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Zinc in PDB 6kyv: Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs

Enzymatic activity of Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs

All present enzymatic activity of Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs, PDB code: 6kyv was solved by K.-H.Kim, J.Hwang, J.H.Kim, K.-P.Son, Y.Jang, M.Kim, S.-J.Kang, J.-O.Lee, B.-S.Choi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.56 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 112.166, 175.130, 308.965, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs (pdb code 6kyv). 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 and Hairpin Rna with G-U Wobble Base Pairs, PDB code: 6kyv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6kyv

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Zinc binding site 1 out of 6 in the Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs


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 and Hairpin Rna with G-U Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:63.0
occ:1.00
 SG B:CYS813 2.3 53.8 1.0
SG B:CYS864 2.4 62.6 1.0
SG B:CYS869 2.4 56.1 1.0
SG B:CYS810 2.4 62.5 1.0
CB B:CYS864 2.8 64.4 1.0
CB B:CYS869 2.8 70.9 1.0
CB B:CYS810 3.2 57.7 1.0
CB B:CYS813 3.6 56.7 1.0
N B:CYS813 4.0 64.8 1.0
CA B:CYS869 4.3 78.5 1.0
CB B:HIS871 4.3 50.4 1.0
CA B:CYS864 4.3 61.1 1.0
CA B:CYS813 4.4 56.6 1.0
CZ2 B:TRP873 4.5 59.3 1.0
NE1 B:TRP873 4.6 65.2 1.0
CA B:CYS810 4.7 58.1 1.0
CB B:LYS812 4.8 48.8 1.0
C B:CYS869 4.8 69.0 1.0
N B:HIS871 4.8 57.8 1.0
CE2 B:TRP873 4.9 60.0 1.0
C B:CYS864 4.9 64.1 1.0
C B:LYS812 5.0 61.9 1.0
O B:ARG866 5.0 73.3 1.0
CB B:ALA815 5.0 54.2 1.0

Zinc binding site 2 out of 6 in 6kyv

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Zinc binding site 2 out of 6 in the Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs


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 and Hairpin Rna with G-U Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:76.6
occ:1.00
 SG D:CYS810 2.3 56.2 1.0
SG D:CYS813 2.3 72.3 1.0
SG D:CYS869 2.4 69.6 1.0
SG D:CYS864 2.4 64.1 1.0
CB D:CYS864 2.9 62.0 1.0
CB D:CYS810 3.1 60.5 1.0
CB D:CYS813 3.5 67.7 1.0
N D:CYS813 3.8 69.6 1.0
CB D:CYS869 4.0 69.7 1.0
CA D:CYS813 4.2 67.6 1.0
CB D:HIS871 4.4 61.3 1.0
CB D:LYS812 4.4 67.0 1.0
CA D:CYS864 4.4 68.4 1.0
CA D:CYS810 4.6 65.5 1.0
CZ2 D:TRP873 4.6 62.3 1.0
C D:LYS812 4.6 72.2 1.0
NE1 D:TRP873 4.7 61.5 1.0
N D:HIS871 4.7 58.2 1.0
N D:LYS812 4.8 64.9 1.0
O D:ARG866 4.8 86.8 1.0
CA D:LYS812 4.9 68.8 1.0
C D:CYS813 4.9 69.3 1.0
C D:CYS810 5.0 72.8 1.0
CE2 D:TRP873 5.0 67.1 1.0

Zinc binding site 3 out of 6 in 6kyv

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Zinc binding site 3 out of 6 in the Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs


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 and Hairpin Rna with G-U Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:77.7
occ:1.00
 SG F:CYS869 2.3 61.7 1.0
SG F:CYS864 2.3 70.3 1.0
SG F:CYS810 2.4 58.5 1.0
SG F:CYS813 2.4 79.2 1.0
CB F:CYS864 2.9 66.9 1.0
CB F:CYS869 3.0 65.8 1.0
CB F:CYS810 3.0 63.7 1.0
CB F:CYS813 3.5 64.5 1.0
N F:CYS813 3.9 73.4 1.0
CA F:CYS813 4.3 67.0 1.0
CA F:CYS864 4.4 65.5 1.0
CB F:HIS871 4.4 54.8 1.0
CA F:CYS869 4.4 72.6 1.0
CA F:CYS810 4.5 67.5 1.0
NE1 F:TRP873 4.7 64.6 1.0
CZ2 F:TRP873 4.7 66.5 1.0
CB F:LYS812 4.7 58.7 1.0
C F:LYS812 4.8 75.8 1.0
C F:CYS869 4.9 70.8 1.0
C F:CYS813 4.9 68.8 1.0
O F:ARG866 4.9 87.4 1.0
C F:CYS810 4.9 67.8 1.0
N F:HIS871 4.9 57.4 1.0
C F:CYS864 5.0 64.8 1.0

