Magnesium in PDB 8hch: Crystal Structure of MTREX1-Uridine Complex
Enzymatic activity of Crystal Structure of MTREX1-Uridine Complex
All present enzymatic activity of Crystal Structure of MTREX1-Uridine Complex:
3.1.11.2;
Protein crystallography data
The structure of Crystal Structure of MTREX1-Uridine Complex, PDB code: 8hch
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)
|
24.69 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.632,
81.149,
93.653,
90,
103.51,
90
|
R / Rfree (%)
|
18.7 /
22.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of MTREX1-Uridine Complex
(pdb code 8hch). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of MTREX1-Uridine Complex, PDB code: 8hch:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8hch
Go back to
Magnesium Binding Sites List in 8hch
Magnesium binding site 1 out
of 4 in the Crystal Structure of MTREX1-Uridine Complex
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-Uridine Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg301
b:51.3
occ:1.00
|
O
|
A:HOH435
|
2.2
|
38.5
|
1.0
|
O
|
A:HOH477
|
2.2
|
40.1
|
1.0
|
O
|
A:HOH462
|
2.2
|
51.2
|
1.0
|
O
|
A:HOH460
|
2.2
|
33.2
|
1.0
|
O
|
A:HOH513
|
2.2
|
53.4
|
1.0
|
OD1
|
A:ASP18
|
2.3
|
35.6
|
1.0
|
CG
|
A:ASP18
|
3.4
|
35.5
|
1.0
|
O
|
A:HOH515
|
3.9
|
45.0
|
1.0
|
O
|
A:HOH512
|
3.9
|
51.6
|
1.0
|
OE2
|
A:GLU20
|
4.0
|
36.5
|
1.0
|
O
|
A:LEU19
|
4.0
|
30.5
|
1.0
|
OD2
|
A:ASP18
|
4.0
|
33.2
|
1.0
|
OD2
|
A:ASP130
|
4.1
|
38.2
|
1.0
|
OD2
|
A:ASP200
|
4.1
|
43.8
|
1.0
|
H5'1
|
A:URI302
|
4.2
|
48.3
|
1.0
|
H
|
A:LEU19
|
4.2
|
36.4
|
1.0
|
O
|
A:HIS124
|
4.2
|
27.0
|
1.0
|
O
|
A:HOH434
|
4.2
|
27.5
|
1.0
|
OD1
|
A:ASP130
|
4.3
|
35.8
|
1.0
|
HA
|
A:ASP18
|
4.4
|
32.7
|
1.0
|
O5'
|
A:URI302
|
4.4
|
41.1
|
1.0
|
HB3
|
A:ASP200
|
4.4
|
32.9
|
1.0
|
HB3
|
A:HIS124
|
4.5
|
35.7
|
1.0
|
CB
|
A:ASP18
|
4.6
|
26.9
|
1.0
|
H5'2
|
A:URI302
|
4.6
|
48.3
|
1.0
|
C5'
|
A:URI302
|
4.6
|
40.2
|
1.0
|
HB2
|
A:ASP18
|
4.7
|
32.3
|
1.0
|
CG
|
A:ASP130
|
4.7
|
35.3
|
1.0
|
O
|
A:HOH470
|
4.7
|
28.6
|
1.0
|
N
|
A:LEU19
|
4.8
|
30.3
|
1.0
|
HO5'
|
A:URI302
|
4.9
|
49.4
|
1.0
|
CD
|
A:GLU20
|
5.0
|
31.3
|
1.0
|
CA
|
A:ASP18
|
