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Zinc 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:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Rig-I in Complex with Cap-0 Rna, PDB code: 5f98:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5f98

Go back to Zinc Binding Sites List in 5f98
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:46.8
occ:1.00
 SG A:CYS813 2.3 63.3 1.0
SG A:CYS869 2.4 31.6 1.0
SG A:CYS864 2.5 67.1 1.0
SG A:CYS810 2.7 38.9 1.0
CB A:CYS864 3.0 58.1 1.0
CB A:CYS869 3.3 77.5 1.0
CB A:CYS810 3.4 47.1 1.0
CB A:CYS813 3.5 78.1 1.0
N A:CYS813 4.1 67.2 1.0
CA A:CYS813 4.4 67.4 1.0
NE1 A:TRP873 4.4 52.6 1.0
CA A:CYS864 4.5 65.1 1.0
CB A:HIS871 4.5 48.0 1.0
CZ2 A:TRP873 4.6 73.2 1.0
CB A:ARG866 4.6 74.8 1.0
CB A:LYS812 4.7 45.9 1.0
CA A:CYS869 4.8 76.2 1.0
CE2 A:TRP873 4.8 67.1 1.0
N A:HIS871 4.9 48.2 1.0
CA A:CYS810 4.9 55.0 1.0
N A:ARG866 4.9 80.2 1.0

Zinc binding site 2 out of 6 in 5f98

Go back to Zinc Binding Sites List in 5f98
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:50.2
occ:1.00
 SG C:CYS813 2.3 46.5 1.0
SG C:CYS810 2.4 35.9 1.0
SG C:CYS864 2.4 53.3 1.0
SG C:CYS869 2.6 38.1 1.0
CB C:CYS864 3.0 42.9 1.0
CB C:CYS810 3.3 45.0 1.0
CB C:CYS813 3.5 61.0 1.0
CB C:CYS869 3.6 50.5 1.0
N C:CYS813 3.8 69.1 1.0
CA C:CYS813 4.2 56.6 1.0
CB C:HIS871 4.3 37.8 1.0
NE1 C:TRP873 4.3 51.6 1.0
CZ2 C:TRP873 4.3 61.8 1.0
CA C:CYS864 4.5 46.8 1.0
CB C:LYS812 4.6 50.4 1.0
CE2 C:TRP873 4.7 62.8 1.0
CA C:CYS810 4.7 43.0 1.0
CB C:ARG866 4.8 60.2 1.0
C C:CYS813 4.8 59.0 1.0
CB C:ALA815 4.9 48.9 1.0
N C:HIS871 4.9 39.4 1.0
C C:LYS812 4.9 69.8 1.0
N C:LYS814 4.9 53.3 1.0
N C:LYS812 4.9 45.7 1.0

Zinc binding site 3 out of 6 in 5f98

Go back to Zinc Binding Sites List in 5f98
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:73.2
occ:1.00
 SG E:CYS813 2.4 58.9 1.0
SG E:CYS864 2.4 72.2 1.0
SG E:CYS810 2.5 89.1 1.0
SG E:CYS869 2.7 61.0 1.0
CB E:CYS810 3.0 77.6 1.0
CB E:CYS864 3.2 69.9 1.0
CB E:CYS813 3.9 81.5 1.0
CB E:CYS869 3.9 89.1 1.0
N E:CYS813 4.0 86.4 1.0
CZ2 E:TRP873 4.1 73.5 1.0
NE1 E:TRP873 4.3 77.2 1.0
CB E:ALA815 4.4 69.7 1.0
CA E:CYS813 4.5 79.9 1.0
CB E:LYS812 4.5 62.8 1.0
CA E:CYS810 4.6 73.9 1.0
CE2 E:TRP873 4.6 81.4 1.0
CA E:CYS864 4.7 71.5 1.0
CB E:HIS871 4.7 84.2 1.0
N E:LYS812 4.8 62.6 1.0
N E:ALA815 4.8 70.9 1.0
C E:LYS812 4.9 91.9 1.0
C E:CYS813 4.9 79.5 1.0
CB E:ARG866 4.9 53.6 1.0

