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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 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 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 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 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 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

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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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