Magnesium in PDB 6szu: Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
Enzymatic activity of Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
All present enzymatic activity of Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence:
2.7.7.48;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
(pdb code 6szu). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence, PDB code: 6szu:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6szu
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Magnesium Binding Sites List in 6szu
Magnesium binding site 1 out
of 6 in the Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:49.6
occ:1.00
|
OD1
|
A:ASP108
|
2.0
|
53.8
|
1.0
|
O8
|
A:M4H801
|
2.0
|
65.6
|
1.0
|
O10
|
A:M4H801
|
2.4
|
65.6
|
1.0
|
OE1
|
A:GLU80
|
2.8
|
53.5
|
1.0
|
O
|
A:PRO107
|
3.0
|
49.1
|
1.0
|
C7
|
A:M4H801
|
3.1
|
65.6
|
1.0
|
CG
|
A:ASP108
|
3.1
|
53.8
|
1.0
|
C1
|
A:M4H801
|
3.3
|
65.6
|
1.0
|
C
|
A:PRO107
|
3.5
|
49.1
|
1.0
|
O
|
A:LEU106
|
3.6
|
45.8
|
1.0
|
C6
|
A:M4H801
|
3.6
|
65.6
|
1.0
|
OD2
|
A:ASP108
|
3.8
|
53.8
|
1.0
|
OE1
|
A:GLU119
|
3.9
|
61.8
|
1.0
|
MG
|
A:MG803
|
3.9
|
59.3
|
1.0
|
N
|
A:ASP108
|
4.0
|
53.8
|
1.0
|
CD
|
A:GLU80
|
4.1
|
53.5
|
1.0
|
CA
|
A:ASP108
|
4.1
|
53.8
|
1.0
|
CB
|
A:ASP108
|
4.2
|
53.8
|
1.0
|
O9
|
A:M4H801
|
4.2
|
65.6
|
1.0
|
CA
|
A:PRO107
|
4.4
|
49.1
|
1.0
|
C
|
A:LEU106
|
4.5
|
45.8
|
1.0
|
CB
|
A:GLU80
|
4.5
|
53.5
|
1.0
|
OE2
|
A:GLU119
|
4.5
|
61.8
|
1.0
|
CE1
|
A:HIS41
|
4.5
|
63.9
|
1.0
|
CD
|
A:GLU119
|
4.6
|
61.8
|
1.0
|
C2
|
A:M4H801
|
4.7
|
65.6
|
1.0
|
CG
|
A:GLU80
|
4.8
|
53.5
|
1.0
|
N
|
A:PRO107
|
4.9
|
49.1
|
1.0
|
CA
|
A:GLU80
|
4.9
|
53.5
|
1.0
|
C5
|
A:M4H801
|
5.0
|
65.6
|
1.0
|
NE2
|
A:HIS41
|
5.0
|
63.9
|
1.0
|
OE2
|
A:GLU80
|
5.0
|
53.5
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6szu
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Magnesium Binding Sites List in 6szu
Magnesium binding site 2 out
of 6 in the Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:59.3
occ:1.00
|
OD2
|
A:ASP108
|
2.0
|
53.8
|
1.0
|
O11
|
A:M4H801
|
2.0
|
65.6
|
1.0
|
O10
|
A:M4H801
|
2.1
|
65.6
|
1.0
|
O
|
A:ILE120
|
2.1
|
61.2
|
1.0
|
NE2
|
A:HIS41
|
2.2
|
63.9
|
1.0
|
OE2
|
A:GLU119
|
2.4
|
61.8
|
1.0
|
C2
|
A:M4H801
|
2.6
|
65.6
|
1.0
|
C1
|
A:M4H801
|
2.6
|
65.6
|
1.0
|
CE1
|
A:HIS41
|
2.9
|
63.9
|
1.0
|
CG
|
A:ASP108
|
2.9
|
53.8
|
1.0
|
OD1
|
A:ASP108
|
3.2
|
53.8
|
1.0
|
C
|
A:ILE120
|
3.3
|
61.2
|
1.0
|
CD2
|
A:HIS41
|
3.3
|
63.9
|
1.0
|
CD
|
A:GLU119
|
3.4
|
61.8
|
1.0
|
N
|
A:ILE120
|
3.8
|
61.2
|
1.0
|
OE1
|
A:GLU119
|
3.8
|
61.8
|
1.0
|
C3
|
A:M4H801
|
3.9
|
65.6
|
1.0
|
MG
|
A:MG802
|
3.9
|
49.6
|
1.0
|
CA
|
A:ILE120
|
4.0
|
61.2
|
1.0
|
C6
|
A:M4H801
|
4.0
|
65.6
|
1.0
|
ND1
|
A:HIS41
|
4.1
|
63.9
|
1.0
|
CB
|
A:ILE120
|
4.3
|
61.2
|
1.0
|
CG
|
A:HIS41
|
4.3
|
63.9
|
1.0
|
CB
|
A:ASP108
|
4.3
|
53.8
|
1.0
|
N
|
A:GLY121
|
4.3
|
67.9
|
1.0
|
CG
|
A:GLU119
|
4.6
|
61.8
|
1.0
|
CA
|
A:GLY121
|
4.6
|
67.9
|
1.0
|
CG2
|
A:ILE120
|
4.8
|
61.2
|
1.0
|
CE
|
A:LYS134
|
4.8
|
74.7
|
1.0
|
C
|
A:GLU119
|
4.8
|
61.8
|
1.0
|
NZ
|
A:LYS134
|
4.8
|
74.7
|
1.0
|
O8
|
A:M4H801
|
4.8
|
65.6
|
1.0
|
N4
|
A:M4H801
|
4.8
|
65.6
|
1.0
|
C5
|
A:M4H801
|
4.9
|
65.6
|
1.0
|
OE1
|
A:GLU80
|
4.9
|
53.5
|
1.0
|
C7
|
A:M4H801
|
4.9
|
65.6
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6szu
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Magnesium Binding Sites List in 6szu
Magnesium binding site 3 out
of 6 in the Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg801
b:11.7
occ:1.00
|
OD1
|
B:ASP445
|
2.1
|
14.8
|
1.0
|
OD1
|
B:ASP446
|
2.1
|
15.1
|
1.0
|
OD1
|
B:ASP305
|
2.1
|
14.4
|
1.0
|
O3'
|
M:C36
|
2.4
|
20.3
|
1.0
|
O
|
B:HOH1021
|
2.6
|
17.1
|
1.0
|
OP1
|
M:A37
|
2.7
|
19.6
|
1.0
|
CG
|
B:ASP445
|
2.8
|
14.8
|
1.0
|
OD2
|
B:ASP445
|
2.8
|
14.8
|
1.0
|
P
|
M:A37
|
3.2
|
19.6
|
1.0
|
CG
|
B:ASP446
|
3.2
|
15.1
|
1.0
|
CG
|
B:ASP305
|
3.3
|
14.4
|
1.0
|
O
|
B:HOH962
|
3.4
|
17.6
|
1.0
|
C3'
|
M:C36
|
3.6
|
20.3
|
1.0
|
OD2
|
B:ASP305
|
3.8
|
14.4
|
1.0
|
MG
|
B:MG802
|
3.8
|
8.9
|
1.0
|
C4'
|
M:C36
|
3.9
|
20.3
|
1.0
|
OD2
|
B:ASP446
|
3.9
|
15.1
|
1.0
|
O2'
|
M:C36
|
4.1
|
20.3
|
1.0
|
N
|
B:ASP446
|
4.1
|
15.1
|
1.0
|
O5'
|
M:A37
|
4.2
|
19.6
|
1.0
|
C5'
|
M:A37
|
4.2
|
19.6
|
1.0
|
CB
|
B:ASP445
|
4.2
|
14.8
|
1.0
|
CB
|
B:ASP446
|
4.3
|
15.1
|
1.0
|
OP2
|
M:A37
|
4.3
|
19.6
|
1.0
|
C5'
|
M:C36
|
4.3
|
20.3
|
1.0
|
CA
|
B:ASP446
|
4.3
|
15.1
|
1.0
|
C
|
B:ASP445
|
4.4
|
14.8
|
1.0
|
C2'
|
M:C36
|
4.5
|
20.3
|
1.0
|
CB
|
B:ASP305
|
4.5
|
14.4
|
1.0
|
O
|
M:HOH206
|
4.5
|
14.4
|
1.0
|
O
|
B:ASP445
|
4.8
|
14.8
|
1.0
|
CA
|
B:ASP445
|
4.8
|
14.8
|
1.0
|
CA
|
B:ASP305
|
4.9
|
14.4
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6szu
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Magnesium Binding Sites List in 6szu
Magnesium binding site 4 out
of 6 in the Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg802
b:8.9
occ:1.00
|
O
|
B:ASN306
|
2.2
|
13.0
|
1.0
|
OD2
|
B:ASP445
|
2.4
|
14.8
|
1.0
|
OP1
|
M:A37
|
2.5
|
19.6
|
1.0
|
O4
|
B:POP803
|
2.6
|
18.5
|
1.0
|
OD2
|
B:ASP305
|
2.6
|
14.4
|
1.0
|
O3
|
B:POP803
|
2.7
|
18.5
|
1.0
|
O1
|
B:POP803
|
3.3
|
18.5
|
1.0
|
CG
|
B:ASP305
|
3.3
|
14.4
|
1.0
|
P1
|
B:POP803
|
3.3
|
18.5
|
1.0
|
C
|
B:ASN306
|
3.4
|
13.0
|
1.0
|
OD1
|
B:ASP305
|
3.5
|
14.4
|
1.0
|
O
|
B:POP803
|
3.5
|
18.5
|
1.0
|
CG
|
B:ASP445
|
3.6
|
14.8
|
1.0
|
P2
|
B:POP803
|
3.6
|
18.5
|
1.0
|
MG
|
B:MG801
|
3.8
|
11.7
|
1.0
|
N
|
B:ASN306
|
3.9
|
13.0
|
1.0
|
P
|
M:A37
|
4.0
|
19.6
|
1.0
|
NZ
|
B:LYS481
|
4.0
|
14.2
|
1.0
|
OD1
|
B:ASP445
|
4.2
|
14.8
|
1.0
|
CA
|
B:ASN306
|
4.2
|
13.0
|
1.0
|
O
|
B:HOH929
|
4.3
|
16.3
|
1.0
|
C5'
|
M:A37
|
4.3
|
19.6
|
1.0
|
O5'
|
M:A37
|
4.5
|
19.6
|
1.0
|
N
|
B:THR307
|
4.5
|
13.8
|
1.0
|
O5
|
B:POP803
|
4.5
|
18.5
|
1.0
|
CB
|
B:ASP445
|
4.6
|
14.8
|
1.0
|
CB
|
B:ASP305
|
4.6
|
14.4
|
1.0
|
N
|
B:LYS308
|
4.7
|
16.2
|
1.0
|
CA
|
B:THR307
|
4.7
|
13.8
|
1.0
|
O6
|
B:POP803
|
4.7
|
18.5
|
1.0
|
CE
|
B:LYS481
|
4.8
|
14.2
|
1.0
|
O2
|
B:POP803
|
4.8
|
18.5
|
1.0
|
O3'
|
M:C36
|
4.8
|
20.3
|
1.0
|
CB
|
B:ASN306
|
4.9
|
13.0
|
1.0
|
C
|
B:ASP305
|
4.9
|
14.4
|
1.0
|
O
|
B:HOH1021
|
4.9
|
17.1
|
1.0
|
OP2
|
M:A37
|
4.9
|
19.6
|
1.0
|
C
|
B:THR307
|
4.9
|
13.8
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6szu
