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Magnesium in PDB 5f98: Crystal Structure of Rig-I in Complex with Cap-0 Rna

Enzymatic activity of Crystal Structure of Rig-I in Complex with Cap-0 Rna

All present enzymatic activity of Crystal Structure of Rig-I in Complex with Cap-0 Rna:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Rig-I in Complex with Cap-0 Rna, PDB code: 5f98 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) 84.00 / 3.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.180, 174.570, 309.260, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27.7

Other elements in 5f98:

The structure of Crystal Structure of Rig-I in Complex with Cap-0 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 in Complex with Cap-0 Rna (pdb code 5f98). 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 in Complex with Cap-0 Rna, PDB code: 5f98:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5f98

Go back to Magnesium Binding Sites List in 5f98
Magnesium binding site 1 out of 6 in the Crystal Structure of Rig-I in Complex with Cap-0 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 in Complex with Cap-0 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:29.0
occ:1.00
 NE2 A:HIS830 2.9 57.1 1.0
OG A:SER854 3.5 51.6 1.0
CE1 A:HIS830 3.6 45.9 1.0
N2 B:G2 3.7 28.4 1.0
CD2 A:HIS830 3.9 59.3 1.0
OE1 A:GLU827 4.0 77.3 1.0
CB A:CYS829 4.3 42.0 1.0
CB A:SER854 4.3 64.8 1.0
SG A:CYS829 4.4 53.1 1.0
O2 B:C25 4.4 38.3 1.0
ND1 A:HIS830 4.8 41.5 1.0
CG A:HIS830 4.9 49.9 1.0
C2 B:G2 4.9 36.5 1.0

Magnesium binding site 2 out of 6 in 5f98

Go back to Magnesium Binding Sites List in 5f98
Magnesium binding site 2 out of 6 in the Crystal Structure of Rig-I in Complex with Cap-0 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 in Complex with Cap-0 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:21.9
occ:1.00
 NE2 C:HIS830 3.4 46.7 1.0
OE1 C:GLU827 3.9 70.2 1.0
CB C:SER854 4.0 54.6 1.0
N2 D:G2 4.1 32.7 1.0
OG C:SER854 4.2 58.4 1.0
O2 D:C25 4.2 16.6 1.0
CE1 C:HIS830 4.3 42.8 1.0
CD2 C:HIS830 4.3 39.0 1.0
O2' D:C25 4.6 39.3 1.0
SG C:CYS829 4.8 79.6 1.0
CB C:CYS829 4.8 44.0 1.0

Magnesium binding site 3 out of 6 in 5f98

Go back to Magnesium Binding Sites List in 5f98
Magnesium binding site 3 out of 6 in the Crystal Structure of Rig-I in Complex with Cap-0 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 in Complex with Cap-0 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:46.1
occ:1.00
 NE2 E:HIS830 3.4 51.5 1.0
OE1 E:GLU827 3.9 81.0 1.0
N2 F:G2 4.0 56.5 1.0
O2 F:C25 4.0 51.5 1.0
CB E:SER854 4.1 82.0 1.0
CE1 E:HIS830 4.2 43.9 1.0
OG E:SER854 4.2 89.0 1.0
CD2 E:HIS830 4.3 56.8 1.0
CB E:CYS829 4.5 54.1 1.0
SG E:CYS829 4.6 0.3 1.0

Magnesium binding site 4 out of 6 in 5f98

Go back to Magnesium Binding Sites List in 5f98
Magnesium binding site 4 out of 6 in the Crystal Structure of Rig-I in Complex with Cap-0 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 in Complex with Cap-0 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1002

b:27.9
occ:1.00
 NE2 G:HIS830 3.2 49.0 1.0
OG G:SER854 3.5 78.0 1.0
N2 H:G2 3.7 40.7 1.0
CE1 G:HIS830 3.9 42.9 1.0
OE1 G:GLU827 4.0 80.9 1.0
O2 H:C25 4.1 35.0 1.0
CD2 G:HIS830 4.2 60.2 1.0
CB G:SER854 4.4 64.4 1.0
O2' H:C25 4.9 31.1 1.0
CB G:CYS829 4.9 59.4 1.0
C2 H:G2 5.0 43.9 1.0

Magnesium binding site 5 out of 6 in 5f98

Go back to Magnesium Binding Sites List in 5f98
Magnesium binding site 5 out of 6 in the Crystal Structure of Rig-I in Complex with Cap-0 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 in Complex with Cap-0 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1002

b:47.5
occ:1.00
 NE2 I:HIS830 3.1 53.5 1.0
OE1 I:GLU827 3.3 85.8 1.0
OG I:SER854 3.9 75.0 1.0
CD2 I:HIS830 4.0 56.9 1.0
CE1 I:HIS830 4.1 40.8 1.0
O2 J:C25 4.2 32.7 1.0
N2 J:G2 4.2 28.4 1.0
CB I:SER854 4.3 77.0 1.0
CD I:GLU827 4.6 76.9 1.0
O2' J:C25 4.7 54.8 1.0
CD2 I:PHE853 4.9 45.0 1.0
SG I:CYS829 5.0 98.0 1.0
CE1 I:PHE856 5.0 71.7 1.0
CB I:CYS829 5.0 44.2 1.0

Magnesium binding site 6 out of 6 in 5f98

Go back to Magnesium Binding Sites List in 5f98
Magnesium binding site 6 out of 6 in the Crystal Structure of Rig-I in Complex with Cap-0 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 in Complex with Cap-0 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1002

b:18.7
occ:1.00
 CE1 K:HIS830 3.2 55.3 1.0
SG K:CYS829 3.2 0.3 1.0
NE2 K:HIS830 3.6 54.0 1.0
N2 L:G2 3.9 31.9 1.0
ND1 K:HIS830 4.1 66.0 1.0
OE1 K:GLU827 4.1 81.4 1.0
OG K:SER854 4.3 73.3 1.0
O2 L:C25 4.6 44.6 1.0
CB K:CYS829 4.6 70.8 1.0
CB K:SER854 4.7 69.8 1.0
CD2 K:HIS830 4.7 48.4 1.0
O2' L:C25 4.8 45.2 1.0
CG K:HIS830 5.0 58.3 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: Mon Dec 14 20:17:33 2020

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