26.6
|
1.0
|
|
H
|
D:HIS195
|
4.5
|
60.5
|
1.0
|
|
HG2
|
D:GLU20
|
4.5
|
44.8
|
1.0
|
|
O
|
D:HOH436
|
4.5
|
37.5
|
1.0
|
|
CG
|
D:GLU20
|
4.5
|
37.4
|
1.0
|
|
HD1
|
D:HIS195
|
4.5
|
63.6
|
1.0
|
|
O
|
D:HOH415
|
4.5
|
29.8
|
1.0
|
|
HB3
|
D:ASP18
|
4.6
|
30.8
|
1.0
|
|
C
|
D:THR196
|
4.6
|
28.9
|
1.0
|
|
N
|
D:THR196
|
4.7
|
41.8
|
1.0
|
|
C
|
D:LEU19
|
4.7
|
26.9
|
1.0
|
|
HB2
|
D:ASP18
|
4.8
|
30.8
|
1.0
|
|
C5'
|
D:AMP301
|
4.8
|
56.8
|
1.0
|
|
H
|
D:LEU19
|
4.8
|
32.0
|
1.0
|
|
N
|
D:HIS195
|
4.8
|
50.4
|
1.0
|
|
H
|
D:THR196
|
4.9
|
50.1
|
1.0
|
|
CA
|
D:ALA197
|
4.9
|
23.7
|
1.0
|
|
N
|
D:ALA197
|
4.9
|
24.8
|
1.0
|
|
HA
|
D:GLU20
|
4.9
|
31.7
|
1.0
|
|
O
|
D:HIS195
|
4.9
|
48.3
|
1.0
|
|
H
|
D:ASP200
|
5.0
|
26.9
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 8hcc
Go back to
Magnesium Binding Sites List in 8hcc
Magnesium binding site 8 out
of 8 in the Crystal Structure of MTREX1-Rna Product Complex (Amp)
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of MTREX1-Rna Product Complex (Amp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg303
b:34.3
occ:1.00
|
O2P
|
D:AMP301
|
2.0
|
44.5
|
1.0
|
|
O
|
D:HOH425
|
2.0
|
26.6
|
1.0
|
|
O
|
D:HOH411
|
2.1
|
26.1
|
1.0
|
|
OD1
|
D:ASP18
|
2.1
|
29.2
|
1.0
|
|
O
|
D:HOH415
|
2.1
|
29.8
|
1.0
|
|
O
|
D:HOH461
|
2.1
|
25.7
|
1.0
|
|
CG
|
D:ASP18
|
3.2
|
28.1
|
1.0
|
|
P
|
D:AMP301
|
3.3
|
55.4
|
1.0
|
|
MG
|
D:MG302
|
3.3
|
41.9
|
1.0
|
|
O3P
|
D:AMP301
|
3.4
|
57.7
|
1.0
|
|
OD2
|
D:ASP18
|
3.8
|
29.4
|
1.0
|
|
OD2
|
D:ASP130
|
3.9
|
30.1
|
1.0
|
|
H5'2
|
D:AMP301
|
3.9
|
68.2
|
1.0
|
|
O
|
D:HOH426
|
4.0
|
23.3
|
1.0
|
|
O
|
D:HIS124
|
4.0
|
26.5
|
1.0
|
|
H
|
D:LEU19
|
4.0
|
32.0
|
1.0
|
|
OD1
|
D:ASP130
|
4.1
|
31.9
|
1.0
|
|
O
|
D:HOH436
|
4.1
|
37.5
|
1.0
|
|
O5'
|
D:AMP301
|
4.2
|
56.9
|
1.0
|
|
O
|
D:LEU19
|
4.2
|
26.2
|
1.0
|
|
H5'1
|
D:AMP301
|
4.2
|
68.2
|
1.0
|
|
HA
|
D:ASP18
|
4.3
|
29.6
|
1.0
|
|
C5'
|
D:AMP301
|
4.3
|
56.8
|
1.0
|
|
CG
|
D:ASP130
|
4.4
|
29.5
|
1.0
|
|
HB3
|
D:HIS124
|
4.4
|
24.6
|
1.0
|
|
CB
|
D:ASP18
|
4.5
|
25.7
|
1.0
|
|
O1P
|
D:AMP301
|
4.5
|
57.3
|
1.0
|
|
O
|
D:HOH482
|
4.5
|
25.7
|
1.0
|
|
HB2
|
D:ASP18
|
4.6
|
30.8
|
1.0
|
|
HB3
|
D:ASP200
|
4.7
|
27.4
|
1.0
|
|
N
|
D:LEU19
|
4.8
|
26.6
|
1.0
|
|
OD2
|
D:ASP200
|
4.8
|
27.1
|
1.0
|
|
HD12
|
D:LEU19
|
4.8
|
37.0
|
1.0
|
|
CA
|
D:ASP18
|
4.9
|
24.6
|
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: Fri Aug 15 06:20:37 2025
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