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Magnesium in PDB 5f9h: Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna

Enzymatic activity of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna

All present enzymatic activity of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna, PDB code: 5f9h was solved by C.Wang, J.Marcotrigiano, M.Miller, F.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.44 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.180, 174.810, 309.280, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.6

Other elements in 5f9h:

The structure of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna also contains other interesting chemical elements:

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 5' Triphosphate Hairpin Rna (pdb code 5f9h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna, PDB code: 5f9h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5f9h

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Magnesium binding site 1 out of 8 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:28.7
occ:1.00
 O A:PRO286 2.5 35.3 1.0
O A:GLN289 2.5 38.7 1.0
C A:PRO286 3.5 36.0 1.0
O A:PHE285 3.6 35.4 1.0
O A:GLN287 3.6 61.9 1.0
C A:GLN289 3.7 30.6 1.0
CA A:GLN287 3.9 57.4 1.0
C A:GLN287 4.0 57.5 1.0
C A:PHE285 4.1 31.0 1.0
N A:GLN287 4.1 52.7 1.0
CB A:PHE285 4.2 28.5 1.0
N A:GLN289 4.5 30.0 1.0
CA A:LYS290 4.5 30.6 1.0
N A:PRO286 4.6 30.8 1.0
CA A:PRO286 4.6 30.7 1.0
N A:LYS290 4.6 28.3 1.0
CA A:GLN289 4.7 29.4 1.0
CA A:PHE285 4.8 29.0 1.0
CB A:LYS290 4.8 34.1 1.0

Magnesium binding site 2 out of 8 in 5f9h

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Magnesium binding site 2 out of 8 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:56.9
occ:1.00
 OE1 A:GLN349 2.6 35.5 1.0
O2' B:A3 3.1 36.4 1.0
CG A:PRO382 3.4 23.6 1.0
CD A:GLN349 3.5 30.7 1.0
O4' B:U4 3.8 35.7 1.0
CD A:PRO382 3.8 23.8 1.0
NE2 A:GLN349 3.9 30.0 1.0
C4' B:U4 4.1 35.6 1.0
C5' B:U4 4.3 36.1 1.0
C2' B:A3 4.3 37.0 1.0
CB A:PRO382 4.4 23.6 1.0
N A:PRO382 4.5 24.0 1.0
O A:GLN380 4.6 59.0 1.0
CA A:PRO382 4.7 23.9 1.0
C1' B:U4 4.7 35.6 1.0
CG A:GLN349 4.9 25.6 1.0

Magnesium binding site 3 out of 8 in 5f9h

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Magnesium binding site 3 out of 8 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:50.1
occ:1.00
 CB A:LYS270 3.0 39.6 1.0
CA A:LYS270 3.8 40.1 1.0
CG2 A:ILE262 4.0 25.5 1.0
CB A:ALA264 4.1 25.6 1.0
CG A:LYS270 4.2 36.3 1.0
CD A:LYS270 4.2 33.5 1.0
SG A:CYS268 4.3 48.7 1.0
CD2 A:LEU408 4.4 24.2 1.0
O A:ILE262 4.5 36.5 1.0
N A:LYS270 4.6 43.0 1.0
CB A:ILE262 4.7 24.8 1.0
N A:ALA264 4.8 35.0 1.0
CB A:LEU408 4.8 23.9 1.0
CA A:ALA264 5.0 30.1 1.0
O A:ALA264 5.0 25.8 1.0
C A:LYS270 5.0 38.4 1.0

Magnesium binding site 4 out of 8 in 5f9h

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Magnesium binding site 4 out of 8 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:46.0
occ:1.00
 OD1 E:ASN376 2.3 52.5 1.0
O2' F:A5 2.8 43.9 1.0
CG E:ASN376 3.2 47.9 1.0
CA E:ASN376 3.5 48.1 1.0
CB E:ASN376 3.6 45.6 1.0
O3' F:A5 3.7 44.5 1.0
C4' F:A5 3.8 44.2 1.0
C2' F:A5 3.9 44.5 1.0
C3' F:A5 4.0 44.6 1.0
O E:ASN376 4.2 46.5 1.0
C E:ASN376 4.3 47.2 1.0
ND2 E:ASN376 4.4 46.7 1.0
O4' F:A5 4.4 44.3 1.0
N E:ASN376 4.5 45.0 1.0
CD2 E:HIS381 4.5 33.5 1.0
C1' F:A5 4.5 44.4 1.0
O E:HIS375 4.6 32.8 1.0
C5' F:U6 4.7 44.5 1.0
CD2 E:HIS375 4.7 32.8 1.0
C5' F:A5 4.9 44.5 1.0
C E:HIS375 4.9 32.7 1.0
OG E:SER378 5.0 51.3 1.0

