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Manganese in PDB 4avg: Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2

Protein crystallography data

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2, PDB code: 4avg 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) 43.96 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.590, 120.810, 128.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.2

Other elements in 4avg:

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2 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 2 (pdb code 4avg). 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 2, PDB code: 4avg:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4avg

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Manganese binding site 1 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:28.8
occ:1.00
 OE2 A:GLU119 2.1 32.9 1.0
O28 A:SL6801 2.2 33.8 1.0
O A:ILE120 2.2 18.4 1.0
OD2 A:ASP108 2.2 16.7 1.0
NE2 A:HIS41 2.3 19.6 1.0
O26 A:SL6801 2.5 33.5 1.0
C23 A:SL6801 3.0 41.3 1.0
CE1 A:HIS41 3.0 20.0 1.0
CG A:ASP108 3.1 17.5 1.0
C24 A:SL6801 3.1 41.4 1.0
CD A:GLU119 3.2 30.5 1.0
OD1 A:ASP108 3.2 17.4 1.0
CD2 A:HIS41 3.3 20.3 1.0
C A:ILE120 3.4 19.2 1.0
MN A:MN902 3.7 36.4 1.0
OE1 A:GLU119 3.7 28.0 1.0
N A:ILE120 3.8 20.9 1.0
CA A:ILE120 4.1 20.6 1.0
O A:HOH2037 4.1 23.8 1.0
ND1 A:HIS41 4.2 17.6 1.0
C22 A:SL6801 4.3 39.3 1.0
O25 A:SL6801 4.4 41.5 1.0
CG A:GLU119 4.4 28.5 1.0
CG A:HIS41 4.4 18.6 1.0
CB A:ILE120 4.4 21.1 1.0
N A:GLY121 4.5 18.1 1.0
CB A:ASP108 4.5 17.0 1.0
OH A:TYR130 4.6 49.2 1.0
C A:GLU119 4.7 20.2 1.0
OE2 A:GLU80 4.7 28.0 1.0
CA A:GLY121 4.7 16.1 1.0
O27 A:SL6801 5.0 38.9 1.0

Manganese binding site 2 out of 8 in 4avg

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn902

b:36.4
occ:1.00
 OE2 A:GLU80 2.1 28.0 1.0
O27 A:SL6801 2.1 38.9 1.0
OD1 A:ASP108 2.2 17.4 1.0
O28 A:SL6801 2.3 33.8 1.0
O A:HOH2037 2.3 23.8 1.0
O A:HOH2028 2.5 23.8 1.0
C14 A:SL6801 3.0 45.4 1.0
CG A:ASP108 3.1 17.5 1.0
CD A:GLU80 3.2 26.9 1.0
C23 A:SL6801 3.3 41.3 1.0
C22 A:SL6801 3.5 39.3 1.0
OD2 A:ASP108 3.6 16.7 1.0
MN A:MN901 3.7 28.8 1.0
CE1 A:HIS41 4.0 20.0 1.0
CG A:GLU80 4.0 24.4 1.0
O A:PRO107 4.1 15.2 1.0
OE1 A:GLU80 4.1 24.4 1.0
CB A:ASP108 4.3 17.0 1.0
CA A:ASP108 4.3 17.7 1.0
C A:PRO107 4.3 18.8 1.0
OE1 A:GLU119 4.4 28.0 1.0
O A:LEU106 4.4 24.4 1.0
C11 A:SL6801 4.4 55.5 1.0
CB A:GLU80 4.5 23.5 1.0
N A:ASP108 4.5 19.1 1.0
NE2 A:HIS41 4.5 19.6 1.0
C24 A:SL6801 4.6 41.4 1.0
OE2 A:GLU119 4.7 32.9 1.0
C12 A:SL6801 4.7 55.2 1.0
O A:HOH2026 4.8 41.6 1.0
C21 A:SL6801 4.8 63.4 1.0
CA A:GLU80 4.9 22.9 1.0
CD A:GLU119 4.9 30.5 1.0
C13 A:SL6801 4.9 52.9 1.0

