Magnesium in PDB 6szv: Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only)
Enzymatic activity of Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only)
All present enzymatic activity of Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only):
2.7.7.48;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only)
(pdb code 6szv). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only), PDB code: 6szv:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6szv
Go back to
Magnesium Binding Sites List in 6szv
Magnesium binding site 1 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only)
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 Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:48.2
occ:1.00
|
O8
|
A:M4H801
|
1.8
|
27.1
|
1.0
|
O10
|
A:M4H801
|
2.1
|
26.3
|
1.0
|
OD1
|
A:ASP108
|
2.2
|
51.0
|
1.0
|
OE1
|
A:GLU80
|
2.2
|
51.0
|
1.0
|
C7
|
A:M4H801
|
2.6
|
26.8
|
1.0
|
C1
|
A:M4H801
|
2.9
|
26.2
|
1.0
|
C6
|
A:M4H801
|
3.1
|
26.3
|
1.0
|
CG
|
A:ASP108
|
3.3
|
51.0
|
1.0
|
CD
|
A:GLU80
|
3.5
|
51.0
|
1.0
|
O9
|
A:M4H801
|
3.5
|
27.4
|
1.0
|
OD2
|
A:ASP108
|
3.9
|
51.0
|
1.0
|
MG
|
A:MG803
|
4.0
|
56.4
|
1.0
|
O
|
A:LEU106
|
4.0
|
44.1
|
1.0
|
CE1
|
A:HIS41
|
4.2
|
61.5
|
1.0
|
O
|
A:PRO107
|
4.2
|
46.3
|
1.0
|
OE2
|
A:GLU80
|
4.2
|
51.0
|
1.0
|
C2
|
A:M4H801
|
4.3
|
25.9
|
1.0
|
OE1
|
A:GLU119
|
4.3
|
59.5
|
1.0
|
C
|
A:PRO107
|
4.4
|
46.3
|
1.0
|
CG
|
A:GLU80
|
4.4
|
51.0
|
1.0
|
CB
|
A:ASP108
|
4.5
|
51.0
|
1.0
|
CA
|
A:ASP108
|
4.5
|
51.0
|
1.0
|
CB
|
A:GLU80
|
4.5
|
51.0
|
1.0
|
C5
|
A:M4H801
|
4.5
|
25.7
|
1.0
|
N
|
A:ASP108
|
4.6
|
51.0
|
1.0
|
OE2
|
A:GLU119
|
4.7
|
59.5
|
1.0
|
NE2
|
A:HIS41
|
4.7
|
61.5
|
1.0
|
O11
|
A:M4H801
|
4.9
|
26.0
|
1.0
|
CD
|
A:GLU119
|
5.0
|
59.5
|
1.0
|
C
|
A:LEU106
|
5.0
|
44.1
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6szv
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Magnesium Binding Sites List in 6szv
Magnesium binding site 2 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only)
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 Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:56.4
occ:1.00
|
O
|
A:ILE120
|
1.9
|
59.2
|
1.0
|
O11
|
A:M4H801
|
2.0
|
26.0
|
1.0
|
OD2
|
A:ASP108
|
2.1
|
51.0
|
1.0
|
NE2
|
A:HIS41
|
2.2
|
61.5
|
1.0
|
O10
|
A:M4H801
|
2.3
|
26.3
|
1.0
|
OE2
|
A:GLU119
|
2.4
|
59.5
|
1.0
|
C2
|
A:M4H801
|
2.8
|
25.9
|
1.0
|
C1
|
