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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy