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Magnesium in PDB 4a8f: Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation

Enzymatic activity of Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation

All present enzymatic activity of Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation:
2.7.7.48;

Protein crystallography data

The structure of Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation, PDB code: 4a8f was solved by S.Wright, M.M.Poranen, D.H.Bamford, D.I.Stuart, J.M.Grimes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.01 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.915, 91.766, 140.461, 90.00, 101.25, 90.00
R / Rfree (%) 24.27 / 28.96

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation (pdb code 4a8f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation, PDB code: 4a8f:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4a8f

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Magnesium binding site 1 out of 4 in the Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1665

b:29.1
occ:0.50
 MG A:MG1665 0.0 29.1 0.5
O2B A:ATP1666 2.3 0.1 1.0
OD2 A:ASP454 3.2 86.1 1.0
O2G A:ATP1666 3.4 0.6 1.0
N A:GLY498 3.6 60.9 1.0
O A:ALA495 3.8 70.0 1.0
N A:LEU497 3.9 61.6 1.0
PB A:ATP1666 3.9 0.7 1.0
C A:ALA495 4.0 70.0 1.0
CB A:ALA495 4.0 70.4 1.0
OE2 A:GLU491 4.1 0.9 1.0
CG A:ASP454 4.1 89.0 1.0
NH2 A:ARG81 4.2 0.8 1.0
CA A:GLY498 4.3 60.6 1.0
N A:PHE496 4.3 62.8 1.0
OD1 A:ASP454 4.4 95.0 1.0
O3A A:ATP1666 4.4 0.9 1.0
CA A:LEU497 4.4 61.5 1.0
C A:PHE496 4.5 64.0 1.0
O3B A:ATP1666 4.5 0.6 1.0
CA A:PHE496 4.5 59.5 1.0
C A:LEU497 4.5 65.3 1.0
CA A:ALA495 4.6 70.3 1.0
O1A A:ATP1666 4.6 0.2 1.0
PG A:ATP1666 4.7 0.8 1.0
MG A:MG1665 4.8 57.2 0.5
OE1 A:GLU491 4.8 0.3 1.0
CD A:GLU491 4.9 0.3 1.0

Magnesium binding site 2 out of 4 in 4a8f

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Magnesium binding site 2 out of 4 in the Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1665

b:57.2
occ:0.50
 MG A:MG1665 0.0 57.2 0.5
OD1 A:ASP454 2.1 95.0 1.0
OE1 A:GLU491 2.3 0.3 1.0
O A:ALA495 2.6 70.0 1.0
CG A:ASP454 3.3 89.0 1.0
CD A:GLU491 3.4 0.3 1.0
O A:THR323 3.5 84.0 1.0
O A:ALA455 3.6 71.1 1.0
C A:ALA495 3.9 70.0 1.0
OD2 A:ASP454 3.9 86.1 1.0
OE2 A:GLU491 3.9 0.9 1.0
N A:ALA455 4.1 63.1 1.0
CB A:ALA322 4.3 78.9 1.0
CB A:ASP454 4.4 76.5 1.0
CG A:GLU491 4.5 0.0 1.0
CA A:ASP454 4.5 74.6 1.0
CB A:GLU491 4.5 90.4 1.0
N A:ALA495 4.5 73.4 1.0
C A:ALA455 4.6 70.8 1.0
CA A:PHE496 4.6 59.5 1.0
C A:THR323 4.7 85.7 1.0
N A:PHE496 4.7 62.8 1.0
N A:THR323 4.7 79.0 1.0
MG A:MG1665 4.8 29.1 0.5
C A:ASP454 4.8 68.8 1.0
CA A:ALA495 4.8 70.3 1.0
CA A:ALA322 4.9 78.0 1.0
C A:ALA322 4.9 82.1 1.0
CA A:ALA455 5.0 62.8 1.0
CD1 A:PHE496 5.0 61.5 1.0

Magnesium binding site 3 out of 4 in 4a8f

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Magnesium binding site 3 out of 4 in the Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1667

b:49.3
occ:1.00
 O2G B:ATP1666 3.2 0.8 1.0
CE B:LYS223 3.9 84.3 1.0
PG B:ATP1666 4.3 0.2 1.0
NH1 B:ARG225 4.5 85.5 1.0
CD B:LYS223 4.5 71.9 1.0
O3B B:ATP1666 4.6 0.0 1.0
O1G B:ATP1666 4.6 0.3 1.0
NH2 B:ARG225 4.7 99.4 1.0
O1A B:ATP1666 4.9 0.8 1.0

Magnesium binding site 4 out of 4 in 4a8f

Go back to Magnesium Binding Sites List in 4a8f
Magnesium binding site 4 out of 4 in the Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Non-Catalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Dsrna Virus PHI6 From De Novo Initiation to Elongation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1667

b:56.1
occ:1.00
 O2B C:ATP1666 2.0 0.7 1.0
OD2 C:ASP454 3.0 63.7 1.0
OE2 C:GLU491 3.2 73.4 1.0
PB C:ATP1666 3.5 0.4 1.0
O C:ALA495 3.5 61.8 1.0
CG C:ASP454 3.8 80.0 1.0
C C:ALA495 3.8 60.2 1.0
OD1 C:ASP454 3.9 86.0 1.0
N C:GLY498 4.0 56.7 1.0
N C:LEU497 4.0 54.4 1.0
CB C:ALA495 4.0 59.6 1.0
NH2 C:ARG81 4.2 82.0 1.0
CD C:GLU491 4.2 94.3 1.0
N C:PHE496 4.3 54.2 1.0
O3B C:ATP1666 4.3 0.5 1.0
O1B C:ATP1666 4.4 0.9 1.0
O2G C:ATP1666 4.4 0.6 1.0
CA C:PHE496 4.4 53.4 1.0
OE1 C:GLU491 4.5 71.0 1.0
CA C:ALA495 4.5 59.4 1.0
C C:PHE496 4.6 58.2 1.0
CA C:LEU497 4.7 52.6 1.0
O3A C:ATP1666 4.7 0.6 1.0
CA C:GLY498 4.7 58.1 1.0
C C:LEU497 4.9 58.5 1.0

Reference:

S.Wright, M.M.Poranen, D.H.Bamford, D.I.Stuart, J.M.Grimes. Noncatalytic Ions Direct the Rna-Dependent Rna Polymerase of Bacterial Double-Stranded Rna Virus PHI6 From De Novo Initiation to Elongation. J.Virol. V. 86 2837 2012.
ISSN: ISSN 0022-538X
PubMed: 22205747
DOI: 10.1128/JVI.05168-11
Page generated: Mon Dec 14 09:06:41 2020

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