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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Aug 11 22:07:35 2025

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