Magnesium in PDB 7oma: Thosea Asigna Virus Rdrp Domain Elongation Complex
Protein crystallography data
The structure of Thosea Asigna Virus Rdrp Domain Elongation Complex, PDB code: 7oma
was solved by
D.S.Ferrero,
M.Falqui,
N.Verdaguer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
67.78 /
3.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.794,
207.305,
115.98,
90,
91.1,
90
|
R / Rfree (%)
|
23.1 /
25.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Thosea Asigna Virus Rdrp Domain Elongation Complex
(pdb code 7oma). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Thosea Asigna Virus Rdrp Domain Elongation Complex, PDB code: 7oma:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7oma
Go back to
Magnesium Binding Sites List in 7oma
Magnesium binding site 1 out
of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Thosea Asigna Virus Rdrp Domain Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg702
b:47.3
occ:1.00
|
OD2
|
B:ASP369
|
1.9
|
59.0
|
1.0
|
CG
|
B:ASP369
|
2.8
|
66.0
|
1.0
|
OD1
|
B:ASP369
|
3.1
|
79.6
|
1.0
|
OD2
|
B:ASP352
|
3.3
|
41.5
|
1.0
|
CG
|
B:ASP352
|
3.3
|
47.2
|
1.0
|
OP1
|
G:U8
|
3.3
|
37.8
|
1.0
|
CB
|
B:ASP352
|
3.5
|
47.4
|
1.0
|
OD1
|
B:ASP351
|
3.7
|
44.1
|
1.0
|
C5'
|
G:U8
|
3.7
|
39.0
|
1.0
|
OD1
|
B:ASP352
|
3.8
|
51.0
|
1.0
|
CA
|
B:ASP352
|
4.0
|
44.9
|
1.0
|
CB
|
B:ASP369
|
4.2
|
57.7
|
1.0
|
O5'
|
G:U8
|
4.3
|
37.6
|
1.0
|
OP1
|
G:U9
|
4.3
|
40.7
|
1.0
|
N
|
B:ASP352
|
4.4
|
46.1
|
1.0
|
P
|
G:U8
|
4.4
|
38.9
|
1.0
|
O3'
|
G:U8
|
4.5
|
43.8
|
1.0
|
C4'
|
G:U8
|
4.7
|
41.0
|
1.0
|
CG
|
B:ASP351
|
4.7
|
46.1
|
1.0
|
P
|
G:U9
|
4.9
|
44.1
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7oma
Go back to
Magnesium Binding Sites List in 7oma
Magnesium binding site 2 out
of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Thosea Asigna Virus Rdrp Domain Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg703
b:48.2
occ:1.00
|
OD2
|
B:ASP351
|
2.0
|
47.0
|
1.0
|
O
|
B:PHE370
|
2.1
|
45.9
|
1.0
|
O1
|
B:POP701
|
2.5
|
66.4
|
1.0
|
OP1
|
G:U9
|
2.8
|
40.7
|
1.0
|
O4
|
B:POP701
|
3.0
|
44.7
|
1.0
|
CG
|
B:ASP351
|
3.1
|
46.1
|
1.0
|
C
|
B:PHE370
|
3.2
|
45.3
|
1.0
|
N
|
B:PHE370
|
3.4
|
49.0
|
1.0
|
CB
|
B:ASP369
|
3.6
|
57.7
|
1.0
|
OD1
|
B:ASP351
|
3.7
|
44.1
|
1.0
|
OD2
|
