Magnesium in PDB 8hcd: Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
Enzymatic activity of Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
All present enzymatic activity of Crystal Structure of MTREX1-Dna Product Complex (Dnmp):
3.1.11.2;
Protein crystallography data
The structure of Crystal Structure of MTREX1-Dna Product Complex (Dnmp), PDB code: 8hcd
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)
|
29.29 /
2.00
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.68,
81.284,
93.209,
90,
103.69,
90
|
|
R / Rfree (%)
|
19.5 /
24
|
Other elements in 8hcd:
The structure of Crystal Structure of MTREX1-Dna Product Complex (Dnmp) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
(pdb code 8hcd). 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-Dna Product Complex (Dnmp), PDB code: 8hcd:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 8hcd
Go back to
Magnesium Binding Sites List in 8hcd
Magnesium binding site 1 out
of 8 in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
 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-Dna Product Complex (Dnmp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:25.4
occ:1.00
|
OE2
|
B:GLU20
|
2.0
|
25.6
|
1.0
|
|
OD2
|
B:ASP200
|
2.2
|
28.7
|
1.0
|
|
O3P
|
B:DCM302
|
2.3
|
35.8
|
1.0
|
|
OD2
|
B:ASP18
|
2.3
|
29.9
|
1.0
|
|
OD1
|
B:ASP18
|
2.9
|
25.6
|
1.0
|
|
CG
|
B:ASP18
|
2.9
|
26.1
|
1.0
|
|
CD
|
B:GLU20
|
3.0
|
26.9
|
1.0
|
|
HA
|
B:HIS195
|
3.1
|
32.2
|
1.0
|
|
HB2
|
B:ASP200
|
3.1
|
29.2
|
1.0
|
|
CG
|
B:ASP200
|
3.2
|
27.1
|
1.0
|
|
O2P
|
B:DCM302
|
3.3
|
41.5
|
1.0
|
|
P
|
B:DCM302
|
3.3
|
40.7
|
1.0
|
|
OE1
|
B:GLU20
|
3.5
|
28.8
|
1.0
|
|
CB
|
B:ASP200
|
3.6
|
24.4
|
1.0
|
|
O
|
B:HOH443
|
3.6
|
42.9
|
1.0
|
|
HB3
|
B:ASP200
|
3.7
|
29.2
|
1.0
|
|
O
|
B:THR196
|
3.8
|
21.8
|
1.0
|
|
O
|
B:LEU19
|
3.9
|
32.1
|
1.0
|
|
H5'2
|
B:DCM302
|
4.0
|
44.2
|
1.0
|
|
CA
|
B:HIS195
|
4.0
|
26.8
|
1.0
|
|
MG
|
B:MG303
|
4.0
|
47.1
|
1.0
|
|
HA
|
B:ALA197
|
4.0
|
26.0
|
1.0
|
|
C
|
B:HIS195
|
4.2
|
27.6
|
1.0
|
|
O
|
B:HOH476
|
4.2
|
41.6
|
1.0
|
|
O1P
|
B:DCM302
|
4.2
|
42.5
|
1.0
|
|
HG2
|
B:GLU20
|
4.2
|
29.6
|
1.0
|
|
H
|
B:HIS195
|
4.2
|
31.8
|
1.0
|
|
C
|
B:THR196
|
4.2
|
21.6
|
1.0
|
|
CG
|
B:GLU20
|
4.3
|
24.6
|
1.0
|
|
OD1
|
B:ASP200
|
4.3
|
25.8
|
1.0
|
|
N
|
B:THR196
|
4.3
|
25.2
|
1.0
|
|
CB
|
B:ASP18
|
4.4
|
22.4
|
1.0
|
|
HD1
|
B:HIS195
|
4.4
|
37.1
|
1.0
|
|
H
|
B:THR196
|
4.5
|
30.2
|
1.0
|
|
O5'
|
B:DCM302
|
4.6
|
39.1
|
1.0
|
|
N
|
B:HIS195
|
4.6
|
26.5
|
1.0
|
|
C
|
B:LEU19
|
4.6
|
27.8
|
1.0
|
|
O
|
B:HIS195
|
4.7
|
28.7
|
1.0
|
|
C5'
|
B:DCM302
|
4.7
|
36.9
|
1.0
|
|
HB3
|
B:ASP18
|
4.7
|
26.9
|
1.0
|
|
N
|
B:ALA197
|
4.7
|
22.9
|
1.0
|
|
O
|
B:HOH446
|
4.7
|
40.5
|
1.0
|
|
HG3
|
B:GLU20
|
4.8
|
29.6
|
1.0
|
|
H
|
B:LEU19
|
4.8
|
30.9
|
1.0
|
|
H
|
B:ASP200
|
4.8
|
29.1
|
1.0
|
|
CA
|
B:ALA197
|
4.8
|
21.7
|
1.0
|
|
HB2
|
B:ASP18
|
4.8
|
26.9
|
1.0
|
|
HA
|
B:GLU20
|
4.8
|
27.3
|
1.0
|
|
CA
|
B:THR196
|
4.8
|
22.8
|
1.0
|
|
O
|
B:HOH504
|
4.9
|
48.5
|
1.0
|
|
O
|
B:HOH434
|
4.9
|
43.8
|
1.0
|
|
H5'1
|
B:DCM302
|
5.0
|
44.2
|
1.0
|
|
HA
|
B:THR196
|
5.0
|
27.4
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 8hcd
Go back to
Magnesium Binding Sites List in 8hcd
Magnesium binding site 2 out
of 8 in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
 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-Dna Product Complex (Dnmp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:47.1
occ:1.00
|
O
|
B:HOH476
|
1.8
|
41.6
|
1.0
|
|
O
|
B:HOH504
|
1.8
|
48.5
|
1.0
|
|
O
|
B:HOH443
|
1.8
|
42.9
|
1.0
|
|
O
|
B:HOH434
|
1.8
|
43.8
|
1.0
|
|
OD1
|
B:ASP18
|
2.7
|
25.6
|
1.0
|
|
O3P
|
B:DCM302
|
2.9
|
35.8
|
1.0
|
|
O
|
B:HIS124
|
3.7
|
31.1
|
1.0
|
|
OD1
|
B:ASP130
|
3.9
|
35.8
|
1.0
|
|
CG
|
B:ASP18
|
4.0
|
26.1
|
1.0
|
|
OD2
|
B:ASP130
|
4.0
|
34.4
|
1.0
|
|
MG
|
B:MG301
|
4.0
|
25.4
|
1.0
|
|
P
|
B:DCM302
|
4.1
|
40.7
|
1.0
|
|
H5'1
|
B:DCM302
|
4.1
|
44.2
|
1.0
|
|
HB3
|
B:HIS124
|
4.1
|
37.6
|
1.0
|
|
O
|
B:HOH446
|
4.1
|
40.5
|
1.0
|
|
O1P
|
B:DCM302
|
4.2
|
42.5
|
1.0
|
|
H
|
B:LEU19
|
4.2
|
30.9
|
1.0
|
|
O
|
B:HOH418
|
4.3
|
23.8
|
1.0
|
|
CG
|
B:ASP130
|
4.4
|
34.1
|
1.0
|
|
H5'2
|
B:DCM302
|
4.4
|
44.2
|
1.0
|
|
HA
|
B:ASP18
|
4.5
|
24.3
|
1.0
|
|
O
|
B:LEU19
|
4.5
|
32.1
|
1.0
|
|
O
|
B:HOH485
|
4.6
|
28.3
|
1.0
|
|
C5'
|
B:DCM302
|
4.6
|
36.9
|
1.0
|
|
O5'
|
B:DCM302
|
4.6
|
39.1
|
1.0
|
|
HB3
|
B:ASN125
|
4.6
|
36.1
|
1.0
|
|
OD2
|
B:ASP18
|
4.7
|
29.9
|
1.0
|
|
C
|
B:HIS124
|
4.8
|
31.3
|
1.0
|
|
O
|
B:HOH424
|
4.8
|
44.9
|
1.0
|
|
H
|
B:HIS124
|
4.8
|
35.2
|
1.0
|
|
HD2
|
B:TYR129
|
4.9
|
39.6
|
1.0
|
|
HB3
|
B:ASP200
|
5.0
|
29.2
|
1.0
|
|
CB
|
B:ASP18
|
5.0
|
22.4
|
1.0
|
|
CB
|
B:HIS124
|
5.0
|
31.3
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 8hcd
Go back to
Magnesium Binding Sites List in 8hcd
Magnesium binding site 3 out
of 8 in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
 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-Dna Product Complex (Dnmp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg302
b:20.8
occ:1.00
|
OE2
|
C:GLU20
|
1.9
|
25.4
|
1.0
|
|
OP3
|
C:DGP301
|
2.1
|
34.7
|
1.0
|
|
OD2
|
C:ASP200
|
2.1
|
29.6
|
1.0
|
|
OD2
|
C:ASP18
|
2.2
|
29.0
|
1.0
|
|
CG
|
C:ASP18
|
3.0
|
28.7
|
1.0
|
|
CD
|
C:GLU20
|
3.0
|
25.7
|
1.0
|
|
OD1
|
C:ASP18
|
3.1
|
27.8
|
1.0
|
|
CG
|
C:ASP200
|
3.1
|
30.2
|
1.0
|
|
HB2
|
C:ASP200
|
3.2
|
33.6
|
1.0
|
|
P
|
C:DGP301
|
3.2
|
38.5
|
1.0
|
|
OP2
|
C:DGP301
|
3.3
|
39.8
|
1.0
|
|
HA
|
C:HIS195
|
3.3
|
38.2
|
1.0
|
|
O
|
C:HOH633
|
3.4
|
47.9
|
1.0
|
|
OE1
|
C:GLU20
|
3.4
|
26.2
|
1.0
|
|
CB
|
C:ASP200
|
3.6
|
28.0
|
1.0
|
|
O
|
C:HOH625
|
3.6
|
48.1
|
1.0
|
|
HB3
|
C:ASP200
|
3.8
|
33.6
|
1.0
|
|
O
|
C:LEU19
|
3.8
|
23.8
|
1.0
|
|
H5'
|
C:DGP301
|
3.8
|
42.2
|
1.0
|
|
MG
|
C:MG303
|
3.8
|
50.4
|
1.0
|
|
O
|
C:THR196
|
3.8
|
22.4
|
1.0
|
|
HA
|
C:ALA197
|
3.8
|
26.6
|
1.0
|
|
OP1
|
C:DGP301
|
4.1
|
40.0
|
1.0
|
|
CA
|
C:HIS195
|
4.1
|
31.9
|
1.0
|
|
HG2
|
C:GLU20
|
4.2
|
29.8
|
1.0
|
|
C
|
C:THR196
|
4.2
|
24.4
|
1.0
|
|
C
|
C:HIS195
|
4.2
|
29.2
|
1.0
|
|
CG
|
C:GLU20
|
4.2
|
24.8
|
1.0
|
|
OD1
|
C:ASP200
|
4.2
|
28.7
|
1.0
|
|
N
|
C:THR196
|
4.3
|
25.6
|
1.0
|
|
H
|
C:HIS195
|
4.4
|
36.1
|
1.0
|
|
CB
|
C:ASP18
|
4.4
|
25.2
|
1.0
|
|
O5'
|
C:DGP301
|
4.4
|
36.1
|
1.0
|
|
H
|
C:THR196
|
4.5
|
30.7
|
1.0
|
|
C5'
|
C:DGP301
|
4.5
|
35.2
|
1.0
|
|
C
|
C:LEU19
|
4.5
|
22.5
|
1.0
|
|
HB3
|
C:ASP18
|
4.6
|
30.2
|
1.0
|
|
N
|
C:ALA197
|
4.6
|
23.5
|
1.0
|
|
CA
|
C:ALA197
|
4.6
|
22.2
|
1.0
|
|
HA
|
C:GLU20
|
4.7
|
25.5
|
1.0
|
|
N
|
C:HIS195
|
4.7
|
30.1
|
1.0
|
|
HG3
|
C:GLU20
|
4.7
|
29.8
|
1.0
|
|
O
|
C:HIS195
|
4.7
|
28.8
|
1.0
|
|
H
|
C:LEU19
|
4.8
|
26.3
|
1.0
|
|
HD1
|
C:HIS195
|
4.8
|
46.2
|
1.0
|
|
CA
|
C:THR196
|
4.8
|
25.3
|
1.0
|
|
H
|
C:ASP200
|
4.8
|
28.1
|
1.0
|
|
O
|
C:HOH709
|
4.8
|
44.3
|
1.0
|
|
H5''
|
C:DGP301
|
4.9
|
42.2
|
1.0
|
|
HB2
|
C:ASP18
|
4.9
|
30.2
|
1.0
|
|
HA
|
C:THR196
|
4.9
|
30.4
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 8hcd
Go back to
Magnesium Binding Sites List in 8hcd
Magnesium binding site 4 out
of 8 in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
 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-Dna Product Complex (Dnmp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg303
b:50.4
occ:1.00
|
O
|
C:HOH714
|
1.8
|
50.1
|
1.0
|
|
O
|
C:HOH614
|
1.8
|
50.8
|
1.0
|
|
O
|
C:HOH625
|
1.8
|
48.1
|
1.0
|
|
O
|
C:HOH633
|
1.8
|
47.9
|
1.0
|
|
OD1
|
C:ASP18
|
2.7
|
27.8
|
1.0
|
|
OP3
|
C:DGP301
|
2.8
|
34.7
|
1.0
|
|
MG
|
C:MG302
|
3.8
|
20.8
|
1.0
|
|
CG
|
C:ASP18
|
3.8
|
28.7
|
1.0
|
|
P
|
C:DGP301
|
4.0
|
38.5
|
1.0
|
|
H5''
|
C:DGP301
|
4.0
|
42.2
|
1.0
|
|
O
|
C:HIS124
|
4.0
|
25.0
|
1.0
|
|
OD1
|
C:ASP130
|
4.0
|
23.6
|
1.0
|
|
OD2
|
C:ASP130
|
4.0
|
22.5
|
1.0
|
|
O
|
C:HOH672
|
4.1
|
23.0
|
1.0
|
|
HB3
|
C:HIS124
|
4.2
|
33.3
|
1.0
|
|
OP1
|
C:DGP301
|
4.2
|
40.0
|
1.0
|
|
H5'
|
C:DGP301
|
4.3
|
42.2
|
1.0
|
|
H
|
C:LEU19
|
4.3
|
26.3
|
1.0
|
|
O
|
C:HOH716
|
4.3
|
26.3
|
1.0
|
|
OD2
|
C:ASP18
|
4.3
|
29.0
|
1.0
|
|
O
|
C:LEU19
|
4.4
|
23.8
|
1.0
|
|
O5'
|
C:DGP301
|
4.4
|
36.1
|
1.0
|
|
O
|
C:HOH709
|
4.4
|
44.3
|
1.0
|
|
C5'
|
C:DGP301
|
4.4
|
35.2
|
1.0
|
|
O
|
C:HOH676
|
4.5
|
36.3
|
1.0
|
|
CG
|
C:ASP130
|
4.5
|
23.2
|
1.0
|
|
HA
|
C:ASP18
|
4.6
|
27.2
|
1.0
|
|
HB3
|
C:ASP200
|
4.7
|
33.6
|
1.0
|
|
OD2
|
C:ASP200
|
4.8
|
29.6
|
1.0
|
|
CB
|
C:ASP18
|
5.0
|
25.2
|
1.0
|
|
HD2
|
C:TYR129
|
5.0
|
31.4
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 8hcd
Go back to
Magnesium Binding Sites List in 8hcd
Magnesium binding site 5 out
of 8 in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
 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-Dna Product Complex (Dnmp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:29.3
occ:1.00
|
OE2
|
D:GLU20
|
2.0
|
31.0
|
1.0
|
|
OD2
|
D:ASP18
|
2.2
|
34.3
|
1.0
|
|
OD2
|
D:ASP200
|
2.2
|
33.8
|
1.0
|
|
O2P
|
D:DCM301
|
2.3
|
49.2
|
1.0
|
|
CD
|
D:GLU20
|
3.0
|
30.5
|
1.0
|
|
CG
|
D:ASP18
|
3.1
|
34.0
|
1.0
|
|
HB2
|
D:ASP200
|
3.1
|
34.8
|
1.0
|
|
HA
|
D:HIS195
|
3.1
|
49.9
|
1.0
|
|
CG
|
D:ASP200
|
3.2
|
32.1
|
1.0
|
|
OD1
|
D:ASP18
|
3.2
|
35.8
|
1.0
|
|
P
|
D:DCM301
|
3.4
|
54.4
|
1.0
|
|
OE1
|
D:GLU20
|
3.4
|
32.5
|
1.0
|
|
O1P
|
D:DCM301
|
3.4
|
52.0
|
1.0
|
|
CB
|
D:ASP200
|
3.6
|
29.0
|
1.0
|
|
O
|
D:HOH497
|
3.7
|
52.7
|
1.0
|
|
O
|
D:THR196
|
3.8
|
28.8
|
1.0
|
|
O
|
D:LEU19
|
3.8
|
33.1
|
1.0
|
|
HB3
|
D:ASP200
|
3.9
|
34.8
|
1.0
|
|
MG
|
D:MG303
|
3.9
|
50.8
|
1.0
|
|
HA
|
D:ALA197
|
3.9
|
31.7
|
1.0
|
|
CA
|
D:HIS195
|
3.9
|
41.6
|
1.0
|
|
O
|
D:HOH462
|
4.0
|
50.2
|
1.0
|
|
C
|
D:HIS195
|
4.0
|
38.9
|
1.0
|
|
C
|
D:THR196
|
4.1
|
28.5
|
1.0
|
|
H5'2
|
D:DCM301
|
4.1
|
54.0
|
1.0
|
|
N
|
D:THR196
|
4.1
|
32.7
|
1.0
|
|
O3P
|
D:DCM301
|
4.1
|
52.3
|
1.0
|
|
HG2
|
D:GLU20
|
4.2
|
35.1
|
1.0
|
|
H
|
D:HIS195
|
4.2
|
49.7
|
1.0
|
|
CG
|
D:GLU20
|
4.2
|
29.3
|
1.0
|
|
H
|
D:THR196
|
4.3
|
39.2
|
1.0
|
|
OD1
|
D:ASP200
|
4.4
|
33.5
|
1.0
|
|
CB
|
D:ASP18
|
4.4
|
30.9
|
1.0
|
|
HB3
|
D:ASP18
|
4.5
|
37.1
|
1.0
|
|
N
|
D:HIS195
|
4.5
|
41.5
|
1.0
|
|
N
|
D:ALA197
|
4.6
|
25.7
|
1.0
|
|
H
|
D:ASP200
|
4.6
|
30.6
|
1.0
|
|
O
|
D:HIS195