A:M4H801
|
2.9
|
26.2
|
1.0
|
CE1
|
A:HIS41
|
3.0
|
61.5
|
1.0
|
CG
|
A:ASP108
|
3.0
|
51.0
|
1.0
|
C
|
A:ILE120
|
3.0
|
59.2
|
1.0
|
OD1
|
A:ASP108
|
3.2
|
51.0
|
1.0
|
CD2
|
A:HIS41
|
3.2
|
61.5
|
1.0
|
CD
|
A:GLU119
|
3.4
|
59.5
|
1.0
|
NZ
|
A:LYS134
|
3.5
|
72.2
|
1.0
|
N
|
A:ILE120
|
3.6
|
59.2
|
1.0
|
CA
|
A:ILE120
|
3.8
|
59.2
|
1.0
|
OE1
|
A:GLU119
|
3.9
|
59.5
|
1.0
|
MG
|
A:MG802
|
4.0
|
48.2
|
1.0
|
ND1
|
A:HIS41
|
4.1
|
61.5
|
1.0
|
N
|
A:GLY121
|
4.1
|
63.7
|
1.0
|
C3
|
A:M4H801
|
4.1
|
25.7
|
1.0
|
CG
|
A:HIS41
|
4.2
|
61.5
|
1.0
|
CB
|
A:ILE120
|
4.3
|
59.2
|
1.0
|
C6
|
A:M4H801
|
4.3
|
26.3
|
1.0
|
CB
|
A:ASP108
|
4.3
|
51.0
|
1.0
|
CA
|
A:GLY121
|
4.4
|
63.7
|
1.0
|
CG
|
A:GLU119
|
4.6
|
59.5
|
1.0
|
C
|
A:GLU119
|
4.6
|
59.5
|
1.0
|
CE
|
A:LYS134
|
4.9
|
72.2
|
1.0
|
CG2
|
A:ILE120
|
4.9
|
59.2
|
1.0
|
OE1
|
A:GLU80
|
5.0
|
51.0
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6szv
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Magnesium Binding Sites List in 6szv
Magnesium binding site 3 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only)
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 Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg802
b:20.4
occ:1.00
|
O
|
B:ASN306
|
2.2
|
22.7
|
1.0
|
OD2
|
B:ASP305
|
2.2
|
23.6
|
1.0
|
O2A
|
B:2KH801
|
2.2
|
27.5
|
1.0
|
O2G
|
B:2KH801
|
2.2
|
27.5
|
1.0
|
O1B
|
B:2KH801
|
2.2
|
27.5
|
1.0
|
OD2
|
B:ASP445
|
2.3
|
24.1
|
1.0
|
CG
|
B:ASP305
|
3.2
|
23.6
|
1.0
|
CG
|
B:ASP445
|
3.3
|
24.1
|
1.0
|
C
|
B:ASN306
|
3.3
|
22.7
|
1.0
|
PB
|
B:2KH801
|
3.3
|
27.5
|
1.0
|
PA
|
B:2KH801
|
3.4
|
27.5
|
1.0
|
PG
|
B:2KH801
|
3.5
|
27.5
|
1.0
|
N
|
B:ASN306
|
3.5
|
22.7
|
1.0
|
OD1
|
B:ASP305
|
3.7
|
23.6
|
1.0
|
N3A
|
B:2KH801
|
3.7
|
27.5
|
1.0
|
O3B
|
B:2KH801
|
3.8
|
27.5
|
1.0
|
OD1
|
B:ASP445
|
3.9
|
24.1
|
1.0
|
MG
|
B:MG803
|
3.9
|
21.3
|
1.0
|
NZ
|
B:LYS481
|
3.9
|
24.1
|
1.0
|
CA
|
B:ASN306
|
3.9
|
22.7
|
1.0
|
O3G
|
B:2KH801
|
4.2
|
27.5
|
1.0
|
CB
|
B:ASP445
|
4.3
|
24.1
|
1.0
|
CB
|
B:ASP305
|
4.3
|
23.6
|
1.0
|
C5'
|
B:2KH801
|
4.4
|
27.5
|
1.0
|
O5'
|
B:2KH801
|
4.4
|
27.5
|
1.0
|
N
|
B:THR307
|
4.4
|
24.1
|
1.0
|
O1A
|
B:2KH801
|
4.4
|
27.5
|
1.0
|
CB
|
B:ASN306
|
4.5
|
22.7
|
1.0
|
O2B
|
B:2KH801
|
4.6
|
27.5
|
1.0
|
O1G
|
B:2KH801
|
4.6
|
27.5
|
1.0
|
C
|
B:ASP305
|
4.6
|
23.6
|
1.0
|
CA
|
B:THR307
|
4.7
|
24.1
|
1.0
|
N
|
B:LYS308
|
4.7
|
24.3
