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

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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 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 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 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 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 Dec 15 00:06:56 2020

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