Magnesium in PDB 4pqv: Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
Protein crystallography data
The structure of Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus), PDB code: 4pqv
was solved by
E.G.Chapman,
D.A.Costantino,
J.L.Rabe,
S.L.Moon,
J.Wilusz,
J.C.Nix,
J.S.Kieft,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.14 /
2.46
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.698,
76.698,
76.448,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23 /
28.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
(pdb code 4pqv). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus), PDB code: 4pqv:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 1 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 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 An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg101
b:69.2
occ:1.00
|
N7
|
A:G21
|
4.2
|
58.3
|
1.0
|
N4
|
A:C20
|
4.4
|
56.8
|
1.0
|
C8
|
A:G21
|
4.9
|
59.8
|
1.0
|
C4
|
A:C20
|
4.9
|
54.9
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 2 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 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 An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg102
b:55.9
occ:1.00
|
OP2
|
A:C23
|
1.8
|
51.4
|
1.0
|
O
|
A:HOH201
|
2.0
|
48.5
|
1.0
|
O
|
A:HOH202
|
2.1
|
57.8
|
1.0
|
O
|
A:HOH203
|
2.2
|
42.0
|
1.0
|
OP2
|
A:C5
|
2.2
|
45.3
|
1.0
|
O
|
A:HOH207
|
2.2
|
43.3
|
1.0
|
P
|
A:C23
|
3.0
|
49.2
|
1.0
|
OP1
|
A:C23
|
3.4
|
58.3
|
1.0
|
P
|
A:C5
|
3.7
|
50.8
|
1.0
|
O3'
|
A:C22
|
3.7
|
52.1
|
1.0
|
N7
|
A:A6
|
4.0
|
45.4
|
1.0
|
C4'
|
A:U4
|
4.1
|
50.0
|
1.0
|
C5'
|
A:U4
|
4.1
|
50.1
|
1.0
|
O5'
|
A:C23
|
4.2
|
49.8
|
1.0
|
C5'
|
A:C23
|
4.4
|
50.0
|
1.0
|
O5'
|
A:C5
|
4.5
|
47.4
|
1.0
|
O3'
|
A:U4
|
4.5
|
44.6
|
1.0
|
OP2
|
A:A6
|
4.6
|
46.5
|
1.0
|
OP1
|
A:C5
|
4.6
|
49.2
|
1.0
|
C3'
|
A:U4
|
4.6
|
47.1
|
1.0
|
C8
|
A:A6
|
4.7
|
46.4
|
1.0
|
C5
|
A:C5
|
4.9
|
45.2
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 3 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 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 An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg103
b:48.3
occ:1.00
|
N7
|
A:G51
|
3.4
|
44.5
|
1.0
|
O6
|
A:G51
|
3.7
|
44.2
|
1.0
|
N4
|
A:C52
|
3.8
|
42.5
|
1.0
|
N7
|
A:G50
|
4.2
|
47.0
|
1.0
|
C5
|
A:G51
|
4.2
|
43.9
|
1.0
|
O2'
|
A:G48
|
4.2
|
46.4
|
1.0
|
C6
|
A:G51
|
4.4
|
43.5
|
1.0
|
C8
|
A:G51
|
4.5
|
43.2
|
1.0
|
C5
|
A:G50
|
4.5
|
42.2
|
1.0
|
O6
|
A:G50
|
4.7
|
41.6
|
1.0
|
C4
|
A:C52
|
4.7
|
42.8
|
1.0
|
C6
|
A:G50
|
4.7
|
41.7
|
1.0
|
C8
|
A:G50
|
4.8
|
43.4
|
1.0
|
C5
|
A:C52
|
5.0
|
42.5
|
1.0
|
OP2
|
A:G51
|
5.0
|
44.4
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 4 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 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 An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg104
b:52.9
occ:1.00
|
O
|
A:HOH204
|
2.2
|
39.8
|
1.0
|
O
|
A:HOH205
|
2.4
|
39.5
|
1.0
|
O
|
A:HOH206
|
2.8
|
45.5
|
1.0
|
OP1
|
A:A16
|
3.0
|
58.0
|
1.0
|
O6
|
A:G14
|
3.5
|
51.6
|
1.0
|
N7
|
A:G14
|
3.9
|
49.0
|
1.0
|
P
|
A:A16
|
4.0
|
50.8
|
1.0
|
OP2
|
A:A16
|
4.0
|
46.3
|
1.0
|
C6
|
A:G14
|
4.1
|
47.0
|
1.0
|
C5
|
A:G14
|
4.3
|
42.7
|
1.0
|
MG
|
A:MG108
|
4.4
|
59.7
|
1.0
|
O3'
|
A:A15
|
4.9