Zinc binding site 4 out of 6 in 6kyv

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Zinc binding site 4 out of 6 in the Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs


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 and Hairpin Rna with G-U Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1001

b:65.0
occ:1.00
 SG H:CYS810 2.3 61.3 1.0
SG H:CYS813 2.4 67.3 1.0
SG H:CYS864 2.4 82.1 1.0
SG H:CYS869 2.4 66.0 1.0
CB H:CYS864 2.7 60.6 1.0
CB H:CYS810 3.1 54.9 1.0
CB H:CYS869 3.2 62.2 1.0
CB H:CYS813 3.8 57.0 1.0
N H:CYS813 4.1 67.7 1.0
CA H:CYS864 4.2 61.5 1.0
NE1 H:TRP873 4.3 52.9 1.0
CB H:HIS871 4.4 53.1 1.0
CA H:CYS813 4.5 64.3 1.0
CA H:CYS810 4.6 55.2 1.0
CA H:CYS869 4.6 64.9 1.0
CZ2 H:TRP873 4.7 68.6 1.0
CB H:LYS812 4.7 52.8 1.0
CB H:ALA815 4.7 65.6 1.0
N H:HIS871 4.8 52.6 1.0
C H:CYS864 4.9 66.8 1.0
CE2 H:TRP873 4.9 61.7 1.0
C H:CYS869 4.9 64.6 1.0
C H:LYS812 5.0 68.0 1.0

Zinc binding site 5 out of 6 in 6kyv

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Zinc binding site 5 out of 6 in the Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs


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 and Hairpin Rna with G-U Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1001

b:0.1
occ:1.00
 SG J:CYS864 2.3 84.2 1.0
SG J:CYS813 2.4 72.8 1.0
SG J:CYS869 2.4 86.5 1.0
SG J:CYS810 2.4 96.1 1.0
CB J:CYS864 2.7 76.9 1.0
CB J:CYS810 3.1 76.9 1.0
CB J:CYS869 3.2 88.6 1.0
CB J:CYS813 3.7 76.2 1.0
N J:CYS813 4.1 82.1 1.0
CA J:CYS864 4.2 77.9 1.0
CB J:HIS871 4.4 77.2 1.0
NE1 J:TRP873 4.5 77.0 1.0
CA J:CYS813 4.5 79.2 1.0
CZ2 J:TRP873 4.5 76.5 1.0
CA J:CYS810 4.6 80.0 1.0
CB J:LYS812 4.6 83.1 1.0
CA J:CYS869 4.7 85.5 1.0
C J:CYS864 4.8 81.9 1.0
CE2 J:TRP873 4.8 77.6 1.0
N J:HIS871 5.0 75.3 1.0
N J:CYS864 5.0 80.0 1.0

Zinc binding site 6 out of 6 in 6kyv

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Zinc binding site 6 out of 6 in the Crystal Structure of Rig-I and Hairpin Rna with G-U Wobble Base Pairs


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 and Hairpin Rna with G-U Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:89.8
occ:1.00
 SG L:CYS813 2.4 88.5 1.0
SG L:CYS864 2.4 75.4 1.0
SG L:CYS869 2.5 89.4 1.0
CB L:CYS813 2.6 75.2 1.0
SG L:CYS810 2.9 88.1 1.0
CB L:CYS869 3.0 91.7 1.0
CB L:CYS864 3.0 74.9 1.0
N L:CYS813 3.4 84.7 1.0
CA L:CYS813 3.6 79.2 1.0
CB L:CYS810 3.6 76.6 1.0
CZ2 L:TRP873 4.3 77.3 1.0
CB L:HIS871 4.4 75.5 1.0
CA L:CYS869 4.5 93.3 1.0
C L:LYS812 4.5 90.4 1.0
C L:CYS813 4.5 86.2 1.0
CB L:LYS812 4.5 84.6 1.0
NE1 L:TRP873 4.5 69.8 1.0
CA L:CYS864 4.5 74.4 1.0
CE2 L:TRP873 4.7 79.0 1.0
N L:LYS814 4.9 82.8 1.0
C L:CYS869 4.9 87.1 1.0
CA L:LYS812 4.9 84.2 1.0
N L:HIS871 5.0 74.8 1.0
O L:ARG866 5.0 0.7 1.0

Reference:

K.-H.Kim, J.Hwang, J.H.Kim, K.-P.Son, Y.Jang, M.Kim, S.-J.Kang, J.-O.Lee, B.-S.Choi. Structure of Rig-I Dcard and Hairpin Rna with G-U Wobble Base Pairs To Be Published.
Page generated: Tue Oct 29 02:09:05 2024

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