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Magnesium in PDB 1hi0: Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex

Protein crystallography data

The structure of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex, PDB code: 1hi0 was solved by J.M.Grimes, S.J.Butcher, E.V.Makeyev, D.H.Bamford, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.0 / 3.0
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.650, 92.700, 140.790, 90.00, 101.09, 90.00
R / Rfree (%) 21.4 / 23.9

Other elements in 1hi0:

The structure of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex (pdb code 1hi0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex, PDB code: 1hi0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1hi0

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Magnesium binding site 1 out of 6 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg668

b:73.1
occ:1.00
 OD1 P:ASP453 2.7 64.8 1.0
O P:VAL325 2.9 65.0 1.0
O2B P:GTP667 3.0 0.0 1.0
O2G P:GTP667 3.1 0.4 1.0
O3B P:GTP667 3.4 0.6 1.0
O1A P:GTP667 3.4 0.5 1.0
PG P:GTP667 3.7 0.8 1.0
PB P:GTP667 3.7 0.2 1.0
CG P:ASP453 3.8 73.0 1.0
OD1 P:ASP324 3.9 90.1 1.0
O3G P:GTP667 4.0 0.3 1.0
MG P:MG669 4.0 83.8 1.0
C P:VAL325 4.0 51.1 1.0
O3A P:GTP667 4.1 0.3 1.0
PA P:GTP667 4.2 0.4 1.0
O5' P:GTP667 4.4 0.7 1.0
OD2 P:ASP453 4.5 71.0 1.0
N P:VAL325 4.6 51.2 1.0
CB P:ASP453 4.7 68.6 1.0
CA P:VAL325 4.9 50.7 1.0
N P:SER326 4.9 53.0 1.0
CA P:SER326 4.9 57.9 1.0
N P:ASP327 5.0 47.9 1.0

Magnesium binding site 2 out of 6 in 1hi0

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Magnesium binding site 2 out of 6 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg669

b:83.8
occ:1.00
 O1A P:GTP667 2.6 0.5 1.0
O2G P:GTP667 2.9 0.4 1.0
C5' P:GTP666 3.1 0.5 1.0
O3' P:GTP666 3.8 0.9 1.0
PA P:GTP667 3.9 0.4 1.0
C4' P:GTP666 3.9 0.5 1.0
MG P:MG668 4.0 73.1 1.0
C3' P:GTP666 4.3 0.4 1.0
O5' P:GTP666 4.5 0.5 1.0
PG P:GTP667 4.5 0.8 1.0
O2A P:GTP667 4.5 0.6 1.0
O3A P:GTP667 4.6 0.3 1.0
O2G P:GTP666 4.7 0.9 1.0
O2A P:GTP666 4.7 0.4 1.0

Magnesium binding site 3 out of 6 in 1hi0

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Magnesium binding site 3 out of 6 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg668

b:73.1
occ:1.00
 OD1 Q:ASP453 2.7 64.8 1.0
O Q:VAL325 2.9 65.0 1.0
O2B Q:GTP667 3.0 0.0 1.0
O2G Q:GTP667 3.1 0.4 1.0
O3B Q:GTP667 3.4 0.6 1.0
O1A Q:GTP667 3.4 0.5 1.0
PG Q:GTP667 3.7 0.8 1.0
PB Q:GTP667 3.7 0.2 1.0
CG Q:ASP453 3.8 73.0 1.0
OD1 Q:ASP324 3.9 90.1 1.0
O3G Q:GTP667 4.0 0.3 1.0
MG Q:MG669 4.0 83.8 1.0
C Q:VAL325 4.0 51.1 1.0
O3A Q:GTP667 4.1 0.3 1.0
PA Q:GTP667 4.2 0.4 1.0
O5' Q:GTP667 4.4 0.7 1.0
OD2 Q:ASP453 4.5 71.0 1.0
N Q:VAL325 4.6 51.2 1.0
CB Q:ASP453 4.7 68.6 1.0
CA Q:VAL325 4.9 50.7 1.0
N Q:SER326 4.9 53.0 1.0
CA Q:SER326 4.9 57.9 1.0
N Q:ASP327 5.0 47.9 1.0