|
4.6
|
39.5
|
1.0
|
|
C
|
D:LEU19
|
4.6
|
31.8
|
1.0
|
|
CA
|
D:THR196
|
4.7
|
30.8
|
1.0
|
|
O5'
|
D:DCM301
|
4.7
|
50.1
|
1.0
|
|
CA
|
D:ALA197
|
4.7
|
26.5
|
1.0
|
|
HD1
|
D:HIS195
|
4.7
|
56.9
|
1.0
|
|
HG3
|
D:GLU20
|
4.7
|
35.1
|
1.0
|
|
HA
|
D:GLU20
|
4.8
|
34.6
|
1.0
|
|
HA
|
D:THR196
|
4.8
|
36.9
|
1.0
|
|
C5'
|
D:DCM301
|
4.8
|
45.0
|
1.0
|
|
H
|
D:LEU19
|
4.9
|
38.5
|
1.0
|
|
O
|
D:HOH532
|
4.9
|
52.2
|
1.0
|
|
HB2
|
D:ASP18
|
4.9
|
37.1
|
1.0
|
|
CA
|
D:ASP200
|
5.0
|
27.6
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 8hcd
Go back to
Magnesium Binding Sites List in 8hcd
Magnesium binding site 6 out
of 8 in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
 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-Dna Product Complex (Dnmp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg303
b:50.8
occ:1.00
|
O
|
D:HOH428
|
1.8
|
51.6
|
1.0
|
|
O
|
D:HOH532
|
1.8
|
52.2
|
1.0
|
|
O
|
D:HOH497
|
1.8
|
52.7
|
1.0
|
|
O
|
D:HOH462
|
1.8
|
50.2
|
1.0
|
|
OD1
|
D:ASP18
|
2.6
|
35.8
|
1.0
|
|
O2P
|
D:DCM301
|
3.0
|
49.2
|
1.0
|
|
CG
|
D:ASP18
|
3.5
|
34.0
|
1.0
|
|
OD2
|
D:ASP18
|
3.8
|
34.3
|
1.0
|
|
MG
|
D:MG302
|
3.9
|
29.3
|
1.0
|
|
OD2
|
D:ASP130
|
3.9
|
34.3
|
1.0
|
|
O
|
D:HOH444
|
4.0
|
24.7
|
1.0
|
|
O
|
D:HIS124
|
4.0
|
33.2
|
1.0
|
|
HB3
|
D:HIS124
|
4.1
|
38.2
|
1.0
|
|
OD1
|
D:ASP130
|
4.1
|
35.6
|
1.0
|
|
H
|
D:LEU19
|
4.1
|
38.5
|
1.0
|
|
P
|
D:DCM301
|
4.2
|
54.4
|
1.0
|
|
H5'1
|
D:DCM301
|
4.2
|
54.0
|
1.0
|
|
HA
|
D:ASP18
|
4.3
|
34.7
|
1.0
|
|
O
|
D:HOH499
|
4.3
|
24.9
|
1.0
|
|
O
|
D:LEU19
|
4.4
|
33.1
|
1.0
|
|
CG
|
D:ASP130
|
4.4
|
33.9
|
1.0
|
|
O3P
|
D:DCM301
|
4.4
|
52.3
|
1.0
|
|
H5'2
|
D:DCM301
|
4.6
|
54.0
|
1.0
|
|
HB3
|
D:ASP200
|
4.6
|
34.8
|
1.0
|
|
O5'
|
D:DCM301
|
4.6
|
50.1
|
1.0
|
|
CB
|
D:ASP18
|
4.7
|
30.9
|
1.0
|
|
C5'
|
D:DCM301
|
4.7
|
45.0
|
1.0
|
|
O
|
D:HOH523
|
4.8
|
40.1
|
1.0
|
|
OD2
|
D:ASP200
|
4.8
|
33.8
|
1.0
|
|
H
|
D:HIS124
|
4.8
|
34.4
|
1.0
|
|
HB2
|
D:ASP18
|
4.8
|
37.1
|
1.0
|
|
N
|
D:LEU19
|
4.9
|
32.1
|
1.0
|
|