Manganese binding site 3 out of 8 in 4avg

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn901

b:25.6
occ:1.00
 OD2 B:ASP108 2.1 19.5 1.0
O B:ILE120 2.2 22.9 1.0
O26 B:SL6801 2.2 29.1 1.0
NE2 B:HIS41 2.2 17.2 1.0
OE2 B:GLU119 2.2 21.9 1.0
O28 B:SL6801 2.3 29.1 1.0
C24 B:SL6801 2.9 38.2 1.0
C23 B:SL6801 3.0 37.3 1.0
CG B:ASP108 3.0 17.7 1.0
CE1 B:HIS41 3.1 20.8 1.0
CD B:GLU119 3.2 22.8 1.0
CD2 B:HIS41 3.2 18.9 1.0
C B:ILE120 3.3 22.6 1.0
OD1 B:ASP108 3.3 19.7 1.0
NZ B:LYS134 3.6 55.1 1.0
N B:ILE120 3.6 20.3 1.0
OE1 B:GLU119 3.7 21.7 1.0
MN B:MN902 3.7 33.3 1.0
CA B:ILE120 3.9 20.5 1.0
O25 B:SL6801 4.1 39.0 1.0
O B:HOH2031 4.1 18.0 1.0
CB B:ILE120 4.2 21.8 1.0
O B:HOH2036 4.2 17.1 1.0
ND1 B:HIS41 4.2 18.8 1.0
CG B:GLU119 4.3 20.6 1.0
C22 B:SL6801 4.3 40.2 1.0
CG B:HIS41 4.3 18.5 1.0
N B:GLY121 4.4 20.8 1.0
CB B:ASP108 4.4 16.3 1.0
C B:GLU119 4.6 19.6 1.0
CA B:GLY121 4.7 21.8 1.0
OE1 B:GLU80 4.8 26.9 1.0
CE B:LYS134 4.9 49.0 1.0
CA B:GLU119 4.9 20.2 1.0
CG2 B:ILE120 5.0 24.1 1.0

Manganese binding site 4 out of 8 in 4avg

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn902

b:33.3
occ:1.00
 O28 B:SL6801 2.1 29.1 1.0
OD1 B:ASP108 2.1 19.7 1.0
O27 B:SL6801 2.2 43.7 1.0
OE1 B:GLU80 2.3 26.9 1.0
O B:HOH2031 2.3 18.0 1.0
O B:HOH2019 2.4 19.5 1.0
CG B:ASP108 3.0 17.7 1.0
C23 B:SL6801 3.1 37.3 1.0
C14 B:SL6801 3.1 42.0 1.0
CD B:GLU80 3.4 26.8 1.0
OD2 B:ASP108 3.4 19.5 1.0
C22 B:SL6801 3.5 40.2 1.0
MN B:MN901 3.7 25.6 1.0
O B:HOH2020 3.8 34.0 1.0
CE1 B:HIS41 3.8 20.8 1.0
O B:PRO107 4.1 14.2 1.0
OE2 B:GLU80 4.2 33.9 1.0
CB B:ASP108 4.2 16.3 1.0
OE1 B:GLU119 4.3 21.7 1.0
NE2 B:HIS41 4.3 17.2 1.0
CA B:ASP108 4.3 16.2 1.0
CG B:GLU80 4.3 24.4 1.0
C B:PRO107 4.4 16.3 1.0
C24 B:SL6801 4.4 38.2 1.0
CB B:GLU80 4.5 22.9 1.0
O B:LEU106 4.5 24.5 1.0
C11 B:SL6801 4.5 46.4 1.0
N B:ASP108 4.5 17.1 1.0
OE2 B:GLU119 4.5 21.9 1.0
O26 B:SL6801 4.8 29.1 1.0
CD B:GLU119 4.8 22.8 1.0
C21 B:SL6801 4.8 55.6 1.0
ND1 B:HIS41 4.9 18.8 1.0
CA B:GLU80 5.0 21.0 1.0
C12 B:SL6801 5.0 43.6 1.0
C15 B:SL6801 5.0 47.9 1.0

