Magnesium in PDB 6t0v: Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Complete Polymerase)
Enzymatic activity of Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Complete Polymerase)
All present enzymatic activity of Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Complete Polymerase):
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 (Complete Polymerase)
(pdb code 6t0v). 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 (Complete Polymerase), PDB code: 6t0v:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6t0v
Go back to
Magnesium Binding Sites List in 6t0v
Magnesium binding site 1 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Complete Polymerase)
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 (Complete Polymerase) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:66.6
occ:1.00
|
O11
|
A:M4H801
|
1.9
|
59.6
|
1.0
|
OE2
|
A:GLU119
|
1.9
|
54.9
|
1.0
|
OD2
|
A:ASP108
|
1.9
|
50.1
|
1.0
|
O
|
A:ILE120
|
1.9
|
56.7
|
1.0
|
C
|
A:ILE120
|
2.8
|
56.7
|
1.0
|
CD
|
A:GLU119
|
2.9
|
54.9
|
1.0
|
CG
|
A:ASP108
|
3.0
|
50.1
|
1.0
|
NE2
|
A:HIS41
|
3.0
|
59.8
|
1.0
|
N
|
A:ILE120
|
3.0
|
56.7
|
1.0
|
C2
|
A:M4H801
|
3.1
|
59.6
|
1.0
|
CA
|
A:ILE120
|
3.5
|
56.7
|
1.0
|
CG
|
A:GLU119
|
3.5
|
54.9
|
1.0
|
OD1
|
A:ASP108
|
3.7
|
50.1
|
1.0
|
N
|
A:GLY121
|
3.8
|
61.2
|
1.0
|
CE1
|
A:HIS41
|
3.8
|
59.8
|
1.0
|
OE1
|
A:GLU119
|
3.8
|
54.9
|
1.0
|
C
|
A:GLU119
|
4.0
|
54.9
|
1.0
|
C3
|
A:M4H801
|
4.0
|
59.6
|
1.0
|
O10
|
A:M4H801
|
4.0
|
59.6
|
1.0
|
CB
|
A:ASP108
|
4.0
|
50.1
|
1.0
|
C1
|
A:M4H801
|
4.0
|
59.6
|
1.0
|
CD2
|
A:HIS41
|
4.1
|
59.8
|
1.0
|
CA
|
A:GLY121
|
4.1
|
61.2
|
1.0
|
CB
|
A:ILE120
|
4.3
|
56.7
|
1.0
|
CA
|
A:GLU119
|
4.4
|
54.9
|
1.0
|
CB
|
A:GLU119
|
4.5
|
54.9
|
1.0
|
MG
|
A:MG803
|
4.6
|
61.6
|
1.0
|
NZ
|
A:LYS134
|
4.7
|
67.0
|
1.0
|
O
|
A:GLU119
|
4.9
|
54.9
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6t0v
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Magnesium Binding Sites List in 6t0v
Magnesium binding site 2 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Complete Polymerase)
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 (Complete Polymerase) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:61.6
occ:1.00
|
OD1
|
A:ASP108
|
1.9
|
50.1
|
1.0
|
O10
|
A:M4H801
|
1.9
|
59.6
|
1.0
|
OE1
|
A:GLU80
|
2.2
|
51.1
|
1.0
|
CG
|
A:ASP108
|
2.9
|
50.1
|
1.0
|
C1
|
A:M4H801
|
2.9
|
59.6
|
1.0
|
CD
|
A:GLU80
|
3.4
|
51.1
|
1.0
|
OD2
|
A:ASP108
|
3.5
|
50.1
|
1.0
|