CA
|
D:ASP18
|
4.9
|
28.9
|
1.0
|
|
HB2
|
D:ASP200
|
5.0
|
34.8
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 8hcd
Go back to
Magnesium Binding Sites List in 8hcd
Magnesium binding site 7 out
of 8 in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
 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-Dna Product Complex (Dnmp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg302
b:24.4
occ:1.00
|
O
|
E:HOH431
|
2.1
|
30.0
|
1.0
|
|
O1P
|
E:DCM301
|
2.2
|
34.3
|
1.0
|
|
OD1
|
E:ASP18
|
2.3
|
27.5
|
1.0
|
|
O
|
E:HOH528
|
2.3
|
40.5
|
1.0
|
|
O
|
E:HOH498
|
2.4
|
18.8
|
1.0
|
|
O
|
E:HOH468
|
2.5
|
31.5
|
1.0
|
|
P
|
E:DCM301
|
3.4
|
39.8
|
1.0
|
|
MG
|
E:MG303
|
3.4
|
22.5
|
1.0
|
|
CG
|
E:ASP18
|
3.5
|
28.2
|
1.0
|
|
O2P
|
E:DCM301
|
3.7
|
39.9
|
1.0
|
|
H5'1
|
E:DCM301
|
3.8
|
47.2
|
1.0
|
|
OD2
|
E:ASP18
|
4.0
|
28.2
|
1.0
|
|
O
|
E:HOH432
|
4.0
|
38.0
|
1.0
|
|
O
|
E:LEU19
|
4.0
|
29.1
|
1.0
|
|
H5'2
|
E:DCM301
|
4.0
|
47.2
|
1.0
|
|
H
|
E:LEU19
|
4.0
|
28.1
|
1.0
|
|
O5'
|
E:DCM301
|
4.1
|
40.6
|
1.0
|
|
OD2
|
E:ASP130
|
4.1
|
32.4
|
1.0
|
|
C5'
|
E:DCM301
|
4.2
|
39.3
|
1.0
|
|
OD1
|
E:ASP130
|
4.2
|
32.4
|
1.0
|
|
O
|
E:HIS124
|
4.2
|
26.7
|
1.0
|
|
O
|
E:HOH448
|
4.3
|
17.9
|
1.0
|
|
HB3
|
E:HIS124
|
4.5
|
29.7
|
1.0
|
|
HA
|
E:ASP18
|
4.5
|
26.5
|
1.0
|
|
O
|
E:HOH496
|
4.5
|
47.6
|
1.0
|
|
O3P
|
E:DCM301
|
4.6
|
37.2
|
1.0
|
|
O
|
E:HOH547
|
4.6
|
23.6
|
1.0
|
|
CG
|
E:ASP130
|
4.6
|
31.7
|
1.0
|
|
OD2
|
E:ASP200
|
4.6
|
24.7
|
1.0
|
|
CB
|
E:ASP18
|
4.7
|
24.9
|
1.0
|
|
O
|
E:HOH437
|
4.8
|
45.5
|
1.0
|
|
N
|
E:LEU19
|
4.8
|
23.4
|
1.0
|
|
HB2
|
E:ASP18
|
4.8
|
29.8
|
1.0
|
|
HB3
|
E:ASP200
|
4.8
|
24.4
|
1.0
|
|
HD2
|
E:TYR129
|
5.0
|
30.8
|
1.0
|
|
OE2
|
E:GLU20
|
5.0
|
29.3
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 8hcd
Go back to
Magnesium Binding Sites List in 8hcd
Magnesium binding site 8 out
of 8 in the Crystal Structure of MTREX1-Dna Product Complex (Dnmp)
 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-Dna Product Complex (Dnmp) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg303