Magnesium binding site 4 out of 6 in 1hi0

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Magnesium binding site 4 out of 6 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg669

b:83.8
occ:1.00
 O1A Q:GTP667 2.6 0.5 1.0
O2G Q:GTP667 2.9 0.4 1.0
C5' Q:GTP666 3.1 0.5 1.0
O3' Q:GTP666 3.8 0.9 1.0
PA Q:GTP667 3.9 0.4 1.0
C4' Q:GTP666 3.9 0.5 1.0
MG Q:MG668 4.0 73.1 1.0
C3' Q:GTP666 4.3 0.4 1.0
O5' Q:GTP666 4.5 0.5 1.0
PG Q:GTP667 4.5 0.8 1.0
O2A Q:GTP667 4.5 0.6 1.0
O3A Q:GTP667 4.6 0.3 1.0
O2G Q:GTP666 4.7 0.9 1.0
O2A Q:GTP666 4.7 0.4 1.0

Magnesium binding site 5 out of 6 in 1hi0

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Magnesium binding site 5 out of 6 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg668

b:73.1
occ:1.00
 OD1 R:ASP453 2.7 64.8 1.0
O R:VAL325 2.9 65.0 1.0
O2B R:GTP667 3.0 0.0 1.0
O2G R:GTP667 3.1 0.4 1.0
O3B R:GTP667 3.4 0.6 1.0
O1A R:GTP667 3.4 0.5 1.0
PG R:GTP667 3.7 0.8 1.0
PB R:GTP667 3.7 0.2 1.0
CG R:ASP453 3.8 73.0 1.0
OD1 R:ASP324 3.9 90.1 1.0
O3G R:GTP667 4.0 0.3 1.0
MG R:MG669 4.0 83.8 1.0
C R:VAL325 4.0 51.1 1.0
O3A R:GTP667 4.1 0.3 1.0
PA R:GTP667 4.2 0.4 1.0
O5' R:GTP667 4.4 0.7 1.0
OD2 R:ASP453 4.5 71.0 1.0
N R:VAL325 4.6 51.2 1.0
CB R:ASP453 4.7 68.6 1.0
CA R:VAL325 4.9 50.7 1.0
N R:SER326 4.9 53.0 1.0
CA R:SER326 4.9 57.9 1.0
N R:ASP327 5.0 47.9 1.0

Magnesium binding site 6 out of 6 in 1hi0

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Magnesium binding site 6 out of 6 in the Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rna Dependent Rna Polymerase From Dsrna Bacteriophage PHI6 Plus Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg669

b:83.8
occ:1.00
 O1A R:GTP667 2.6 0.5 1.0
O2G R:GTP667 2.9 0.4 1.0
C5' R:GTP666 3.1 0.5 1.0
O3' R:GTP666 3.8 0.9 1.0
PA R:GTP667 3.9 0.4 1.0
C4' R:GTP666 3.9 0.5 1.0
MG R:MG668 4.0 73.1 1.0
C3' R:GTP666 4.3 0.4 1.0
O5' R:GTP666 4.5 0.5 1.0
PG R:GTP667 4.5 0.8 1.0
O2A R:GTP667 4.5 0.6 1.0
O3A R:GTP667 4.6 0.3 1.0
O2G R:GTP666 4.7 0.9 1.0
O2A R:GTP666 4.7 0.4 1.0

Reference:

S.J.Butcher, J.M.Grimes, E.V.Makeyev, D.H.Bamford, D.I.Stuart. A Mechanism For Initiating Rna-Dependent Rna Polymerization Nature V. 410 235 2001.
ISSN: ISSN 0028-0836
PubMed: 11242087
DOI: 10.1038/35065653
Page generated: Tue Aug 13 03:57:17 2024

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