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Manganese in PDB 4awg: Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3

Protein crystallography data

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3, PDB code: 4awg was solved by E.Kowalinski, C.Zubieta, A.Wolkerstorfer, O.H.Szolar, R.W.Ruigrok, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.10 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.570, 122.540, 129.780, 90.00, 90.00, 90.00
R / Rfree (%) 19.015 / 26.172

Other elements in 4awg:

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 (pdb code 4awg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3, PDB code: 4awg:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4awg

Go back to Manganese Binding Sites List in 4awg
Manganese binding site 1 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:27.1
occ:1.00
 OAO A:CI3801 2.1 30.5 1.0
O A:ILE120 2.1 18.6 1.0
O14 A:CI3801 2.2 26.8 1.0
OD2 A:ASP108 2.2 21.2 1.0
OE2 A:GLU119 2.2 25.7 1.0
NE2 A:HIS41 2.2 15.1 1.0
CE A:CI3801 2.8 30.7 1.0
CA A:CI3801 2.9 30.4 1.0
CE1 A:HIS41 3.0 15.2 1.0
CG A:ASP108 3.0 20.2 1.0
OD1 A:ASP108 3.1 19.7 1.0
C A:ILE120 3.3 18.2 1.0
CD2 A:HIS41 3.3 14.9 1.0
CD A:GLU119 3.4 25.5 1.0
O A:HOH2013 3.6 18.4 1.0
N A:ILE120 3.7 19.3 1.0
MN A:MN902 3.8 29.8 1.0
CA A:ILE120 4.0 18.1 1.0
OAN A:CI3801 4.1 34.1 1.0
OE1 A:GLU119 4.1 27.2 1.0
ND1 A:HIS41 4.2 14.7 1.0
CM A:CI3801 4.2 30.4 1.0
CB A:ILE120 4.3 16.6 1.0
N A:GLY121 4.3 18.6 1.0
CG A:HIS41 4.4 15.2 1.0
CB A:ASP108 4.4 19.9 1.0
CG A:GLU119 4.5 24.5 1.0
O13 A:CI3801 4.6 31.0 1.0
CA A:GLY121 4.6 19.7 1.0
C A:GLU119 4.7 20.7 1.0
OE2 A:GLU80 4.7 21.1 1.0
O A:HOH2016 4.8 15.4 1.0
CE A:LYS134 4.8 50.8 1.0
O A:HOH2015 4.9 36.3 1.0
CB A:CI3801 5.0 32.1 1.0

Manganese binding site 2 out of 8 in 4awg

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Manganese binding site 2 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn902

b:29.8
occ:1.00
 O13 A:CI3801 1.9 31.0 1.0
OD1 A:ASP108 2.1 19.7 1.0
O A:HOH2013 2.2 18.4 1.0
O14 A:CI3801 2.2 26.8 1.0
OE2 A:GLU80 2.4 21.1 1.0
CB A:CI3801 3.1 32.1 1.0
CG A:ASP108 3.3 20.2 1.0
CA A:CI3801 3.3 30.4 1.0
CD A:GLU80 3.3 20.1 1.0
CM A:CI3801 3.7 30.4 1.0
MN A:MN901 3.8 27.1 1.0
OD2 A:ASP108 3.9 21.2 1.0
CE1 A:HIS41 3.9 15.2 1.0
O A:PRO107 4.0 21.4 1.0
OE1 A:GLU80 4.0 21.0 1.0
CG A:GLU80 4.2 19.4 1.0
CF A:CI3801 4.3 34.4 1.0
CB A:GLU80 4.3 19.1 1.0
CH A:CI3801 4.3 33.8 1.0
C A:PRO107 4.3 21.6 1.0
CB A:ASP108 4.4 19.9 1.0
O A:LEU106 4.4 25.4 1.0
CA A:ASP108 4.5 19.9 1.0
OE2 A:GLU119 4.5 25.7 1.0
NE2 A:HIS41 4.5 15.1 1.0
N A:ASP108 4.5 20.5 1.0
CE A:CI3801 4.6 30.7 1.0
O A:HOH2015 4.6 36.3 1.0
CDB A:CI3801 4.7 36.3 1.0
OE1 A:GLU119 4.7 27.2 1.0
CA A:GLU80 4.8 18.9 1.0
CO A:CI3801 4.8 35.4 1.0
ND1 A:HIS41 4.9 14.7 1.0
OAO A:CI3801 4.9 30.5 1.0

