Manganese in PDB 5ize: Hantaan Virus L Protein Cap-Snatching Endonuclease
Enzymatic activity of Hantaan Virus L Protein Cap-Snatching Endonuclease
All present enzymatic activity of Hantaan Virus L Protein Cap-Snatching Endonuclease:
2.7.7.48;
Protein crystallography data
The structure of Hantaan Virus L Protein Cap-Snatching Endonuclease, PDB code: 5ize
was solved by
J.Reguera,
S.Cusack,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.00 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.200,
76.150,
63.720,
90.00,
103.97,
90.00
|
R / Rfree (%)
|
16.6 /
21.6
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Hantaan Virus L Protein Cap-Snatching Endonuclease
(pdb code 5ize). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
Hantaan Virus L Protein Cap-Snatching Endonuclease, PDB code: 5ize:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 5ize
Go back to
Manganese Binding Sites List in 5ize
Manganese binding site 1 out
of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1001
b:18.6
occ:1.00
|
OD2
|
A:ASP97
|
2.2
|
14.0
|
1.0
|
O
|
A:VAL111
|
2.2
|
14.9
|
1.0
|
O
|
A:HOH1198
|
2.2
|
19.0
|
1.0
|
OE2
|
A:GLU110
|
2.2
|
19.6
|
1.0
|
O
|
A:HOH1196
|
2.2
|
20.7
|
1.0
|
NE2
|
A:HIS36
|
2.3
|
15.6
|
1.0
|
CG
|
A:ASP97
|
3.1
|
14.6
|
1.0
|
CD
|
A:GLU110
|
3.2
|
18.3
|
1.0
|
CE1
|
A:HIS36
|
3.3
|
15.6
|
1.0
|
CD2
|
A:HIS36
|
3.3
|
16.2
|
1.0
|
C
|
A:VAL111
|
3.3
|
15.1
|
1.0
|
OD1
|
A:ASP97
|
3.3
|
14.3
|
1.0
|
MN
|
A:MN31002
|
3.7
|
38.4
|
1.0
|
N
|
A:VAL111
|
3.8
|
13.0
|
1.0
|
OE1
|
A:GLU110
|
3.9
|
18.6
|
1.0
|
CA
|
A:VAL111
|
4.0
|
14.6
|
1.0
|
O
|
A:HOH1141
|
4.0
|
21.2
|
1.0
|
CG
|
A:GLU110
|
4.1
|
17.4
|
1.0
|
CB
|
A:VAL111
|
4.2
|
15.2
|
1.0
|
NZ
|
A:LYS124
|
4.3
|
31.0
|
1.0
|
ND1
|
A:HIS36
|
4.4
|
15.5
|
1.0
|
N
|
A:THR112
|
4.4
|
16.3
|
1.0
|
CG
|
A:HIS36
|
4.4
|
14.8
|
1.0
|
CE
|
A:LYS124
|
4.5
|
25.2
|
1.0
|
CB
|
A:ASP97
|
4.5
|
14.6
|
1.0
|
O
|
A:HOH1200
|
4.7
|
28.7
|
1.0
|
CA
|
A:THR112
|
4.7
|
16.4
|
1.0
|
C
|
A:GLU110
|
4.7
|
12.9
|
1.0
|
O
|
A:HOH1167
|
4.8
|
29.6
|
1.0
|
O
|
A:HOH1203
|
4.9
|
31.7
|
1.0
|
|
Manganese binding site 2 out
of 6 in 5ize
Go back to
Manganese Binding Sites List in 5ize
Manganese binding site 2 out
of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1002
b:38.4
occ:1.00
|
O
|
A:HOH1198
|
2.1
|
19.0
|
1.0
|
O
|
A:HOH1130
|
2.1
|
35.2
|
1.0
|
OD1
|
A:ASP97
|
2.2
|
14.3
|
1.0
|
OE2
|
A:GLU54
|
2.3
|
37.6
|
1.0
|
O
|
A:HOH1141
|
2.3
|
21.2
|
1.0
|
O
|
A:HOH1203
|
2.4
|
31.7
|
1.0
|
CG
|
A:ASP97
|
3.2
|
14.6
|
1.0
|
CD
|
A:GLU54
|
3.3
|
39.2
|
1.0
|
OE1
|
A:GLU54
|
3.7
|
43.2
|
1.0
|
MN
|
A:MN31001
|
3.7
|
18.6
|
1.0
|
OD2
|
A:ASP97
|
3.8
|
14.0
|