B:ASP369
|
3.7
|
59.0
|
1.0
|
P1
|
B:POP701
|
3.8
|
62.7
|
1.0
|
CA
|
B:PHE370
|
3.8
|
47.9
|
1.0
|
P2
|
B:POP701
|
3.9
|
55.9
|
1.0
|
O6
|
B:POP701
|
4.0
|
70.3
|
1.0
|
C
|
B:ASP369
|
4.1
|
47.0
|
1.0
|
CG
|
B:ASP369
|
4.1
|
66.0
|
1.0
|
O2
|
B:POP701
|
4.2
|
65.2
|
1.0
|
CE
|
B:LYS488
|
4.2
|
70.5
|
1.0
|
N
|
B:LYS371
|
4.2
|
44.6
|
1.0
|
O
|
B:POP701
|
4.3
|
59.0
|
1.0
|
CB
|
B:ASP351
|
4.3
|
42.1
|
1.0
|
P
|
G:U9
|
4.3
|
44.1
|
1.0
|
CA
|
B:ASP369
|
4.3
|
51.5
|
1.0
|
CA
|
B:LYS371
|
4.6
|
48.9
|
1.0
|
CB
|
B:PHE370
|
4.7
|
48.6
|
1.0
|
O5'
|
G:U9
|
4.8
|
51.8
|
1.0
|
O3
|
B:POP701
|
5.0
|
64.8
|
1.0
|
N
|
B:GLN372
|
5.0
|
44.2
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7oma
Go back to
Magnesium Binding Sites List in 7oma
Magnesium binding site 3 out
of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Thosea Asigna Virus Rdrp Domain Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg702
b:45.8
occ:1.00
|
OD2
|
A:ASP351
|
1.9
|
40.1
|
1.0
|
O4
|
A:POP701
|
2.1
|
69.8
|
1.0
|
OP1
|
E:U9
|
2.2
|
35.0
|
1.0
|
OD2
|
A:ASP369
|
2.3
|
53.3
|
1.0
|
O
|
A:PHE370
|
2.5
|
54.9
|
1.0
|
O3
|
A:POP701
|
2.7
|
45.2
|
1.0
|
CG
|
A:ASP351
|
3.0
|
41.1
|
1.0
|
CG
|
A:ASP369
|
3.0
|
56.4
|
1.0
|
OD1
|
A:ASP369
|
3.1
|
63.9
|
1.0
|
O2
|
A:POP701
|
3.4
|
46.4
|
1.0
|
P2
|
A:POP701
|
3.4
|
69.2
|
1.0
|
P1
|
A:POP701
|
3.4
|
44.6
|
1.0
|
OD1
|
A:ASP351
|
3.4
|
40.6
|
1.0
|
P
|
E:U9
|
3.6
|
35.8
|
1.0
|
C
|
A:PHE370
|
3.7
|
50.5
|
1.0
|
O
|
A:POP701
|
3.7
|
55.3
|
1.0
|
O6
|
A:POP701
|
4.0
|
73.8
|
1.0
|
O5'
|
E:U9
|
4.0
|
33.7
|
1.0
|
N
|
A:PHE370
|
4.0
|
50.6
|
1.0
|
CB
|
A:ASP351
|
4.2
|
40.8
|
1.0
|
CB
|
A:ASP369
|
4.4
|
51.0
|
1.0
|
CA
|
A:PHE370
|
4.4
|
48.4
|
1.0
|
O5
|
A:POP701
|
4.5
|
76.3
|
1.0
|
OP2
|
E:U9
|
4.5
|
36.7
|
1.0
|
O3'
|
E:U8
|
4.6
|
30.4
|
1.0
|
C5'
|
E:U9
|
4.6
|
34.5
|
1.0
|
N
|
A:LYS371
|
4.7
|
49.3
|
1.0
|
CE
|
A:LYS488
|
4.8
|
65.1
|
1.0
|
NZ
|
A:LYS488
|
4.8
|
70.1
|
1.0
|
O1
|
A:POP701
|
4.8
|
62.0
|
1.0
|
CA
|
A:LYS371
|
4.9
|
50.1
|
1.0
|
C
|
A:ASP369
|
4.9
|
44.0
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7oma
Go back to
Magnesium Binding Sites List in 7oma
Magnesium binding site 4 out
of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Thosea Asigna Virus Rdrp Domain Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg701