5.0
|
27.2
|
1.0
|
CG
|
A:ASP200
|
5.0
|
38.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8hch
Go back to
Magnesium Binding Sites List in 8hch
Magnesium binding site 2 out
of 4 in the Crystal Structure of MTREX1-Uridine Complex
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-Uridine Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:48.3
occ:1.00
|
O
|
B:HOH473
|
2.2
|
39.5
|
1.0
|
O
|
B:HOH468
|
2.2
|
51.2
|
1.0
|
O
|
B:HOH420
|
2.2
|
34.2
|
1.0
|
O
|
B:HOH464
|
2.2
|
48.3
|
1.0
|
O
|
B:HOH499
|
2.2
|
55.0
|
1.0
|
OD1
|
B:ASP18
|
2.3
|
36.2
|
1.0
|
CG
|
B:ASP18
|
3.5
|
35.7
|
1.0
|
OD2
|
B:ASP200
|
4.0
|
43.5
|
1.0
|
O
|
B:HOH433
|
4.1
|
25.7
|
1.0
|
OD2
|
B:ASP18
|
4.1
|
32.9
|
1.0
|
OD2
|
B:ASP130
|
4.2
|
38.3
|
1.0
|
O
|
B:HIS124
|
4.2
|
32.6
|
1.0
|
OE2
|
B:GLU20
|
4.2
|
30.6
|
1.0
|
H
|
B:LEU19
|
4.2
|
33.4
|
1.0
|
O
|
B:LEU19
|
4.3
|
34.2
|
1.0
|
OD1
|
B:ASP130
|
4.3
|
35.6
|
1.0
|
HB3
|
B:ASP200
|
4.3
|
35.2
|
1.0
|
O
|
B:HOH482
|
4.4
|
29.9
|
1.0
|
H5'1
|
B:URI302
|
4.4
|
45.8
|
1.0
|
HB3
|
B:HIS124
|
4.5
|
38.4
|
1.0
|
O5'
|
B:URI302
|
4.5
|
38.0
|
1.0
|
HA
|
B:ASP18
|
4.5
|
32.2
|
1.0
|
HO5'
|
B:URI302
|
4.6
|
45.7
|
1.0
|
CB
|
B:ASP18
|
4.7
|
25.6
|
1.0
|
CG
|
B:ASP130
|
4.7
|
32.6
|
1.0
|
HB2
|
B:ASP18
|
4.7
|
30.7
|
1.0
|
H5'2
|
B:URI302
|
4.8
|
45.8
|
1.0
|
C5'
|
B:URI302
|
4.8
|
38.1
|
1.0
|
CG
|
B:ASP200
|
4.9
|
38.2
|
1.0
|
CB
|
B:ASP200
|
5.0
|
29.3
|
1.0
|
N
|
B:LEU19
|
5.0
|
27.7
|
1.0
|
HB2
|
B:ASP200
|
5.0
|
35.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8hch
Go back to
Magnesium Binding Sites List in 8hch
Magnesium binding site 3 out
of 4 in the Crystal Structure of MTREX1-Uridine Complex
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-Uridine Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg301
b:49.5
occ:1.00
|
O
|
C:HOH449
|
2.2
|
37.3
|
1.0
|
O
|
C:HOH427
|
2.2
|
37.3
|
1.0
|
O
|
C:HOH479
|
2.2
|
39.2
|
1.0
|
O
|
C:HOH477
|
2.2
|
53.1
|
1.0
|
O
|
C:HOH499
|
2.2
|
49.3
|
1.0
|
OD1
|
C:ASP18
|
2.2
|
32.8
|
1.0
|
O
|
C:HOH493
|
3.4
|
42.7
|
1.0
|
CG
|
C:ASP18
|
3.4
|
34.6
|
1.0
|
O
|
C:HOH506
|
3.9
|
46.4
|
1.0
|
OD2
|
C:ASP130
|
4.0
|
33.9
|
1.0
|
O
|
C:HOH422
|
