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Magnesium in PDB 5f9f: Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna

Enzymatic activity of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna

All present enzymatic activity of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna, PDB code: 5f9f was solved by C.Wang, J.Marcotrigiano, M.T.Miller, F.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.524, 174.252, 308.288, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.9

Other elements in 5f9f:

The structure of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna (pdb code 5f9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna, PDB code: 5f9f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5f9f

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Magnesium binding site 1 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


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 Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:44.9
occ:1.00
 NZ A:LYS723 3.2 44.1 1.0
O2 B:U20 4.1 33.8 1.0
O2 B:U6 4.2 55.2 1.0
C2 B:A5 4.3 37.3 1.0
C1' B:U6 4.4 30.8 1.0
OG A:SER698 4.4 53.4 1.0
C1' B:A21 4.4 28.3 1.0
O4' B:A21 4.5 30.0 1.0
CE A:LYS723 4.5 40.6 1.0
N3 B:A5 4.6 31.8 1.0
C2 B:U6 4.8 43.4 1.0
O4' B:U6 4.8 31.9 1.0
O2' B:A21 4.9 35.9 1.0
O2' B:U6 4.9 37.9 1.0
N1 B:U6 4.9 38.4 1.0
CB A:SER698 5.0 46.2 1.0

Magnesium binding site 2 out of 6 in 5f9f

Go back to Magnesium Binding Sites List in 5f9f
Magnesium binding site 2 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


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 Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:56.5
occ:1.00
 CB C:ASP550 4.2 57.5 1.0
CG C:ASP550 4.5 61.0 1.0
CB C:ALA638 4.6 41.3 1.0
CG1 C:ILE554 4.6 51.7 1.0
CD1 C:ILE554 4.7 50.6 1.0
CG2 C:THR636 4.7 20.7 1.0
OD1 C:ASP550 4.8 59.1 1.0
OG1 C:THR636 4.8 44.8 1.0
CA C:ASP550 4.8 60.0 1.0
O C:ASP550 4.9 75.9 1.0
CB C:THR636 4.9 44.3 1.0
OH C:TYR566 4.9 41.5 1.0
OD2 C:ASP550 4.9 59.6 1.0

Magnesium binding site 3 out of 6 in 5f9f

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Magnesium binding site 3 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


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 Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg101

b:47.0
occ:1.00
 OG G:SER698 3.9 78.8 1.0
O2 H:U6 4.1 45.0 1.0
C1' H:U6 4.1 52.0 1.0
O2 H:U20 4.2 40.0 1.0
C2 H:A5 4.5 43.3 1.0
O2' H:U6 4.6 41.8 1.0
O4' H:U6 4.7 58.5 1.0
C2 H:U6 4.7 41.5 1.0
N3 H:A5 4.7 35.4 1.0
C1' H:A21 4.7 35.1 1.0
N1 H:U6 4.8 44.4 1.0
O4' H:A21 4.8 32.5 1.0
CB G:SER698 4.9 66.0 1.0

Magnesium binding site 4 out of 6 in 5f9f

Go back to Magnesium Binding Sites List in 5f9f
Magnesium binding site 4 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


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 Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1002

b:51.2
occ:1.00
 CB I:ASP550 4.3 64.5 1.0
CB I:ALA638 4.5 38.6 1.0
CG I:ASP550 4.5 65.6 1.0
OD1 I:ASP550 4.5 62.9 1.0
CG2 I:THR636 4.5 20.0 1.0
OG1 I:THR636 4.7 48.1 1.0
CB I:THR636 4.7 42.3 1.0
CA I:ASP550 4.9 66.8 1.0
CG1 I:ILE554 4.9 49.6 1.0
OH I:TYR566 4.9 61.8 1.0
CD1 I:ILE554 5.0 56.4 1.0

Magnesium binding site 5 out of 6 in 5f9f

Go back to Magnesium Binding Sites List in 5f9f
Magnesium binding site 5 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


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 Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1003

b:57.7
occ:1.00
 NZ I:LYS723 3.1 66.4 1.0
O2 J:U6 4.1 55.4 1.0
C1' J:U6 4.1 41.2 1.0
CE I:LYS723 4.3 54.9 1.0
O2 J:U20 4.4 47.8 1.0
OG I:SER698 4.4 66.6 1.0
C2 J:A5 4.4 56.4 1.0
O2' J:U6 4.4 39.1 1.0
O4' J:U6 4.6 43.6 1.0
N3 J:A5 4.7 56.5 1.0
C2 J:U6 4.7 46.8 1.0
N1 J:U6 4.8 43.2 1.0
C1' J:A21 4.9 36.4 1.0
C2' J:U6 4.9 44.7 1.0
O4' J:A21 4.9 31.0 1.0

Magnesium binding site 6 out of 6 in 5f9f

Go back to Magnesium Binding Sites List in 5f9f
Magnesium binding site 6 out of 6 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna


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 Rig-I Helicase-Rd in Complex with 24-Mer Blunt- End Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1002

b:62.3
occ:1.00
 NZ K:LYS723 3.1 73.7 1.0
OG K:SER698 3.9 58.7 1.0
CE K:LYS723 4.4 63.7 1.0
CA K:ALA700 4.4 63.4 1.0
C1' L:A21 4.5 43.1 1.0
O2 L:U20 4.5 41.0 1.0
O4' L:A21 4.5 44.4 1.0
O2 L:U6 4.6 34.5 1.0
CB K:ALA700 4.6 53.4 1.0
N K:ALA700 4.7 71.0 1.0
C1' L:U6 4.7 39.1 1.0
C2 L:A5 4.7 43.7 1.0
O2' L:A21 4.8 37.8 1.0
CB K:SER698 4.8 57.6 1.0
C K:VAL699 5.0 72.4 1.0

Reference:

S.C.Devarkar, C.Wang, M.T.Miller, A.Ramanathan, F.Jiang, A.G.Khan, S.S.Patel, J.Marcotrigiano. Structural Basis For M7G Recognition and 2'-O-Methyl Discrimination in Capped Rnas By the Innate Immune Receptor Rig-I. Proc.Natl.Acad.Sci.Usa V. 113 596 2016.
ISSN: ESSN 1091-6490
PubMed: 26733676
DOI: 10.1073/PNAS.1515152113
Page generated: Tue Aug 12 08:00:40 2025

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