Manganese binding site 5 out of 8 in 4avg

Go back to Manganese Binding Sites List in 4avg
Manganese binding site 5 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn901

b:27.1
occ:1.00
 O28 C:SL6801 2.0 23.9 1.0
O C:ILE120 2.1 25.3 1.0
OD2 C:ASP108 2.2 21.9 1.0
O26 C:SL6801 2.2 33.4 1.0
OE2 C:GLU119 2.3 26.8 1.0
NE2 C:HIS41 2.3 21.6 1.0
C23 C:SL6801 2.8 33.4 1.0
C24 C:SL6801 2.8 33.4 1.0
CG C:ASP108 3.1 24.7 1.0
CE1 C:HIS41 3.2 22.2 1.0
CD C:GLU119 3.2 23.9 1.0
C C:ILE120 3.3 23.9 1.0
CD2 C:HIS41 3.3 22.7 1.0
OD1 C:ASP108 3.4 24.4 1.0
OE1 C:GLU119 3.7 26.0 1.0
MN C:MN902 3.8 38.8 1.0
N C:ILE120 3.8 23.3 1.0
CA C:ILE120 4.0 25.8 1.0
O25 C:SL6801 4.0 36.8 1.0
C22 C:SL6801 4.1 34.1 1.0
O C:HOH2027 4.2 31.5 1.0
CB C:ILE120 4.2 25.7 1.0
ND1 C:HIS41 4.3 20.2 1.0
N C:GLY121 4.3 29.1 1.0
CG C:HIS41 4.4 21.8 1.0
CG C:GLU119 4.4 23.3 1.0
CB C:ASP108 4.5 22.4 1.0
O C:HOH2031 4.6 28.9 1.0
CA C:GLY121 4.6 24.9 1.0
C C:GLU119 4.7 22.0 1.0
O27 C:SL6801 4.9 38.2 1.0
CA C:GLU119 5.0 22.4 1.0

Manganese binding site 6 out of 8 in 4avg

Go back to Manganese Binding Sites List in 4avg
Manganese binding site 6 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn902

b:38.8
occ:1.00
 O27 C:SL6801 2.0 38.2 1.0
O C:HOH2022 2.1 19.7 1.0
O28 C:SL6801 2.2 23.9 1.0
OD1 C:ASP108 2.2 24.4 1.0
O C:HOH2027 2.3 31.5 1.0
OE2 C:GLU80 2.6 37.2 1.0
C14 C:SL6801 3.0 42.8 1.0
C23 C:SL6801 3.1 33.4 1.0
CG C:ASP108 3.2 24.7 1.0
C22 C:SL6801 3.4 34.1 1.0
OD2 C:ASP108 3.6 21.9 1.0
CD C:GLU80 3.7 32.5 1.0
MN C:MN901 3.8 27.1 1.0
CE1 C:HIS41 3.9 22.2 1.0
O C:PRO107 4.2 22.6 1.0
C11 C:SL6801 4.4 48.5 1.0
CB C:ASP108 4.4 22.4 1.0
NE2 C:HIS41 4.4 21.6 1.0
OE1 C:GLU119 4.4 26.0 1.0
OE1 C:GLU80 4.4 34.3 1.0
C C:PRO107 4.4 21.2 1.0
O C:LEU106 4.4 25.4 1.0
CA C:ASP108 4.4 22.9 1.0
C24 C:SL6801 4.5 33.4 1.0
CG C:GLU80 4.5 30.3 1.0
N C:ASP108 4.5 21.7 1.0
CB C:GLU80 4.6 25.6 1.0
C12 C:SL6801 4.7 46.4 1.0
OE2 C:GLU119 4.8 26.8 1.0
C21 C:SL6801 4.9 50.0 1.0
C15 C:SL6801 4.9 49.5 1.0
ND1 C:HIS41 4.9 20.2 1.0
O26 C:SL6801 5.0 33.4 1.0