4.0
|
26.2
|
1.0
|
O
|
C:HIS124
|
4.1
|
28.9
|
1.0
|
OD2
|
C:ASP18
|
4.1
|
33.9
|
1.0
|
O
|
C:LEU19
|
4.1
|
30.2
|
1.0
|
HO5'
|
C:URI302
|
4.1
|
43.6
|
1.0
|
OE2
|
C:GLU20
|
4.2
|
33.6
|
1.0
|
OD2
|
C:ASP200
|
4.2
|
43.8
|
1.0
|
H
|
C:LEU19
|
4.2
|
32.8
|
1.0
|
OD1
|
C:ASP130
|
4.3
|
39.0
|
1.0
|
HA
|
C:ASP18
|
4.4
|
35.3
|
1.0
|
HB3
|
C:HIS124
|
4.4
|
37.1
|
1.0
|
O5'
|
C:URI302
|
4.4
|
36.3
|
1.0
|
HB3
|
C:ASP200
|
4.5
|
32.2
|
1.0
|
HB2
|
C:ASP18
|
4.5
|
35.4
|
1.0
|
CB
|
C:ASP18
|
4.5
|
29.4
|
1.0
|
O
|
C:HOH467
|
4.6
|
28.8
|
1.0
|
H5'1
|
C:URI302
|
4.6
|
47.8
|
1.0
|
CG
|
C:ASP130
|
4.6
|
36.9
|
1.0
|
H5'2
|
C:URI302
|
4.9
|
47.8
|
1.0
|
N
|
C:LEU19
|
4.9
|
27.3
|
1.0
|
C5'
|
C:URI302
|
4.9
|
39.8
|
1.0
|
CA
|
C:ASP18
|
5.0
|
29.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8hch
Go back to
Magnesium Binding Sites List in 8hch
Magnesium binding site 4 out
of 4 in the Crystal Structure of MTREX1-Uridine Complex
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-Uridine Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg301
b:55.8
occ:1.00
|
O
|
D:HOH461
|
2.2
|
43.9
|
1.0
|
O
|
D:HOH477
|
2.2
|
50.9
|
1.0
|
O
|
D:HOH435
|
2.2
|
37.6
|
1.0
|
O
|
D:HOH464
|
2.2
|
49.8
|
1.0
|
O
|
D:HOH492
|
2.2
|
57.4
|
1.0
|
OD2
|
D:ASP18
|
2.3
|
41.1
|
1.0
|
CG
|
D:ASP18
|
3.5
|
35.2
|
1.0
|
OD2
|
D:ASP130
|
4.0
|
38.8
|
1.0
|
O
|
D:HOH414
|
4.1
|
28.0
|
1.0
|
O
|
D:HIS124
|
4.1
|
37.9
|
1.0
|
O
|
D:LEU19
|
4.1
|
33.0
|
1.0
|
H
|
D:LEU19
|
4.2
|
40.6
|
1.0
|
OD2
|
D:ASP200
|
4.2
|
44.7
|
1.0
|
OE2
|
D:GLU20
|
4.2
|
39.1
|
1.0
|
OD1
|
D:ASP18
|
4.2
|
36.4
|
1.0
|
OD1
|
D:ASP130
|
4.2
|
42.0
|
1.0
|
H5'2
|
D:URI302
|
4.2
|
57.8
|
1.0
|
O
|
D:HOH481
|
4.4
|
30.6
|
1.0
|
HA
|
D:ASP18
|
4.4
|
31.6
|
1.0
|
HB3
|
D:ASP200
|
4.4
|
34.4
|
1.0
|
HB3
|
D:HIS124
|
4.5
|
44.3
|
1.0
|
CG
|
D:ASP130
|
4.5
|
37.0
|
1.0
|
O5'
|
D:URI302
|
4.5
|
61.3
|
1.0
|
HB2
|
D:ASP18
|
4.6
|
37.3
|
1.0
|
CB
|
D:ASP18
|
4.6
|
31.0
|
1.0
|
H5'1
|
D:URI302
|
4.7
|
57.8
|
1.0
|
C5'
|
D:URI302
|
4.7
|
48.1
|
1.0
|
N
|
D:LEU19
|
4.9
|
33.8
|
1.0
|
CA
|
D:ASP18
|
5.0
|
26.3
|
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: Thu Dec 28 09:12:25 2023
|