b:52.9
occ:1.00
|
N
|
D:GLN372
|
3.1
|
56.7
|
1.0
|
OP1
|
L:U9
|
3.3
|
73.3
|
1.0
|
CA
|
D:GLN372
|
3.4
|
60.7
|
1.0
|
O5'
|
L:U9
|
3.7
|
75.7
|
1.0
|
O
|
D:PHE370
|
3.7
|
65.3
|
1.0
|
NH1
|
D:ARG280
|
3.7
|
98.0
|
1.0
|
N
|
D:MET373
|
3.7
|
56.7
|
1.0
|
OD2
|
D:ASP351
|
3.9
|
44.4
|
1.0
|
P
|
L:U9
|
4.0
|
62.2
|
1.0
|
C
|
D:GLN372
|
4.1
|
60.5
|
1.0
|
C
|
D:LYS371
|
4.1
|
60.4
|
1.0
|
C5'
|
L:U9
|
4.3
|
77.9
|
1.0
|
O3'
|
L:U9
|
4.3
|
78.4
|
1.0
|
NH2
|
D:ARG280
|
4.4
|
93.0
|
1.0
|
CA
|
D:LYS371
|
4.5
|
54.5
|
1.0
|
CZ
|
D:ARG280
|
4.5
|
90.6
|
1.0
|
OE1
|
D:GLN372
|
4.6
|
74.1
|
1.0
|
C
|
D:PHE370
|
4.7
|
53.1
|
1.0
|
CB
|
D:GLN372
|
4.7
|
64.9
|
1.0
|
C3'
|
L:U9
|
4.7
|
76.0
|
1.0
|
OP2
|
L:U9
|
4.8
|
56.7
|
1.0
|
NH2
|
D:ARG164
|
4.9
|
74.8
|
1.0
|
CD
|
D:GLN372
|
4.9
|
76.3
|
1.0
|
CA
|
D:MET373
|
5.0
|
54.2
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7oma
Go back to
Magnesium Binding Sites List in 7oma
Magnesium binding site 5 out
of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Thosea Asigna Virus Rdrp Domain Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg101
b:89.4
occ:1.00
|
OP1
|
I:U9
|
1.5
|
90.0
|
1.0
|
OD2
|
C:ASP351
|
1.8
|
65.3
|
1.0
|
O3
|
C:POP701
|
2.0
|
112.7
|
1.0
|
O6
|
C:POP701
|
2.0
|
64.1
|
1.0
|
O
|
C:POP701
|
2.4
|
100.5
|
1.0
|
P1
|
C:POP701
|
2.5
|
129.2
|
1.0
|
CG
|
C:ASP351
|
2.7
|
65.7
|
1.0
|
P2
|
C:POP701
|
2.7
|
67.7
|
1.0
|
P
|
I:U9
|
2.8
|
88.2
|
1.0
|
OD1
|
C:ASP351
|
2.9
|
65.9
|
1.0
|
O1
|
C:POP701
|
3.0
|
136.0
|
1.0
|
O5'
|
I:U9
|
3.3
|
90.1
|
1.0
|
O
|
C:PHE370
|
3.4
|
62.5
|
1.0
|
O4
|
C:POP701
|
3.6
|
62.4
|
1.0
|
O3'
|
I:U8
|
3.9
|
84.1
|
1.0
|
OP2
|
I:U9
|
3.9
|
86.6
|
1.0
|
OD1
|
C:ASP369
|
3.9
|
84.8
|
1.0
|
C5'
|
I:U9
|
3.9
|
89.3
|
1.0
|
O2
|
C:POP701
|
3.9
|
132.0
|
1.0
|
O5
|
C:POP701
|
4.0
|
68.5
|
1.0
|
CB
|
C:ASP351
|
4.0
|
61.6
|
1.0
|
CG
|
C:ASP369
|
4.2
|
84.6
|
1.0
|
OD2
|
C:ASP369
|
4.5
|
90.4
|
1.0
|
C
|
C:PHE370
|
4.6
|
60.2
|
1.0
|
N
|
C:PHE370
|
4.7
|
64.2
|
1.0
|
CB
|
C:ASP369
|
4.8
|
76.5
|
1.0
|
|
Reference:
D.S.Ferrero,
M.Falqui,
N.Verdaguer.
Snapshots of A Non-Canonical Rdrp in Action. Viruses V. 13 2021.
ISSN: ESSN 1999-4915
PubMed: 34203380
DOI: 10.3390/V13071260
Page generated: Thu Oct 3 03:26:07 2024
|