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Magnesium in PDB 6tw1: Bat Influenza A Polymerase Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence

Enzymatic activity of Bat Influenza A Polymerase Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence

All present enzymatic activity of Bat Influenza A Polymerase 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 Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence (pdb code 6tw1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Bat Influenza A Polymerase Termination Complex with Pyrophosphate Using 44-Mer Vrna Template with Mutated Oligo(U) Sequence, PDB code: 6tw1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6tw1

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Magnesium binding site 1 out of 4 in the Bat Influenza A Polymerase 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 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:41.0
occ:1.00
 OD1 A:ASP108 2.0 38.9 1.0
O8 A:M4H801 2.1 50.4 1.0
OE1 A:GLU80 2.1 40.1 1.0
O10 A:M4H801 2.1 50.4 1.0
C7 A:M4H801 2.3 50.4 1.0
C1 A:M4H801 2.5 50.4 1.0
C6 A:M4H801 2.5 50.4 1.0
CG A:ASP108 3.0 38.9 1.0
CD A:GLU80 3.2 40.1 1.0
O9 A:M4H801 3.2 50.4 1.0
MG A:MG803 3.4 41.1 1.0
OD2 A:ASP108 3.4 38.9 1.0
CE1 A:HIS41 3.5 49.2 1.0
C5 A:M4H801 3.8 50.4 1.0
C2 A:M4H801 3.8 50.4 1.0
NE2 A:HIS41 3.9 49.2 1.0
OE2 A:GLU80 3.9 40.1 1.0
CG A:GLU80 4.1 40.1 1.0
CB A:ASP108 4.3 38.9 1.0
CB A:GLU80 4.4 40.1 1.0
ND1 A:HIS41 4.5 49.2 1.0
O A:PRO107 4.5 35.8 1.0
O11 A:M4H801 4.6 50.4 1.0
OE1 A:GLU119 4.6 46.6 1.0
O A:LEU106 4.7 36.0 1.0
N4 A:M4H801 4.7 50.4 1.0
CA A:ASP108 4.7 38.9 1.0
C3 A:M4H801 4.7 50.4 1.0
OE2 A:GLU119 4.7 46.6 1.0
C A:PRO107 4.8 35.8 1.0
N A:ASP108 4.9 38.9 1.0

Magnesium binding site 2 out of 4 in 6tw1

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Magnesium binding site 2 out of 4 in the Bat Influenza A Polymerase 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 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:41.1
occ:1.00
 O11 A:M4H801 2.0 50.4 1.0
OD2 A:ASP108 2.1 38.9 1.0
O10 A:M4H801 2.1 50.4 1.0
O A:ILE120 2.1 46.1 1.0
OE2 A:GLU119 2.1 46.6 1.0
NE2 A:HIS41 2.3 49.2 1.0
C2 A:M4H801 2.5 50.4 1.0
C1 A:M4H801 2.5 50.4 1.0
CG A:ASP108 3.0 38.9 1.0
CE1 A:HIS41 3.0 49.2 1.0
CD A:GLU119 3.1 46.6 1.0
C A:ILE120 3.2 46.1 1.0
MG A:MG802 3.4 41.0 1.0
OD1 A:ASP108 3.4 38.9 1.0
CD2 A:HIS41 3.4 49.2 1.0
N A:ILE120 3.5 46.1 1.0
OE1 A:GLU119 3.6 46.6 1.0
C3 A:M4H801 3.7 50.4 1.0
C6 A:M4H801 3.8 50.4 1.0
CA A:ILE120 3.9 46.1 1.0
N A:GLY121 4.2 52.2 1.0
ND1 A:HIS41 4.2 49.2 1.0
CB A:ASP108 4.3 38.9 1.0
CG A:GLU119 4.3 46.6 1.0
CB A:ILE120 4.4 46.1 1.0
CG A:HIS41 4.4 49.2 1.0
CA A:GLY121 4.5 52.2 1.0
C A:GLU119 4.6 46.6 1.0
N4 A:M4H801 4.6 50.4 1.0
C5 A:M4H801 4.7 50.4 1.0
C7 A:M4H801 4.8 50.4 1.0
O8 A:M4H801 4.8 50.4 1.0
CA A:GLU119 4.9 46.6 1.0
OE1 A:GLU80 5.0 40.1 1.0

