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Magnesium in PDB 2e9t: Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp

Enzymatic activity of Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp

All present enzymatic activity of Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp:
2.7.7.48;

Protein crystallography data

The structure of Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp, PDB code: 2e9t was solved by C.Ferrer-Orta, A.Arias, R.Perez-Luque, C.Escarmis, E.Domingo, N.Verdaguer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.597, 95.597, 201.155, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 28.9

Other elements in 2e9t:

The structure of Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp (pdb code 2e9t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp, PDB code: 2e9t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2e9t

Go back to Magnesium Binding Sites List in 2e9t
Magnesium binding site 1 out of 4 in the Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg780

b:41.4
occ:1.00
 O A:HOH964 2.3 30.6 1.0
OD1 A:ASP339 2.5 38.2 1.0
O A:HOH962 2.9 38.9 1.0
OD1 A:ASP238 2.9 44.9 1.0
O A:THR384 3.2 38.5 1.0
CG A:ASP339 3.6 36.0 1.0
CG A:ASP238 3.9 41.9 1.0
OD1 A:ASP240 4.0 43.5 1.0
C A:THR384 4.0 38.3 1.0
OD2 A:ASP339 4.1 35.3 1.0
OD2 A:ASP238 4.2 41.6 1.0
O A:ILE340 4.5 38.1 1.0
N A:ILE340 4.6 37.1 1.0
CA A:PHE385 4.6 37.1 1.0
O A:VAL239 4.7 40.7 1.0
N A:PHE385 4.7 37.9 1.0
O A:HOH952 4.7 41.9 1.0
CB A:ASP339 4.8 36.1 1.0
CA A:ASP339 4.8 36.4 1.0
CB A:THR384 4.8 38.9 1.0
O A:HOH963 4.8 35.3 1.0
CA A:THR384 4.9 39.0 1.0

Magnesium binding site 2 out of 4 in 2e9t

Go back to Magnesium Binding Sites List in 2e9t
Magnesium binding site 2 out of 4 in the Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg781

b:57.7
occ:1.00
 O32 A:PPV930 1.9 84.2 0.8
P2 A:PPV930 3.1 84.1 0.8
O12 A:PPV930 3.4 83.5 0.8
NZ A:LYS172 3.7 45.0 1.0
O11 A:PPV930 4.1 80.9 0.8
O31 A:PPV930 4.1 81.4 0.8
CE A:LYS172 4.1 44.1 1.0
OPP A:PPV930 4.2 82.8 0.8
O22 A:PPV930 4.2 83.7 0.8
P1 A:PPV930 4.4 81.8 0.8
O A:HOH954 5.0 39.0 1.0

Magnesium binding site 3 out of 4 in 2e9t

Go back to Magnesium Binding Sites List in 2e9t
Magnesium binding site 3 out of 4 in the Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1780

b:38.4
occ:1.00
 O D:HOH1963 2.5 25.9 1.0
OD1 D:ASP339 2.5 38.1 1.0
O D:HOH1961 2.6 49.8 1.0
OD1 D:ASP238 2.9 45.5 1.0
O D:THR384 2.9 38.6 1.0
CG D:ASP339 3.6 35.9 1.0
C D:THR384 3.8 38.4 1.0
CG D:ASP238 3.9 41.7 1.0
OD1 D:ASP240 4.1 43.5 1.0
OD2 D:ASP339 4.1 35.6 1.0
OD2 D:ASP238 4.2 41.4 1.0
CA D:PHE385 4.4 37.0 1.0
O D:ILE340 4.5 38.0 1.0
N D:PHE385 4.5 37.7 1.0
N D:ILE340 4.6 36.9 1.0
CB D:THR384 4.7 38.8 1.0
CA D:THR384 4.8 38.9 1.0
O D:VAL239 4.8 40.3 1.0
CB D:ASP339 4.9 36.2 1.0
CG2 D:THR384 4.9 39.3 1.0
CA D:ASP339 4.9 36.4 1.0
O D:HOH1952 5.0 35.3 1.0

Magnesium binding site 4 out of 4 in 2e9t

Go back to Magnesium Binding Sites List in 2e9t
Magnesium binding site 4 out of 4 in the Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Foot-and-Mouth Disease Virus Rna-Polymerase Rna Dependent in Complex with A Template-Primer Rna and 5F-Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1781

b:66.1
occ:1.00
 O32 D:PPV1930 2.2 79.3 0.8
NZ D:LYS172 3.1 45.1 1.0
P2 D:PPV1930 3.2 80.1 0.8
CE D:LYS172 3.3 44.2 1.0
OPP D:PPV1930 3.4 79.4 0.8
O12 D:PPV1930 3.6 78.8 0.8
O31 D:PPV1930 4.4 79.2 0.8
O22 D:PPV1930 4.6 79.5 0.8
CD D:LYS172 4.6 42.6 1.0
P1 D:PPV1930 4.7 79.5 0.8
O D:HOH1954 4.9 44.0 1.0

Reference:

C.Ferrer-Orta, A.Arias, R.Perez-Luque, C.Escarmis, E.Domingo, N.Verdaguer. Sequential Structures Provide Insights Into the Fidelity of Rna Replication Proc.Natl.Acad.Sci.Usa V. 104 9463 2007.
ISSN: ISSN 0027-8424
PubMed: 17517631
DOI: 10.1073/PNAS.0700518104
Page generated: Tue Aug 13 22:43:44 2024

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