Magnesium binding site 5 out of 8 in 5f9h

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Magnesium binding site 5 out of 8 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1002

b:24.2
occ:1.00
 CD1 G:LEU639 2.6 51.0 1.0
OG1 G:THR636 2.8 40.5 1.0
CG2 G:THR636 3.7 43.9 1.0
CB G:THR636 3.8 40.2 1.0
CG G:LEU639 3.9 47.7 1.0
CD2 G:LEU639 4.1 48.9 1.0
CG2 G:ILE553 4.2 45.4 1.0
CG1 G:ILE554 4.4 43.9 1.0
CD2 G:HIS557 4.4 65.8 1.0
CB G:LEU639 4.7 44.5 1.0
CA G:ILE554 4.7 47.0 1.0
N G:ILE554 4.8 46.2 1.0
N G:LEU639 4.9 49.0 1.0
CB G:ALA638 4.9 45.0 1.0
N G:THR636 5.0 40.3 1.0
CA G:THR636 5.0 39.1 1.0

Magnesium binding site 6 out of 8 in 5f9h

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Magnesium binding site 6 out of 8 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate 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 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1003

b:25.1
occ:1.00
 ND2 G:ASN341 3.4 46.2 1.0
ND2 K:ASN341 3.6 46.2 1.0
CG G:ASN341 4.3 42.7 1.0
OD1 G:ASN341 4.4 40.8 1.0
CA G:ILE337 4.4 38.2 1.0
OD1 K:ASN341 4.4 38.3 1.0
NH1 G:ARG320 4.4 51.9 1.0
CG K:ASN341 4.4 36.8 1.0
CA K:ILE337 4.5 34.3 1.0
CG2 K:ILE337 4.5 33.8 1.0
CG1 K:ILE337 4.5 34.6 1.0
CB G:ASN340 4.5 57.0 1.0
NH1 K:ARG320 4.6 53.2 1.0
CG1 G:ILE337 4.6 40.5 1.0
CB K:ASN340 4.7 36.0 1.0
CG2 G:ILE337 4.7 37.5 1.0
CB K:ILE337 4.7 34.1 1.0
O G:ILE337 4.7 44.8 1.0
CB G:ILE337 4.8 37.7 1.0
ND2 G:ASN340 4.9 53.9 1.0
ND2 K:ASN340 4.9 47.4 1.0

Magnesium binding site 7 out of 8 in 5f9h

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Magnesium binding site 7 out of 8 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1002

b:13.2
occ:1.00
 ND2 I:ASN341 3.5 61.9 1.0
ND2 E:ASN341 3.6 47.0 1.0
NH1 I:ARG320 4.3 42.6 1.0
CA I:ILE337 4.4 41.7 1.0
CG I:ASN341 4.4 61.3 1.0
OD1 I:ASN341 4.4 66.0 1.0
NH1 E:ARG320 4.5 61.3 1.0
CB I:ASN340 4.5 43.1 1.0
CG E:ASN341 4.6 46.8 1.0
CG2 I:ILE337 4.6 46.6 1.0
CA E:ILE337 4.6 39.3 1.0
OD1 E:ASN341 4.6 47.8 1.0
CG2 E:ILE337 4.6 38.5 1.0
CG1 I:ILE337 4.7 41.2 1.0
O I:ILE337 4.7 54.2 1.0
CG1 E:ILE337 4.7 39.4 1.0
CB I:ILE337 4.8 41.2 1.0
CB E:ASN340 4.8 51.7 1.0
ND2 I:ASN340 4.9 50.2 1.0
CB E:ILE337 4.9 38.9 1.0

Magnesium binding site 8 out of 8 in 5f9h

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Magnesium binding site 8 out of 8 in the Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Rig-I Helicase-Rd in Complex with 24-Mer 5' Triphosphate Hairpin Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1002

b:39.1
occ:1.00
 O K:PRO286 2.5 51.1 1.0
O K:GLN289 2.8 53.9 1.0
O K:PHE285 3.3 40.8 1.0
C K:PRO286 3.5 50.9 1.0
C K:PHE285 3.9 37.4 1.0
C K:GLN289 4.0 40.1 1.0
CB K:PHE285 4.1 34.0 1.0
O K:GLN287 4.1 52.4 1.0
CA K:GLN287 4.1 47.1 1.0
N K:GLN287 4.2 44.2 1.0
C K:GLN287 4.3 46.4 1.0
N K:PRO286 4.4 40.0 1.0
CA K:PRO286 4.5 46.8 1.0
CA K:PHE285 4.6 34.8 1.0
CA K:LYS290 4.7 34.2 1.0
N K:LYS290 4.8 34.4 1.0
N K:GLN289 4.8 35.6 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: Sun Sep 29 04:07:00 2024

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