1.0
|
O
|
A:HOH1127
|
3.9
|
32.7
|
1.0
|
O
|
A:HOH1214
|
4.0
|
41.3
|
1.0
|
O
|
A:THR95
|
4.2
|
20.7
|
1.0
|
OE2
|
A:GLU110
|
4.3
|
19.6
|
1.0
|
CE1
|
A:HIS36
|
4.3
|
15.6
|
1.0
|
CB
|
A:ASP97
|
4.4
|
14.6
|
1.0
|
CA
|
A:ASP97
|
4.4
|
14.4
|
1.0
|
OE1
|
A:GLU110
|
4.5
|
18.6
|
1.0
|
N
|
A:ASP97
|
4.5
|
14.2
|
1.0
|
NE2
|
A:HIS36
|
4.6
|
15.6
|
1.0
|
CG
|
A:GLU54
|
4.6
|
34.0
|
1.0
|
O
|
A:HOH1196
|
4.8
|
20.7
|
1.0
|
CD
|
A:GLU110
|
4.8
|
18.3
|
1.0
|
CB
|
A:GLU54
|
4.8
|
30.9
|
1.0
|
|
Manganese binding site 3 out
of 6 in 5ize
Go back to
Manganese Binding Sites List in 5ize
Manganese binding site 3 out
of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1003
b:27.0
occ:1.00
|
OG
|
A:SER15
|
2.1
|
33.9
|
1.0
|
NE2
|
A:HIS8
|
2.3
|
27.2
|
1.0
|
O
|
A:GLY17
|
2.4
|
34.3
|
1.0
|
CD2
|
A:HIS8
|
3.2
|
30.3
|
1.0
|
CE1
|
A:HIS8
|
3.4
|
27.9
|
1.0
|
CB
|
A:SER15
|
3.4
|
36.1
|
1.0
|
C
|
A:GLY17
|
3.5
|
37.1
|
1.0
|
O
|
A:SER15
|
3.9
|
39.0
|
1.0
|
C
|
A:SER15
|
4.0
|
35.0
|
1.0
|
N
|
A:GLY17
|
4.0
|
39.0
|
1.0
|
CA
|
A:SER15
|
4.1
|
33.9
|
1.0
|
CA
|
A:GLY17
|
4.1
|
38.1
|
1.0
|
O
|
A:THR18
|
4.3
|
28.7
|
1.0
|
OE1
|
A:GLU23
|
4.3
|
27.4
|
1.0
|
OE2
|
A:GLU23
|
4.4
|
24.7
|
1.0
|
C
|
A:THR18
|
4.4
|
32.3
|
1.0
|
CG
|
A:HIS8
|
4.4
|
31.3
|
1.0
|
ND1
|
A:HIS8
|
4.4
|
29.3
|
1.0
|
N
|
A:LEU19
|
4.5
|
29.4
|
1.0
|
N
|
A:THR18
|
4.6
|
38.2
|
1.0
|
CA
|
A:LEU19
|
4.7
|
30.9
|
1.0
|
CD
|
A:GLU23
|
4.7
|
28.7
|
1.0
|
N
|
A:PRO16
|
4.8
|
38.3
|
1.0
|
CA
|
A:THR18
|
5.0
|
34.7
|
1.0
|
|
Manganese binding site 4 out
of 6 in 5ize
Go back to
Manganese Binding Sites List in 5ize
Manganese binding site 4 out
of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1001
b:49.8
occ:1.00
|
O
|
B:HOH1170
|
2.1
|
26.2
|
1.0
|
OE2
|
B:GLU54
|
2.2
|
49.1
|
1.0
|
OD1
|
B:ASP97
|
2.3
|
21.0
|
1.0
|
O
|
B:HOH1122
|
2.3
|
31.4
|
1.0
|
O
|
B:HOH1174
|
2.4
|
40.8
|
1.0
|
CD
|
B:GLU54
|
3.3
|
45.8
|
1.0
|
CG
|
B:ASP97
|
3.3
|
20.6
|
1.0
|
OE1
|
B:GLU54
|
3.7
|
55.0
|
1.0
|
MN
|
B:MN31002
|
3.8
|
24.2
|
1.0
|
OD2
|
B:ASP97
|
3.8
|
20.4
|
1.0
|
O
|
B:HOH1127
|
3.9
|
34.2
|
1.0
|
O
|
B:THR95
|
4.1
|
27.3
|
1.0
|
OE2
|
B:GLU110
|
4.3
|
26.4
|
1.0
|
CE1
|
B:HIS36
|
4.3
|
23.6
|
1.0
|
CA
|
B:ASP97
|
4.4
|
20.4
|
1.0
|
CB
|
B:ASP97
|
4.5
|
20.9
|
1.0
|
OE1
|
B:GLU110
|
4.5
|
24.4
|
1.0
|
NE2
|
B:HIS36
|
4.6
|
21.3
|
1.0
|
N
|
B:ASP97
|
4.6
|
19.9
|
1.0
|
CG
|
B:GLU54
|
4.6
|
38.0
|
1.0
|
O
|
B:HOH1163
|
4.8
|
25.8
|
1.0
|
CB
|
B:GLU54
|
4.8
|
33.2
|
1.0
|
CD
|
B:GLU110
|
4.8
|
26.8
|
1.0
|
|
Manganese binding site 5 out
of 6 in 5ize
Go back to
Manganese Binding Sites List in 5ize
Manganese binding site 5 out
of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1002
b:24.2
occ:1.00
|
O
|
B:VAL111
|
2.1
|
20.9
|
1.0
|
OD2
|
B:ASP97
|
2.2
|
20.4
|
1.0
|
O
|
B:HOH1163
|
2.2
|
25.8
|
1.0
|
OE2
|
B:GLU110
|
2.2
|
26.4
|
1.0
|
O
|
B:HOH1170
|
2.3
|
26.2
|
1.0
|
NE2
|
B:HIS36
|
2.3
|
21.3
|
1.0
|
CG
|
B:ASP97
|
3.1
|
20.6
|
1.0
|
CD
|
B:GLU110
|
3.2
|
26.8
|
1.0
|
CE1
|
B:HIS36
|
3.3
|
23.6
|
1.0
|
CD2
|
B:HIS36
|
3.3
|
24.6
|
1.0
|
C
|
B:VAL111
|
3.3
|
21.4
|
1.0
|
OD1
|
B:ASP97
|
3.4
|
21.0
|
1.0
|
N
|
B:VAL111
|
3.8
|
21.7
|
1.0
|
MN
|
B:MN31001
|
3.8
|
49.8
|
1.0
|
OE1
|
B:GLU110
|
3.8
|
24.4
|
1.0
|
CA
|
B:VAL111
|
3.9
|
22.4
|
1.0
|
O
|
B:HOH1122
|
4.0
|
31.4
|
1.0
|
CB
|
B:VAL111
|
4.1
|
23.9
|
1.0
|
CG
|
B:GLU110
|
4.1
|
25.0
|
1.0
|
NZ
|
B:LYS124
|
4.4
|
35.2
|
1.0
|
ND1
|
B:HIS36
|
4.4
|
23.8
|
1.0
|
N
|
B:THR112
|
4.4
|
22.1
|
1.0
|
CG
|
B:HIS36
|
4.4
|
24.1
|
1.0
|
CE
|
B:LYS124
|
4.5
|
31.9
|
1.0
|
CB
|
B:ASP97
|
4.5
|
20.9
|
1.0
|
O
|
B:HOH1168
|
4.6
|
32.1
|
1.0
|
CA
|
B:THR112
|
4.7
|
23.6
|
1.0
|
C
|
B:GLU110
|
4.7
|
20.4
|
1.0
|
O
|
B:HOH1174
|
4.9
|
40.8
|
1.0
|
O
|
B:HOH1110
|
5.0
|
35.7
|
1.0
|
|
Manganese binding site 6 out
of 6 in 5ize
Go back to
Manganese Binding Sites List in 5ize
Manganese binding site 6 out
of 6 in the Hantaan Virus L Protein Cap-Snatching Endonuclease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Hantaan Virus L Protein Cap-Snatching Endonuclease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1003
b:17.6
occ:1.00
|
O
|
B:HOH1117
|
2.2
|
19.4
|
1.0
|
O
|
B:HOH1107
|
2.2
|
16.1
|
1.0
|
NE2
|
B:HIS8
|
2.2
|
16.6
|
1.0
|
OG
|
B:SER15
|
2.3
|
18.1
|
1.0
|
O
|
B:GLY17
|
2.3
|
20.0
|
1.0
|
CD2
|
B:HIS8
|
3.2
|
17.3
|
1.0
|
CE1
|
B:HIS8
|
3.3
|
17.4
|
1.0
|
C
|
B:GLY17
|
3.4
|
20.9
|
1.0
|
CB
|
B:SER15
|
3.5
|
19.1
|
1.0
|
O
|
B:SER15
|
3.8
|
22.8
|
1.0
|
N
|
B:GLY17
|
3.9
|
22.0
|
1.0
|
CA
|
B:GLY17
|
4.0
|
22.5
|
1.0
|
C
|
B:SER15
|
4.0
|
21.6
|
1.0
|
CA
|
B:SER15
|
4.2
|
20.6
|
1.0
|
O
|
B:THR18
|
4.2
|
18.0
|
1.0
|
C
|
B:THR18
|
4.3
|
18.9
|
1.0
|
CG
|
B:HIS8
|
4.3
|
18.3
|
1.0
|
OE1
|
B:GLU23
|
4.3
|
20.7
|
1.0
|
ND1
|
B:HIS8
|
4.3
|
18.2
|
1.0
|
OE2
|
B:GLU23
|
4.4
|
19.9
|
1.0
|
N
|
B:LEU19
|
4.5
|
20.5
|
1.0
|
N
|
B:THR18
|
4.5
|
21.6
|
1.0
|
CA
|
B:LEU19
|
4.7
|
21.9
|
1.0
|
N
|
B:PRO16
|
4.8
|
22.6
|
1.0
|
CD
|
B:GLU23
|
4.8
|
23.1
|
1.0
|
CA
|
B:THR18
|
4.8
|
21.9
|
1.0
|
C
|
B:PRO16
|
5.0
|
24.8
|
1.0
|
|
Reference:
J.Reguera,
P.Gerlach,
M.Rosenthal,
S.Gaudon,
F.Coscia,
S.Gunther,
S.Cusack.
Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases. Plos Pathog. V. 12 05636 2016.
ISSN: ESSN 1553-7374
PubMed: 27304209
DOI: 10.1371/JOURNAL.PPAT.1005636
Page generated: Sun Oct 6 01:28:38 2024
|