Magnesium in PDB 7k05: Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases

Protein crystallography data

The structure of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases, PDB code: 7k05 was solved by R.Thapar, A.S.Andrew, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.25 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.579, 74.346, 96.513, 90, 90, 90
R / Rfree (%) 17.2 / 21.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases (pdb code 7k05). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases, PDB code: 7k05:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7k05

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Magnesium binding site 1 out of 4 in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:35.0
occ:1.00
 O1P A:AMP501 1.9 39.0 1.0
O A:HOH607 2.0 37.2 1.0
O A:HOH644 2.0 30.8 1.0
O A:HOH604 2.1 36.4 1.0
O A:HOH608 2.1 37.9 1.0
OD1 A:ASP150 2.2 49.2 1.0
CG A:ASP150 3.0 46.7 1.0
OD2 A:ASP150 3.2 50.0 1.0
P A:AMP501 3.3 44.4 1.0
MG A:MG503 3.5 40.3 1.0
O5' A:AMP501 3.9 34.7 1.0
O3P A:AMP501 3.9 38.8 1.0
O A:HOH643 3.9 33.5 1.0
OD2 A:ASP249 4.0 39.8 1.0
C5' A:AMP501 4.1 32.4 1.0
OD1 A:ASP249 4.1 36.7 1.0
O A:PHE151 4.2 30.5 1.0
CB A:ASP150 4.4 36.6 1.0
O2P A:AMP501 4.4 46.3 1.0
O A:CYS245 4.4 42.5 1.0
CG A:ASP249 4.5 37.4 1.0
OD2 A:ASP312 4.7 44.7 1.0
CA A:ASP150 4.7 33.0 1.0
N A:PHE151 4.9 29.1 1.0
C A:ASP150 4.9 34.2 1.0
O A:HOH677 5.0 49.3 1.0

Magnesium binding site 2 out of 4 in 7k05

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Magnesium binding site 2 out of 4 in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:40.3
occ:1.00
 OD2 A:ASP150 1.7 50.0 1.0
OE2 A:GLU152 2.0 47.5 1.0
OD2 A:ASP312 2.1 44.7 1.0
O1P A:AMP501 2.3 39.0 1.0
O2P A:AMP501 2.7 46.3 1.0
CG A:ASP150 2.9 46.7 1.0
P A:AMP501 3.1 44.4 1.0
CD A:GLU152 3.1 44.3 1.0
CG A:ASP312 3.2 40.9 1.0
OD1 A:ASP150 3.3 49.2 1.0
MG A:MG502 3.5 35.0 1.0
OE1 A:GLU152 3.6 36.8 1.0
O A:PHE151 3.6 30.5 1.0
CB A:ASP312 3.8 32.9 1.0
O A:HOH604 3.9 36.4 1.0
O A:HOH644 4.0 30.8 1.0
O3P A:AMP501 4.1 38.8 1.0
CA A:HIS307 4.2 42.2 1.0
CB A:ASP150 4.2 36.6 1.0
OD1 A:ASP312 4.2 40.3 1.0
O5' A:AMP501 4.3 34.7 1.0
CA A:GLY309 4.3 32.8 1.0
O A:ASP150 4.4 33.8 1.0
CG A:GLU152 4.4 37.2 1.0
O A:SER308 4.5 40.5 1.0
C A:HIS307 4.5 41.7 1.0
C A:PHE151 4.5 32.6 1.0
C5' A:AMP501 4.6 32.4 1.0
C A:SER308 4.6 38.8 1.0
C A:ASP150 4.6 34.2 1.0
N A:GLY309 4.6 35.5 1.0
O A:HIS307 4.7 41.7 1.0
O A:HOH608 4.8 37.9 1.0
N A:HIS307 4.9 42.5 1.0

Magnesium binding site 3 out of 4 in 7k05

Go back to Magnesium Binding Sites List in 7k05
Magnesium binding site 3 out of 4 in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:46.2
occ:1.00
 O3P B:AMP501 1.9 42.4 1.0
O B:HOH633 2.0 48.4 1.0
O B:HOH606 2.1 44.9 1.0
OD2 B:ASP150 2.1 47.4 1.0
O B:HOH612 2.1 44.2 1.0
O B:HOH629 2.2 39.4 1.0
CG B:ASP150 3.1 46.4 1.0
P B:AMP501 3.2 46.7 1.0
MG B:MG503 3.3 42.9 1.0
OD1 B:ASP150 3.4 47.5 1.0
O1P B:AMP501 3.8 43.5 1.0
O5' B:AMP501 3.8 44.7 1.0
O B:HOH630 4.0 41.2 1.0
O B:HOH626 4.1 45.4 1.0
C5' B:AMP501 4.1 43.3 1.0
OD2 B:ASP249 4.1 46.6 1.0
O B:PHE151 4.2 35.5 1.0
OD1 B:ASP249 4.2 44.3 1.0
O2P B:AMP501 4.3 48.0 1.0
CB B:ASP150 4.4 41.3 1.0
O B:CYS245 4.5 40.4 1.0
OD2 B:ASP312 4.6 42.5 1.0
CG B:ASP249 4.6 44.7 1.0
CA B:ASP150 4.7 39.5 1.0
N B:PHE151 4.9 36.5 1.0
C B:ASP150 4.9 38.6 1.0

Magnesium binding site 4 out of 4 in 7k05

Go back to Magnesium Binding Sites List in 7k05
Magnesium binding site 4 out of 4 in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:42.9
occ:1.00
 OE2 B:GLU152 2.0 46.2 1.0
O3P B:AMP501 2.3 42.4 1.0
OD2 B:ASP312 2.4 42.5 1.0
OD2 B:ASP150 2.5 47.4 1.0
CD B:GLU152 3.0 41.6 1.0
CG B:ASP150 3.1 46.4 1.0
O2P B:AMP501 3.1 48.0 1.0
O B:PHE151 3.2 35.5 1.0
P B:AMP501 3.3 46.7 1.0
MG B:MG502 3.3 46.2 1.0
CG B:ASP312 3.4 40.4 1.0
OE1 B:GLU152 3.6 42.8 1.0
OD1 B:ASP150 3.8 47.5 1.0
CB B:ASP150 3.8 41.3 1.0
CB B:ASP312 3.8 38.5 1.0
O B:ASP150 3.9 36.9 1.0
O B:HOH612 3.9 44.2 1.0
O B:HOH629 3.9 39.4 1.0
O B:HOH626 4.0 45.4 1.0
C B:PHE151 4.1 37.2 1.0
C B:ASP150 4.1 38.6 1.0
CA B:GLY309 4.2 33.3 1.0
CG B:GLU152 4.3 33.8 1.0
O1P B:AMP501 4.4 43.5 1.0
O5' B:AMP501 4.5 44.7 1.0
CA B:ASP150 4.5 39.5 1.0
OD1 B:ASP312 4.5 36.9 1.0
CA B:HIS307 4.5 47.0 1.0
C5' B:AMP501 4.6 43.3 1.0
N B:PHE151 4.6 36.5 1.0
N B:GLY309 4.6 33.7 1.0
O B:SER308 4.7 43.8 1.0
C B:HIS307 4.7 45.4 1.0
N B:GLU152 4.8 29.3 1.0
C B:SER308 4.8 38.0 1.0
O B:HOH633 4.9 48.4 1.0
O B:HIS307 5.0 42.3 1.0
CA B:PHE151 5.0 38.8 1.0

Reference:

R.Thapar, A.S.Arvai, J.A.Tainer. Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3' - 5' Exoribonucleases To Be Published.
Page generated: Fri Nov 5 15:12:35 2021

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