Magnesium binding site 3 out of 4 in 6tw1

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Magnesium binding site 3 out of 4 in the Bat Influenza A Polymerase 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 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:13.7
occ:1.00
 OD1 B:ASP305 2.0 13.1 1.0
OD1 B:ASP445 2.1 16.3 1.0
OD1 B:ASP446 2.1 15.9 1.0
O3' M:A36 2.4 23.3 1.0
OP1 M:U37 2.4 23.3 1.0
P M:U37 2.9 23.3 1.0
CG B:ASP445 3.0 16.3 1.0
CG B:ASP305 3.0 13.1 1.0
CG B:ASP446 3.2 15.9 1.0
OD2 B:ASP445 3.2 16.3 1.0
OD2 B:ASP305 3.3 13.1 1.0
C3' M:A36 3.6 23.3 1.0
OD2 B:ASP446 3.8 15.9 1.0
MG B:MG802 3.8 11.7 1.0
C4' M:A36 3.9 23.3 1.0
OP2 M:U37 4.0 23.3 1.0
O5' M:U37 4.0 23.3 1.0
C5' M:U37 4.2 23.3 1.0
C5' M:A36 4.3 23.3 1.0
O2' M:A36 4.3 23.3 1.0
CB B:ASP446 4.3 15.9 1.0
N B:ASP446 4.3 15.9 1.0
CB B:ASP305 4.4 13.1 1.0
CB B:ASP445 4.4 16.3 1.0
CA B:ASP446 4.5 15.9 1.0
C2' M:A36 4.6 23.3 1.0
C B:ASP445 4.6 16.3 1.0
CA B:ASP305 4.9 13.1 1.0
CA B:ASP445 5.0 16.3 1.0

Magnesium binding site 4 out of 4 in 6tw1

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Magnesium binding site 4 out of 4 in the Bat Influenza A Polymerase 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 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:11.7
occ:1.00
 OD2 B:ASP305 2.2 13.1 1.0
O1 B:POP803 2.3 19.3 1.0
O B:ASN306 2.4 12.2 1.0
OP1 M:U37 2.5 23.3 1.0
OD2 B:ASP445 2.7 16.3 1.0
O B:POP803 3.0 19.3 1.0
P1 B:POP803 3.1 19.3 1.0
CG B:ASP305 3.3 13.1 1.0
O3 B:POP803 3.4 19.3 1.0
O4 B:POP803 3.5 19.3 1.0
CG B:ASP445 3.6 16.3 1.0
C B:ASN306 3.6 12.2 1.0
P2 B:POP803 3.6 19.3 1.0
O6 B:POP803 3.7 19.3 1.0
OD1 B:ASP305 3.8 13.1 1.0
MG B:MG801 3.8 13.7 1.0
P M:U37 3.9 23.3 1.0
OD1 B:ASP445 3.9 16.3 1.0
N B:ASN306 3.9 12.2 1.0
NZ B:LYS481 4.1 12.9 1.0
O B:HOH901 4.2 16.0 1.0
C5' M:U37 4.2 23.3 1.0
O5' M:U37 4.3 23.3 1.0
CA B:ASN306 4.3 12.2 1.0
O2 B:POP803 4.5 19.3 1.0
CB B:ASP305 4.5 13.1 1.0
N B:THR307 4.6 13.8 1.0
CB B:ASP445 4.7 16.3 1.0
N B:LYS308 4.7 15.9 1.0
CA B:THR307 4.8 13.8 1.0
CB B:TRP309 4.8 13.7 1.0
O3' M:A36 4.9 23.3 1.0
CB B:ASN306 4.9 12.2 1.0
OP2 M:U37 4.9 23.3 1.0
N B:TRP309 4.9 13.7 1.0
C B:ASP305 5.0 13.1 1.0
CE B:LYS481 5.0 12.9 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 20:32:56 2024

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