O8
|
A:M4H801
|
3.6
|
59.6
|
1.0
|
O
|
A:LEU106
|
3.7
|
42.3
|
1.0
|
O
|
A:PRO107
|
3.7
|
44.4
|
1.0
|
C2
|
A:M4H801
|
3.8
|
59.6
|
1.0
|
O11
|
A:M4H801
|
3.8
|
59.6
|
1.0
|
C6
|
A:M4H801
|
4.0
|
59.6
|
1.0
|
C
|
A:PRO107
|
4.1
|
44.4
|
1.0
|
OE2
|
A:GLU80
|
4.1
|
51.1
|
1.0
|
CB
|
A:ASP108
|
4.1
|
50.1
|
1.0
|
CA
|
A:ASP108
|
4.2
|
50.1
|
1.0
|
C7
|
A:M4H801
|
4.3
|
59.6
|
1.0
|
N
|
A:ASP108
|
4.3
|
50.1
|
1.0
|
CG
|
A:GLU80
|
4.4
|
51.1
|
1.0
|
C
|
A:LEU106
|
4.5
|
42.3
|
1.0
|
CB
|
A:GLU80
|
4.6
|
51.1
|
1.0
|
OE2
|
A:GLU119
|
4.6
|
54.9
|
1.0
|
MG
|
A:MG802
|
4.6
|
66.6
|
1.0
|
OE1
|
A:GLU119
|
4.7
|
54.9
|
1.0
|
CA
|
A:PRO107
|
4.9
|
44.4
|
1.0
|
CE1
|
A:HIS41
|
4.9
|
59.8
|
1.0
|
CB
|
A:LEU106
|
4.9
|
42.3
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6t0v
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Magnesium Binding Sites List in 6t0v
Magnesium binding site 3 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Complete Polymerase)
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 (Complete Polymerase) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg802
b:22.5
occ:1.00
|
O1B
|
B:2KH801
|
2.1
|
26.8
|
1.0
|
O2A
|
B:2KH801
|
2.1
|
26.8
|
1.0
|
O2G
|
B:2KH801
|
2.1
|
26.8
|
1.0
|
O
|
B:ASN306
|
2.3
|
20.2
|
1.0
|
OD2
|
B:ASP445
|
2.8
|
20.5
|
1.0
|
OD2
|
B:ASP305
|
2.8
|
20.4
|
1.0
|
OD1
|
B:ASP305
|
3.2
|
20.4
|
1.0
|
PB
|
B:2KH801
|
3.2
|
26.8
|
1.0
|
CG
|
B:ASP305
|
3.3
|
20.4
|
1.0
|
PA
|
B:2KH801
|
3.3
|
26.8
|
1.0
|
PG
|
B:2KH801
|
3.4
|
26.8
|
1.0
|
CG
|
B:ASP445
|
3.4
|
20.5
|
1.0
|
C
|
B:ASN306
|
3.5
|
20.2
|
1.0
|
N3A
|
B:2KH801
|
3.6
|
26.8
|
1.0
|
OD1
|
B:ASP445
|
3.7
|
20.5
|
1.0
|
O3B
|
B:2KH801
|
3.7
|
26.8
|
1.0
|
C5'
|
B:2KH801
|
4.0
|
26.8
|
1.0
|
MG
|
B:MG804
|
4.0
|
21.5
|
1.0
|
N
|
B:ASN306
|
4.1
|
20.2
|
1.0
|
O5'
|
B:2KH801
|
4.2
|
26.8
|
1.0
|
O1G
|
B:2KH801
|
4.3
|
26.8
|
1.0
|
CA
|
B:ASN306
|
4.4
|
20.2
|
1.0
|
O1A
|
B:2KH801
|
4.4
|
26.8
|
1.0
|
O2B
|
B:2KH801
|
4.4
|
26.8
|
1.0
|
N
|
B:THR307
|
4.4
|
21.1
|
1.0
|
O3G
|
B:2KH801
|
4.5
|
26.8
|
1.0
|
CA
|
B:THR307
|
4.5
|
21.1
|
1.0
|
CB
|
B:TRP309
|
4.5
|
21.2
|
1.0
|
N
|
B:LYS308
|
4.6
|
23.7
|
1.0
|
CB
|
B:ASP445
|
4.6
|
20.5
|
1.0
|
NZ
|
B:LYS481
|
4.7
|
19.5
|
1.0
|
CB
|
B:ASP305
|
4.7
|
20.4
|
1.0
|
N
|
B:TRP309
|
4.8
|
21.2
|
1.0
|
C
|
B:ASP305
|
4.9
|
20.4
|
1.0
|
C
|
B:THR307
|
4.9
|
21.1
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6t0v
Go back to
Magnesium Binding Sites List in 6t0v
