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
Go back to
Zinc Binding Sites List in 6kyv
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
Go back to
Zinc Binding Sites List in 6kyv
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
Go back to
Zinc Binding Sites List in 6kyv
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
Go back to
Zinc Binding Sites List in 6kyv
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
Go back to
Zinc Binding Sites List in 6kyv
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
Go back to
Zinc Binding Sites List in 6kyv
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
|