|
50.2
|
1.0
|
C8
|
A:G14
|
4.9
|
49.9
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 5 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 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 An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg105
b:65.5
occ:1.00
|
O6
|
A:G58
|
3.3
|
60.6
|
1.0
|
C6
|
A:G58
|
4.3
|
61.3
|
1.0
|
OP2
|
A:G61
|
4.7
|
71.1
|
1.0
|
N1
|
A:G58
|
4.8
|
60.1
|
1.0
|
O6
|
A:G57
|
4.8
|
57.3
|
1.0
|
N7
|
A:A56
|
4.9
|
47.5
|
1.0
|
N7
|
A:G57
|
5.0
|
53.2
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 6 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 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 An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg106
b:70.3
occ:1.00
|
OP2
|
A:G34
|
4.1
|
49.8
|
1.0
|
N6
|
A:A36
|
4.1
|
62.1
|
1.0
|
N7
|
A:G34
|
4.2
|
55.2
|
1.0
|
N4
|
A:C25
|
4.5
|
60.9
|
1.0
|
O4
|
A:U26
|
4.6
|
63.2
|
1.0
|
N7
|
A:G35
|
4.6
|
54.1
|
1.0
|
C8
|
A:G34
|
4.7
|
54.1
|
1.0
|
C5
|
A:G34
|
4.7
|
49.4
|
1.0
|
O6
|
A:G35
|
4.8
|
58.1
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 7 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 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 An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg107
b:75.5
occ:1.00
|
O6
|
A:G11
|
3.0
|
64.2
|
1.0
|
N7
|
A:G11
|
3.8
|
70.3
|
1.0
|
C6
|
A:G11
|
3.9
|
67.0
|
1.0
|
C5
|
A:G11
|
4.2
|
70.4
|
1.0
|
O6
|
A:G12
|
4.3
|
58.5
|
1.0
|
N7
|
A:G12
|
4.4
|
61.7
|
1.0
|
N4
|
A:C10
|
4.9
|
67.6
|
1.0
|
C8
|
A:G11
|
5.0
|
72.5
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 8 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 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 An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg108
b:59.7
occ:1.00
|
OP1
|
A:A16
|
3.8
|
58.0
|
1.0
|
OP1
|
A:A17
|
4.2
|
52.7
|
1.0
|
O6
|
A:G14
|
4.3
|
51.6
|
1.0
|
MG
|
A:MG104
|
4.4
|
52.9
|
1.0
|
O3'
|
A:A16
|
4.5
|
47.3
|
1.0
|
OP2
|
A:A17
|
4.6
|
46.4
|
1.0
|
C5'
|
A:A16
|
4.6
|
52.2
|
1.0
|
P
|
A:A17
|
4.6
|
50.9
|
1.0
|
O5'
|
A:A16
|
4.9
|
47.3
|
1.0
|
P
|
A:A16
|
5.0
|
50.8
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 4pqv
Go back to
Magnesium Binding Sites List in 4pqv
Magnesium binding site 9 out
of 9 in the Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of An XRN1-Resistant Rna From the 3' Untranslated Region of A Flavivirus (Murray Valley Encephalitis Virus) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg109
b:58.7
occ:1.00
|
O6
|
A:G67
|
2.2
|
45.4
|
1.0
|
N7
|
A:G67
|
2.9
|
49.2
|
1.0
|
C6
|
A:G67
|
3.0
|
44.6
|
1.0
|
C5
|
A:G67
|
3.3
|
42.2
|
1.0
|
O6
|
A:G66
|
3.5
|
47.2
|
1.0
|
C6
|
A:G66
|
3.8
|
45.4
|
1.0
|
N7
|
A:G66
|
3.9
|
49.6
|
1.0
|
C5
|
A:G66
|
4.0
|
49.2
|
1.0
|
N4
|
A:C53
|
4.1
|
42.0
|
1.0
|
C8
|
A:G67
|
4.2
|
50.8
|
1.0
|
N1
|
A:G67
|
4.4
|
47.0
|
1.0
|
C4
|
A:G67
|
4.7
|
46.5
|
1.0
|
N1
|
A:G66
|
4.8
|
43.0
|
1.0
|
C8
|
A:G66
|
4.8
|
49.3
|
1.0
|
N4
|
A:C52
|
4.9
|
42.5
|
1.0
|
C4
|
A:G66
|
5.0
|
48.2
|
1.0
|
|
Reference:
E.G.Chapman,
D.A.Costantino,
J.L.Rabe,
S.L.Moon,
J.Wilusz,
J.C.Nix,
J.S.Kieft.
The Structural Basis of Pathogenic Subgenomic Flavivirus Rna (Sfrna) Production. Science V. 344 307 2014.
ISSN: ISSN 0036-8075
PubMed: 24744377
DOI: 10.1126/SCIENCE.1250897
Page generated: Tue Aug 20 01:37:38 2024
|