Zinc binding site 4 out of 6 in 5f98

Go back to Zinc Binding Sites List in 5f98
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:96.0
occ:1.00
 SG G:CYS810 2.4 34.0 1.0
SG G:CYS864 2.5 68.1 1.0
CB G:CYS813 2.6 51.8 1.0
SG G:CYS869 2.6 56.7 1.0
SG G:CYS813 2.7 95.2 1.0
CB G:CYS810 3.3 41.9 1.0
CB G:CYS864 3.3 47.4 1.0
N G:CYS813 3.5 68.0 1.0
CA G:CYS813 3.6 53.6 1.0
CB G:CYS869 3.7 68.2 1.0
C G:LYS812 4.4 66.2 1.0
CB G:LYS812 4.6 46.1 1.0
CZ2 G:TRP873 4.7 58.4 1.0
NE1 G:TRP873 4.7 52.4 1.0
CA G:CYS810 4.7 45.1 1.0
C G:CYS813 4.7 56.8 1.0
CB G:HIS871 4.8 50.0 1.0
CA G:CYS864 4.8 39.0 1.0
CA G:LYS812 4.9 48.5 1.0
CB G:ARG866 4.9 63.7 1.0
N G:LYS812 4.9 40.3 1.0

Zinc binding site 5 out of 6 in 5f98

Go back to Zinc Binding Sites List in 5f98
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:44.8
occ:1.00
 SG I:CYS813 2.6 82.3 1.0
CB I:CYS813 2.6 55.3 1.0
SG I:CYS864 2.6 77.3 1.0
SG I:CYS869 2.6 70.8 1.0
SG I:CYS810 2.7 51.1 1.0
CB I:CYS864 3.1 71.2 1.0
CB I:CYS869 3.4 58.3 1.0
N I:CYS813 3.6 72.7 1.0
CB I:CYS810 3.6 43.8 1.0
CA I:CYS813 3.7 66.1 1.0
C I:LYS812 4.4 75.4 1.0
CB I:HIS871 4.5 54.3 1.0
CB I:LYS812 4.6 49.8 1.0
CZ2 I:TRP873 4.6 85.4 1.0
CA I:CYS864 4.6 67.7 1.0
NE1 I:TRP873 4.6 60.6 1.0
CB I:ARG866 4.8 60.4 1.0
C I:CYS813 4.9 69.7 1.0
CA I:LYS812 4.9 52.7 1.0
CA I:CYS869 4.9 78.7 1.0
CE2 I:TRP873 5.0 80.3 1.0

Zinc binding site 6 out of 6 in 5f98

Go back to Zinc Binding Sites List in 5f98
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:69.4
occ:1.00
 SG K:CYS864 2.4 72.6 1.0
SG K:CYS813 2.4 60.4 1.0
SG K:CYS869 2.4 83.2 1.0
SG K:CYS810 2.7 80.3 1.0
CB K:CYS864 2.9 57.6 1.0
CB K:CYS810 3.3 71.5 1.0
CZ2 K:TRP873 3.8 62.6 1.0
CB K:CYS813 3.8 54.3 1.0
CB K:CYS869 3.9 0.8 1.0
NE1 K:TRP873 4.0 45.2 1.0
CB K:HIS871 4.2 66.8 1.0
CE2 K:TRP873 4.2 57.2 1.0
CA K:CYS864 4.4 65.6 1.0
CG K:LYS812 4.5 82.5 1.0
N K:CYS813 4.5 75.9 1.0
N K:HIS871 4.7 77.5 1.0
CA K:CYS813 4.7 65.0 1.0
CA K:CYS810 4.8 66.2 1.0
CH2 K:TRP873 4.9 75.0 1.0
CB K:ARG866 4.9 52.6 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 Oct 27 15:54:00 2024

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