Manganese binding site 3 out of 8 in 4awg

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Manganese binding site 3 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn901

b:34.0
occ:1.00
 O B:ILE120 2.1 20.8 1.0
OD2 B:ASP108 2.2 18.1 1.0
NE2 B:HIS41 2.2 20.7 1.0
OE2 B:GLU119 2.2 26.3 1.0
O14 B:CI3801 2.3 36.3 1.0
OAO B:CI3801 2.3 30.3 1.0
CE1 B:HIS41 3.0 20.8 1.0
CG B:ASP108 3.1 17.8 1.0
CA B:CI3801 3.1 36.5 1.0
CE B:CI3801 3.1 33.8 1.0
C B:ILE120 3.2 21.1 1.0
CD2 B:HIS41 3.2 21.2 1.0
CD B:GLU119 3.3 25.4 1.0
OD1 B:ASP108 3.3 16.8 1.0
N B:ILE120 3.5 20.7 1.0
O B:HOH2014 3.6 19.4 1.0
MN B:MN902 3.8 34.0 1.0
CA B:ILE120 3.9 20.2 1.0
OE1 B:GLU119 3.9 25.3 1.0
ND1 B:HIS41 4.2 20.8 1.0
CB B:ILE120 4.2 19.7 1.0
N B:GLY121 4.3 21.0 1.0
OAN B:CI3801 4.3 32.8 1.0
CG B:GLU119 4.3 24.9 1.0
CG B:HIS41 4.3 20.8 1.0
NZ B:LYS134 4.4 40.7 1.0
CM B:CI3801 4.4 37.9 1.0
CB B:ASP108 4.4 18.0 1.0
O B:HOH2017 4.5 28.3 1.0
CA B:GLY121 4.6 21.8 1.0
C B:GLU119 4.6 22.0 1.0
O13 B:CI3801 4.7 39.8 1.0
OE1 B:GLU80 4.9 25.1 1.0
CE B:LYS134 4.9 41.7 1.0
CA B:GLU119 5.0 22.3 1.0

Manganese binding site 4 out of 8 in 4awg

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Manganese binding site 4 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn902

b:34.0
occ:1.00
 O13 B:CI3801 1.9 39.8 1.0
OE1 B:GLU80 2.1 25.1 1.0
OD1 B:ASP108 2.2 16.8 1.0
O14 B:CI3801 2.3 36.3 1.0
O B:HOH2012 2.3 19.1 1.0
O B:HOH2014 2.5 19.4 1.0
CB B:CI3801 3.0 40.0 1.0
CG B:ASP108 3.3 17.8 1.0
CA B:CI3801 3.3 36.5 1.0
CD B:GLU80 3.3 23.8 1.0
CM B:CI3801 3.6 37.9 1.0
O B:HOH2013 3.6 31.2 1.0
CE1 B:HIS41 3.7 20.8 1.0
OD2 B:ASP108 3.8 18.1 1.0
MN B:MN901 3.8 34.0 1.0
OE2 B:GLU80 4.2 26.9 1.0
CG B:GLU80 4.2 21.7 1.0
NE2 B:HIS41 4.2 20.7 1.0
CF B:CI3801 4.2 42.2 1.0
CH B:CI3801 4.3 42.7 1.0
CB B:GLU80 4.4 20.6 1.0
O B:PRO107 4.4 21.4 1.0
CB B:ASP108 4.5 18.0 1.0
O B:LEU106 4.5 22.8 1.0
CDB B:CI3801 4.6 46.7 1.0
CE B:CI3801 4.6 33.8 1.0
CA B:ASP108 4.6 18.7 1.0
OE2 B:GLU119 4.6 26.3 1.0
C B:PRO107 4.6 20.4 1.0
OE1 B:GLU119 4.7 25.3 1.0
ND1 B:HIS41 4.7 20.8 1.0
N B:ASP108 4.8 19.8 1.0
OAO B:CI3801 4.9 30.3 1.0
CO B:CI3801 4.9 44.4 1.0
CA B:GLU80 4.9 19.4 1.0

Manganese binding site 5 out of 8 in 4awg

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Manganese binding site 5 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn901

b:27.3
occ:1.00
 OD2 C:ASP108 2.0 20.8 1.0
O C:ILE120 2.1 19.0 1.0
OAO C:CI3801 2.1 31.3 1.0
O14 C:CI3801 2.3 32.3 1.0
NE2 C:HIS41 2.5 17.4 1.0
OE2 C:GLU119 2.5 26.4 1.0
CE C:CI3801 2.8 33.4 1.0
CA C:CI3801 2.8 35.7 1.0
CG C:ASP108 3.1 19.3 1.0
C C:ILE120 3.2 19.9 1.0
CE1 C:HIS41 3.2 17.5 1.0
CD C:GLU119 3.3 24.1 1.0
CD2 C:HIS41 3.5 17.1 1.0
N C:ILE120 3.5 19.6 1.0
OD1 C:ASP108 3.6 19.1 1.0
CA C:ILE120 3.8 19.6 1.0
O C:HOH2017 3.8 18.3 1.0
OE1 C:GLU119 3.9 24.0 1.0
OAN C:CI3801 4.0 32.1 1.0
MN C:MN902 4.0 37.1 1.0
CG C:GLU119 4.1 23.6 1.0
CB C:ILE120 4.2 19.2 1.0
CM C:CI3801 4.2 40.6 1.0
N C:GLY121 4.3 20.8 1.0
ND1 C:HIS41 4.4 17.1 1.0
CB C:ASP108 4.4 19.4 1.0
C C:GLU119 4.4 21.5 1.0
OE2 C:GLU80 4.6 25.2 1.0
CG C:HIS41 4.6 17.2 1.0
CE C:LYS134 4.6 36.0 1.0
O C:HOH2021 4.7 34.8 1.0
CA C:GLY121 4.8 21.1 1.0
CA C:GLU119 4.8 21.8 1.0
CG2 C:ILE120 5.0 18.5 1.0

Manganese binding site 6 out of 8 in 4awg

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Manganese binding site 6 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn902

b:37.1
occ:1.00
 O13 C:CI3801 2.1 40.9 1.0
OD1 C:ASP108 2.1 19.1 1.0
O14 C:CI3801 2.1 32.3 1.0
OE2 C:GLU80 2.2 25.2 1.0
O C:HOH2017 2.3 18.3 1.0
CD C:GLU80 3.0 26.1 1.0
CB C:CI3801 3.1 42.5 1.0
CG C:ASP108 3.1 19.3 1.0
CA C:CI3801 3.2 35.7 1.0
CM C:CI3801 3.5 40.6 1.0
OE1 C:GLU80 3.5 30.3 1.0
OD2 C:ASP108 3.5 20.8 1.0
O C:PRO107 3.9 19.0 1.0
MN C:MN901 4.0 27.3 1.0
CG C:GLU80 4.0 25.5 1.0
CE1 C:HIS41 4.2 17.5 1.0
O C:LEU106 4.2 21.7 1.0
CB C:GLU80 4.3 24.6 1.0
C C:PRO107 4.3 20.1 1.0
CB C:ASP108 4.4 19.4 1.0
CF C:CI3801 4.4 45.5 1.0
CA C:ASP108 4.5 20.0 1.0
OE1 C:GLU119 4.5 24.0 1.0
CDA C:CI3801 4.5 51.2 1.0
CE C:CI3801 4.6 33.4 1.0
N C:ASP108 4.6 19.6 1.0
CH C:CI3801 4.6 44.8 1.0
OE2 C:GLU119 4.6 26.4 1.0
NE2 C:HIS41 4.7 17.4 1.0
CEA C:CI3801 4.9 57.0 1.0
CD C:GLU119 4.9 24.1 1.0
O C:HOH2021 5.0 34.8 1.0
CA C:GLU80 5.0 23.3 1.0

Manganese binding site 7 out of 8 in 4awg

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Manganese binding site 7 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn901

b:25.6
occ:1.00
 O14 D:CI3801 1.9 28.6 1.0
OD2 D:ASP108 2.2 19.8 1.0
O D:ILE120 2.2 21.9 1.0
OE2 D:GLU119 2.3 26.6 1.0
NE2 D:HIS41 2.3 17.0 1.0
OAO D:CI3801 2.4 31.0 1.0
CA D:CI3801 2.8 32.4 1.0
CE D:CI3801 3.0 31.2 1.0
CG D:ASP108 3.0 20.9 1.0
CE1 D:HIS41 3.0 17.2 1.0
CD D:GLU119 3.1 25.0 1.0
OD1 D:ASP108 3.2 19.9 1.0
C D:ILE120 3.3 21.0 1.0
CD2 D:HIS41 3.4 17.6 1.0
OE1 D:GLU119 3.6 27.4 1.0
MN D:MN902 3.6 42.3 1.0
N D:ILE120 3.8 21.2 1.0
O D:HOH2014 3.9 21.6 1.0
CA D:ILE120 4.0 20.7 1.0
CM D:CI3801 4.1 35.5 1.0
CB D:ILE120 4.1 21.3 1.0
OAN D:CI3801 4.2 31.9 1.0
ND1 D:HIS41 4.3 17.5 1.0
CG D:GLU119 4.3 24.2 1.0
CB D:ASP108 4.4 21.2 1.0
N D:GLY121 4.4 21.8 1.0
CG D:HIS41 4.5 17.9 1.0
CE D:LYS134 4.5 36.6 1.0
O13 D:CI3801 4.6 37.3 1.0
CA D:GLY121 4.7 22.0 1.0
C D:GLU119 4.7 22.0 1.0
CB D:CI3801 4.8 39.5 1.0
CG2 D:ILE120 4.9 20.6 1.0
OE1 D:GLU80 5.0 26.8 1.0

Manganese binding site 8 out of 8 in 4awg

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Manganese binding site 8 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn902

b:42.3
occ:1.00
 O13 D:CI3801 1.8 37.3 1.0
OD1 D:ASP108 1.9 19.9 1.0
O D:HOH2014 2.0 21.6 1.0
O D:HOH2011 2.3 23.4 1.0
O14 D:CI3801 2.3 28.6 1.0
OE1 D:GLU80 2.4 26.8 1.0
CB D:CI3801 2.9 39.5 1.0
CG D:ASP108 3.0 20.9 1.0
CA D:CI3801 3.3 32.4 1.0
CM D:CI3801 3.5 35.5 1.0
OD2 D:ASP108 3.5 19.8 1.0
CD D:GLU80 3.6 26.7 1.0
MN D:MN901 3.6 25.6 1.0
CE1 D:HIS41 3.8 17.2 1.0
OE1 D:GLU119 4.0 27.4 1.0
CF D:CI3801 4.1 43.1 1.0
O D:HOH2015 4.1 33.5 1.0
O D:LEU106 4.2 22.5 1.0
CB D:ASP108 4.2 21.2 1.0
O D:PRO107 4.2 21.5 1.0
OE2 D:GLU119 4.3 26.6 1.0
CH D:CI3801 4.3 44.2 1.0
CG D:GLU80 4.3 25.3 1.0
CB D:GLU80 4.3 24.2 1.0
C D:PRO107 4.4 21.9 1.0
CA D:ASP108 4.4 21.5 1.0
N D:ASP108 4.4 22.3 1.0
NE2 D:HIS41 4.4 17.0 1.0
OE2 D:GLU80 4.5 30.6 1.0
CO D:CI3801 4.6 44.8 1.0
CD D:GLU119 4.6 25.0 1.0
CE D:CI3801 4.6 31.2 1.0
ND1 D:HIS41 4.8 17.5 1.0

Reference:

E.Kowalinski, C.Zubieta, A.Wolkerstorfer, O.H.Szolar, R.W.Ruigrok, S.Cusack. Structural Analysis of Specific Metal Chelating Inhibitor Binding to the Endonuclease Domain of Influenza PH1N1 (2009) Polymerase. Plos Pathog. V. 8 2831 2012.
ISSN: ISSN 1553-7366
PubMed: 22876177
DOI: 10.1371/JOURNAL.PPAT.1002831
Page generated: Sat Oct 5 18:46:06 2024

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