|
1.0
|
CA
|
B:ASP305
|
4.8
|
23.6
|
1.0
|
CB
|
B:TRP309
|
5.0
|
23.5
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6szv
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Magnesium Binding Sites List in 6szv
Magnesium binding site 4 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only)
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 Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg803
b:21.3
occ:1.00
|
O3'
|
M:G26
|
2.1
|
25.3
|
1.0
|
OD1
|
B:ASP445
|
2.2
|
24.1
|
1.0
|
OD1
|
B:ASP305
|
2.4
|
23.6
|
1.0
|
O2A
|
B:2KH801
|
2.8
|
27.5
|
1.0
|
OD1
|
B:ASP446
|
3.0
|
23.7
|
1.0
|
CG
|
B:ASP445
|
3.0
|
24.1
|
1.0
|
OD2
|
B:ASP445
|
3.0
|
24.1
|
1.0
|
OD2
|
B:ASP446
|
3.2
|
23.7
|
1.0
|
CG
|
B:ASP446
|
3.3
|
23.7
|
1.0
|
CG
|
B:ASP305
|
3.4
|
23.6
|
1.0
|
C3'
|
M:G26
|
3.5
|
25.3
|
1.0
|
OD2
|
B:ASP305
|
3.6
|
23.6
|
1.0
|
PA
|
B:2KH801
|
3.7
|
27.5
|
1.0
|
O1A
|
B:2KH801
|
3.9
|
27.5
|
1.0
|
O5'
|
B:2KH801
|
3.9
|
27.5
|
1.0
|
MG
|
B:MG802
|
3.9
|
20.4
|
1.0
|
C4'
|
M:G26
|
4.1
|
25.3
|
1.0
|
O2'
|
M:G26
|
4.2
|
25.3
|
1.0
|
N
|
B:ASP446
|
4.3
|
23.7
|
1.0
|
CB
|
B:ASP445
|
4.4
|
24.1
|
1.0
|
C2'
|
M:G26
|
4.4
|
25.3
|
1.0
|
C5'
|
B:2KH801
|
4.5
|
27.5
|
1.0
|
CB
|
B:ASP446
|
4.5
|
23.7
|
1.0
|
C5'
|
M:G26
|
4.5
|
25.3
|
1.0
|
C
|
B:ASP445
|
4.6
|
24.1
|
1.0
|
CA
|
B:ASP446
|
4.6
|
23.7
|
1.0
|
CB
|
B:ASP305
|
4.7
|
23.6
|
1.0
|
CA
|
B:ASP445
|
5.0
|
24.1
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6szv
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Magnesium Binding Sites List in 6szv
Magnesium binding site 5 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only)
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 Elongation Complex with Incoming Utp Analogue (Core + Endonuclease Only) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg101
b:31.5
occ:1.00
|
O
|
V:HOH212
|
2.1
|
25.3
|
1.0
|
O
|
V:HOH209
|
2.1
|
26.9
|
1.0
|
O
|
V:HOH233
|
2.1
|
30.8
|
1.0
|
O
|
V:HOH224
|
2.2
|
21.0
|
1.0
|
N7
|
V:G2
|
3.6
|
18.4
|
1.0
|
OP2
|
V:A1
|
3.6
|
30.2
|
1.0
|
O6
|
V:G2
|
3.7
|
18.4
|
1.0
|
C5
|
V:G2
|
4.3
|
18.4
|
1.0
|
OP1
|
V:A1
|
4.3
|
30.2
|
1.0
|
O4
|
V:U3
|
4.3
|
30.2
|
1.0
|
C6
|
V:G2
|
4.4
|
18.4
|
1.0
|
P
|
V:A1
|
4.4
|
30.2
|
1.0
|
C8
|
V:G2
|
4.6
|
18.4
|
1.0
|
O5'
|
V:A1
|
4.8
|
30.2
|
1.0
|
OP2
|
V:G2
|
4.9
|
18.4
|
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 18:30:53 2024
|