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Magnesium Binding Sites List in 6szu
Magnesium binding site 5 out
of 6 in the Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg101
b:21.6
occ:1.00
|
O
|
V:HOH230
|
2.1
|
16.4
|
1.0
|
O
|
V:HOH209
|
2.4
|
17.2
|
1.0
|
O
|
V:HOH252
|
2.5
|
19.4
|
1.0
|
O4
|
V:U3
|
3.6
|
20.3
|
1.0
|
O
|
V:HOH214
|
4.0
|
17.4
|
1.0
|
N7
|
V:G2
|
4.1
|
19.2
|
1.0
|
O6
|
V:G2
|
4.1
|
19.2
|
1.0
|
O
|
V:HOH246
|
4.3
|
16.1
|
1.0
|
C4
|
V:U3
|
4.5
|
20.3
|
1.0
|
C5
|
V:G2
|
4.7
|
19.2
|
1.0
|
C6
|
V:G2
|
4.7
|
19.2
|
1.0
|
N1
|
V:A4
|
4.7
|
20.3
|
1.0
|
O
|
V:HOH234
|
4.8
|
20.4
|
1.0
|
C5
|
V:U3
|
4.9
|
20.3
|
1.0
|
OP2
|
V:A1
|
4.9
|
20.3
|
1.0
|
N6
|
V:A8
|
5.0
|
24.8
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6szu
Go back to
Magnesium Binding Sites List in 6szu
Magnesium binding site 6 out
of 6 in the Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Bat Influenza A Polymerase Pre-Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg101
b:26.3
occ:1.00
|
N7
|
M:A33
|
2.2
|
28.3
|
1.0
|
O
|
M:HOH202
|
2.2
|
20.4
|
1.0
|
C5
|
M:A33
|
3.1
|
28.3
|
1.0
|
N6
|
M:A33
|
3.2
|
28.3
|
1.0
|
C8
|
M:A33
|
3.2
|
28.3
|
1.0
|
N7
|
M:G32
|
3.5
|
24.0
|
1.0
|
C5
|
M:G32
|
3.5
|
24.0
|
1.0
|
C6
|
M:A33
|
3.5
|
28.3
|
1.0
|
C6
|
M:G32
|
3.8
|
24.0
|
1.0
|
N4
|
M:C34
|
4.0
|
20.8
|
1.0
|
C8
|
M:G32
|
4.0
|
24.0
|
1.0
|
O6
|
M:G32
|
4.1
|
24.0
|
1.0
|
C4
|
M:G32
|
4.1
|
24.0
|
1.0
|
C4
|
M:A33
|
4.3
|
28.3
|
1.0
|
N9
|
M:G32
|
4.3
|
24.0
|
1.0
|
N9
|
M:A33
|
4.3
|
28.3
|
1.0
|
N1
|
M:G32
|
4.6
|
24.0
|
1.0
|
C5
|
M:C34
|
4.6
|
20.8
|
1.0
|
C4
|
M:C34
|
4.6
|
20.8
|
1.0
|
O
|
M:HOH203
|
4.7
|
21.7
|
1.0
|
OP2
|
M:A33
|
4.7
|
28.3
|
1.0
|
N3
|
M:G32
|
4.8
|
24.0
|
1.0
|
N1
|
M:A33
|
4.9
|
28.3
|
1.0
|
C2
|
M:G32
|
5.0
|
24.0
|
1.0
|
|
Reference:
J.M.Wandzik,
T.Kouba,
M.Karuppasamy,
A.Pflug,
P.Drncova,
J.Provaznik,
N.Azevedo,
S.Cusack.
A Structure-Based Model For the Complete Transcription Cycle of Influenza Polymerase Cell(Cambridge,Mass.) 2020.
ISSN: ISSN 0092-8674
Page generated: Tue Oct 1 18:30:32 2024
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