Magnesium in PDB 9f37: Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10)

Enzymatic activity of Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10)

All present enzymatic activity of Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10):
2.7.7.48;

Protein crystallography data

The structure of Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10), PDB code: 9f37 was solved by S.Cusack, P.Drncova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.57 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.937, 119.005, 251.381, 90, 90, 90
R / Rfree (%) 18.9 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10) (pdb code 9f37). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10), PDB code: 9f37:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 9f37

Go back to Magnesium Binding Sites List in 9f37
Magnesium binding site 1 out of 2 in the Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg806

b:35.7
occ:1.00
 OD2 B:ASP305 2.2 45.9 1.0
O3' B:GTP805 2.3 42.0 1.0
OD1 B:ASP446 2.3 34.5 1.0
OD1 B:ASP445 2.3 39.2 1.0
O1A B:CTP804 2.5 30.2 1.0
O2' B:GTP805 2.7 39.6 1.0
O B:HOH941 2.9 57.3 1.0
CG B:ASP446 3.2 33.6 1.0
C3' B:GTP805 3.3 47.5 1.0
CG B:ASP445 3.3 36.6 1.0
CG B:ASP305 3.4 33.3 1.0
C2' B:GTP805 3.4 44.1 1.0
PA B:CTP804 3.5 40.1 1.0
OD2 B:ASP446 3.5 34.4 1.0
OD2 B:ASP445 3.6 36.8 1.0
MG B:MG807 3.7 24.9 1.0
O5' B:CTP804 3.8 34.5 1.0
O B:HOH927 3.8 41.5 1.0
C5' B:CTP804 3.9 34.9 1.0
C4' B:GTP805 3.9 45.2 1.0
OD1 B:ASP305 3.9 34.6 1.0
O2A B:CTP804 4.0 33.5 1.0
O B:HOH1148 4.5 56.6 1.0
CB B:ASP446 4.5 31.7 1.0
CB B:ASP305 4.5 32.7 1.0
N B:ASP446 4.6 33.9 1.0
CB B:ASP445 4.7 34.3 1.0
CA B:ASP446 4.7 30.7 1.0
C B:ASP445 4.8 37.8 1.0
O2B B:GTP805 4.8 66.8 1.0
C1' B:GTP805 4.8 43.7 1.0
C5' B:GTP805 4.9 53.4 1.0
O4' B:GTP805 4.9 38.9 1.0
O3A B:CTP804 4.9 33.3 1.0
NZ B:LYS481 4.9 45.6 1.0
O B:ASP445 5.0 37.8 1.0

Magnesium binding site 2 out of 2 in 9f37

Go back to Magnesium Binding Sites List in 9f37
Magnesium binding site 2 out of 2 in the Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Replication-Like Initiation State of Influenza Polymerase with Gtp and Ctp at Respectively the -1 and +1 Positions (Strain A/Little Yellow- Shouldered Bat/Guatemala/060/2010/H17N10) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg807

b:24.9
occ:1.00
 OD2 B:ASP445 2.1 36.8 1.0
O1A B:CTP804 2.1 30.2 1.0
O B:ASN306 2.1 26.4 1.0
O2B B:CTP804 2.2 29.0 1.0
OD1 B:ASP305 2.3 34.6 1.0
O1G B:CTP804 2.3 35.3 1.0
CG B:ASP305 3.1 33.3 1.0
CG B:ASP445 3.1 36.6 1.0
PB B:CTP804 3.2 30.2 1.0
C B:ASN306 3.3 27.1 1.0
PA B:CTP804 3.3 40.1 1.0
OD2 B:ASP305 3.3 45.9 1.0
O3A B:CTP804 3.4 33.3 1.0
PG B:CTP804 3.6 33.9 1.0
OD1 B:ASP445 3.6 39.2 1.0
N B:ASN306 3.7 25.1 1.0
MG B:MG806 3.7 35.7 1.0
O3B B:CTP804 3.7 33.4 1.0
NZ B:LYS481 3.9 45.6 1.0
CA B:ASN306 4.0 28.3 1.0
C5' B:CTP804 4.0 34.9 1.0
O5' B:CTP804 4.2 34.5 1.0
CB B:ASP445 4.4 34.3 1.0
N B:THR307 4.4 29.7 1.0
O2G B:CTP804 4.4 36.6 1.0
CB B:ASP305 4.4 32.7 1.0
O2A B:CTP804 4.5 33.5 1.0
N B:LYS308 4.6 25.3 1.0
C B:ASP305 4.6 27.3 1.0
O1B B:CTP804 4.6 34.4 1.0
CA B:THR307 4.7 29.1 1.0
CE B:LYS481 4.7 41.6 1.0
O3G B:CTP804 4.7 38.4 1.0
CB B:ASN306 4.7 27.7 1.0
C B:THR307 4.8 26.0 1.0
N B:TRP309 4.9 26.9 1.0
CA B:ASP305 4.9 29.6 1.0
CB B:TRP309 4.9 25.9 1.0

Reference:

S.Cusack, P.Drncova, T.Krischuns, N.Naffakh. High-Resolution Structure of A Replication-Initiation Like Configuration of Influenza Polymerase Active Site Visualises the Essential Role of A Conserved Dibasic Motif in the Pa Subunit Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.11.20.567839
Page generated: Sat Oct 5 09:33:26 2024

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