Manganese binding site 7 out of 8 in 4avg

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn901

b:30.7
occ:1.00
 O D:ILE120 2.0 25.5 1.0
OD2 D:ASP108 2.2 18.9 1.0
NE2 D:HIS41 2.3 23.6 1.0
OE2 D:GLU119 2.3 32.3 1.0
O28 D:SL6801 2.3 32.7 1.0
O26 D:SL6801 2.3 35.2 1.0
C24 D:SL6801 3.0 39.9 1.0
C23 D:SL6801 3.1 38.2 1.0
CG D:ASP108 3.1 23.3 1.0
CE1 D:HIS41 3.1 27.2 1.0
C D:ILE120 3.2 22.0 1.0
CD2 D:HIS41 3.3 21.9 1.0
CD D:GLU119 3.3 33.0 1.0
OD1 D:ASP108 3.3 27.5 1.0
N D:ILE120 3.6 24.4 1.0
MN D:MN902 3.7 42.4 1.0
CA D:ILE120 3.9 23.7 1.0
OE1 D:GLU119 3.9 32.2 1.0
NZ D:LYS134 4.1 74.3 1.0
O D:HOH2027 4.1 25.4 1.0
O25 D:SL6801 4.2 36.8 1.0
N D:GLY121 4.2 24.2 1.0
CB D:ILE120 4.2 27.0 1.0
ND1 D:HIS41 4.3 24.9 1.0
O D:HOH2032 4.3 30.1 1.0
CG D:HIS41 4.4 21.1 1.0
CG D:GLU119 4.4 29.0 1.0
C22 D:SL6801 4.4 42.2 1.0
CA D:GLY121 4.4 21.5 1.0
CB D:ASP108 4.5 22.1 1.0
CE D:LYS134 4.6 70.7 1.0
C D:GLU119 4.7 24.4 1.0

Manganese binding site 8 out of 8 in 4avg

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn902

b:42.4
occ:1.00
 O28 D:SL6801 2.0 32.7 1.0
OD1 D:ASP108 2.2 27.5 1.0
O27 D:SL6801 2.2 42.1 1.0
O D:HOH2027 2.2 25.4 1.0
O D:HOH2020 2.2 31.1 1.0
OE2 D:GLU80 2.6 40.2 1.0
C23 D:SL6801 3.0 38.2 1.0
C14 D:SL6801 3.1 44.4 1.0
CG D:ASP108 3.2 23.3 1.0
C22 D:SL6801 3.4 42.2 1.0
OD2 D:ASP108 3.6 18.9 1.0
CD D:GLU80 3.6 36.0 1.0
MN D:MN901 3.7 30.7 1.0
CE1 D:HIS41 3.8 27.2 1.0
NE2 D:HIS41 4.3 23.6 1.0
O D:HOH2019 4.3 42.5 1.0
C24 D:SL6801 4.3 39.9 1.0
O D:PRO107 4.4 22.1 1.0
CB D:ASP108 4.4 22.1 1.0
CG D:GLU80 4.4 32.1 1.0
C D:PRO107 4.4 21.4 1.0
OE1 D:GLU80 4.4 44.1 1.0
OE1 D:GLU119 4.4 32.2 1.0
O D:LEU106 4.5 24.1 1.0
CA D:ASP108 4.5 22.4 1.0
N D:ASP108 4.5 21.9 1.0
C11 D:SL6801 4.5 53.0 1.0
OE2 D:GLU119 4.6 32.3 1.0
CB D:GLU80 4.7 27.5 1.0
O26 D:SL6801 4.8 35.2 1.0
ND1 D:HIS41 4.9 24.9 1.0
CD D:GLU119 5.0 33.0 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 18:44:39 2024

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