Magnesium binding site 4 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Complete Polymerase)
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 (Complete Polymerase) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg803
b:17.0
occ:1.00
|
O
|
B:GLY304
|
2.8
|
17.6
|
1.0
|
CB
|
B:ASP446
|
2.9
|
19.1
|
1.0
|
OD2
|
B:ASP446
|
3.4
|
19.1
|
1.0
|
CG
|
B:ASP446
|
3.6
|
19.1
|
1.0
|
CA
|
B:ASP446
|
3.7
|
19.1
|
1.0
|
C
|
B:GLY304
|
4.0
|
17.6
|
1.0
|
N
|
B:THR493
|
4.0
|
17.2
|
1.0
|
N
|
B:PHE447
|
4.2
|
16.8
|
1.0
|
C
|
B:ASP446
|
4.3
|
19.1
|
1.0
|
O
|
B:GLU491
|
4.4
|
16.2
|
1.0
|
CA
|
B:PHE492
|
4.5
|
16.9
|
1.0
|
OE2
|
B:GLU491
|
4.5
|
16.2
|
1.0
|
O
|
B:PHE447
|
4.6
|
16.8
|
1.0
|
N
|
B:GLY304
|
4.7
|
17.6
|
1.0
|
N
|
B:ASP305
|
4.8
|
20.4
|
1.0
|
C
|
B:PHE492
|
4.8
|
16.9
|
1.0
|
CD1
|
B:PHE492
|
4.8
|
16.9
|
1.0
|
MG
|
B:MG804
|
4.8
|
21.5
|
1.0
|
CB
|
B:ASP305
|
4.8
|
20.4
|
1.0
|
OD1
|
B:ASP446
|
4.8
|
19.1
|
1.0
|
CA
|
B:ASP305
|
4.8
|
20.4
|
1.0
|
CA
|
B:THR493
|
4.8
|
17.2
|
1.0
|
OD1
|
B:ASP305
|
4.8
|
20.4
|
1.0
|
N
|
B:ASP446
|
4.9
|
19.1
|
1.0
|
CA
|
B:GLY304
|
4.9
|
17.6
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6t0v
Go back to
Magnesium Binding Sites List in 6t0v
Magnesium binding site 5 out
of 5 in the Bat Influenza A Polymerase Elongation Complex with Incoming Utp Analogue (Complete Polymerase)
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 (Complete Polymerase) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg804
b:21.5
occ:1.00
|
OD1
|
B:ASP305
|
2.1
|
20.4
|
1.0
|
OD1
|
B:ASP445
|
2.4
|
20.5
|
1.0
|
OD2
|
B:ASP446
|
2.7
|
19.1
|
1.0
|
O3'
|
M:G26
|
2.7
|
22.7
|
1.0
|
O2A
|
B:2KH801
|
3.1
|
26.8
|
1.0
|
CG
|
B:ASP305
|
3.2
|
20.4
|
1.0
|
CG
|
B:ASP446
|
3.4
|
19.1
|
1.0
|
CG
|
B:ASP445
|
3.4
|
20.5
|
1.0
|
OD2
|
B:ASP445
|
3.8
|
20.5
|
1.0
|
OD2
|
B:ASP305
|
3.9
|
20.4
|
1.0
|
OD1
|
B:ASP446
|
3.9
|
19.1
|
1.0
|
C3'
|
M:G26
|
4.0
|
22.7
|
1.0
|
MG
|
B:MG802
|
4.0
|
22.5
|
1.0
|
PA
|
B:2KH801
|
4.0
|
26.8
|
1.0
|
O1A
|
B:2KH801
|
4.2
|
26.8
|
1.0
|
CB
|
B:ASP446
|
4.3
|
19.1
|
1.0
|
CB
|
B:ASP305
|
4.3
|
20.4
|
1.0
|
N
|
B:ASP446
|
4.3
|
19.1
|
1.0
|
O5'
|
B:2KH801
|
4.4
|
26.8
|
1.0
|
C5'
|
B:2KH801
|
4.5
|
26.8
|
1.0
|
CA
|
B:ASP446
|
4.5
|
19.1
|
1.0
|
C4'
|
M:G26
|
4.7
|
22.7
|
1.0
|
C5'
|
M:G26
|
4.7
|
22.7
|
1.0
|
CB
|
B:ASP445
|
4.7
|
20.5
|
1.0
|
MG
|
B:MG803
|
4.8
|
17.0
|
1.0
|
C
|
B:ASP445
|
4.8
|
20.5
|
1.0
|
CA
|
B:ASP305
|
4.9
|
20.4
|
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 18:34:26 2024
|