b:22.5
occ:1.00
|
OE2
|
E:GLU20
|
1.9
|
29.3
|
1.0
|
|
OD2
|
E:ASP18
|
2.2
|
28.2
|
1.0
|
|
OD2
|
E:ASP200
|
2.2
|
24.7
|
1.0
|
|
O1P
|
E:DCM301
|
2.2
|
34.3
|
1.0
|
|
CG
|
E:ASP18
|
2.9
|
28.2
|
1.0
|
|
OD1
|
E:ASP18
|
2.9
|
27.5
|
1.0
|
|
CD
|
E:GLU20
|
3.0
|
30.2
|
1.0
|
|
O3P
|
E:DCM301
|
3.1
|
37.2
|
1.0
|
|
P
|
E:DCM301
|
3.2
|
39.8
|
1.0
|
|
HB2
|
E:ASP200
|
3.2
|
24.4
|
1.0
|
|
HA
|
E:HIS195
|
3.2
|
35.3
|
1.0
|
|
CG
|
E:ASP200
|
3.2
|
22.6
|
1.0
|
|
OE1
|
E:GLU20
|
3.4
|
29.2
|
1.0
|
|
MG
|
E:MG302
|
3.4
|
24.4
|
1.0
|
|
CB
|
E:ASP200
|
3.6
|
20.4
|
1.0
|
|
HB3
|
E:ASP200
|
3.8
|
24.4
|
1.0
|
|
O
|
E:LEU19
|
3.8
|
29.1
|
1.0
|
|
O
|
E:HOH498
|
3.8
|
18.8
|
1.0
|
|
HA
|
E:ALA197
|
3.9
|
22.6
|
1.0
|
|
O
|
E:THR196
|
3.9
|
22.2
|
1.0
|
|
O2P
|
E:DCM301
|
4.0
|
39.9
|
1.0
|
|
CA
|
E:HIS195
|
4.0
|
29.5
|
1.0
|
|
H5'2
|
E:DCM301
|
4.1
|
47.2
|
1.0
|
|
O
|
E:HOH431
|
4.1
|
30.0
|
1.0
|
|
HG2
|
E:GLU20
|
4.2
|
36.9
|
1.0
|
|
CG
|
E:GLU20
|
4.2
|
30.8
|
1.0
|
|
C
|
E:HIS195
|
4.3
|
27.8
|
1.0
|
|
H
|
E:HIS195
|
4.3
|
33.1
|
1.0
|
|
C
|
E:THR196
|
4.3
|
21.7
|
1.0
|
|
CB
|
E:ASP18
|
4.3
|
24.9
|
1.0
|
|
OD1
|
E:ASP200
|
4.3
|
22.2
|
1.0
|
|
N
|
E:THR196
|
4.4
|
23.0
|
1.0
|
|
O5'
|
E:DCM301
|
4.5
|
40.6
|
1.0
|
|
HB3
|
E:ASP18
|
4.5
|
29.8
|
1.0
|
|
HD1
|
E:HIS195
|
4.5
|
38.5
|
1.0
|
|
C
|
E:LEU19
|
4.5
|
29.5
|
1.0
|
|
H
|
E:THR196
|
4.6
|
27.6
|
1.0
|
|
N
|
E:HIS195
|
4.6
|
27.6
|
1.0
|
|
O
|
E:HOH432
|
4.7
|
38.0
|
1.0
|
|
N
|
E:ALA197
|
4.7
|
19.3
|
1.0
|
|
HA
|
E:GLU20
|
4.7
|
31.9
|
1.0
|
|
H
|
E:LEU19
|
4.7
|
28.1
|
1.0
|
|
HB2
|
E:ASP18
|
4.7
|
29.8
|
1.0
|
|
C5'
|
E:DCM301
|
4.7
|
39.3
|
1.0
|
|
HG3
|
E:GLU20
|
4.7
|
36.9
|
1.0
|
|
CA
|
E:ALA197
|
4.7
|
18.9
|
1.0
|
|
O
|
E:HIS195
|
4.8
|
29.3
|
1.0
|
|
H
|
E:ASP200
|
4.8
|
22.7
|
1.0
|
|
CA
|
E:THR196
|
4.9
|
23.4
|
1.0
|
|
N
|
E:LEU19
|
5.0
|
23.4
|
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 Oct 4 04:47:29 2024
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