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Manganese in PDB 4awf: Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba

Protein crystallography data

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba, PDB code: 4awf 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) 46.32 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 260.870, 65.750, 66.030, 90.00, 95.76, 90.00
R / Rfree (%) 22.41 / 28.888

Manganese Binding Sites:

The binding sites of Manganese atom in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba (pdb code 4awf). 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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba, PDB code: 4awf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4awf

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Manganese binding site 1 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba


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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:26.9
occ:1.00
 O14 A:XI7303 1.9 24.1 1.0
OD1 A:ASP108 2.1 15.8 1.0
O A:HOH2024 2.2 15.4 1.0
O8 A:XI7303 2.3 17.7 1.0
O A:HOH2035 2.4 16.9 1.0
OE2 A:GLU80 2.5 25.4 1.0
C7 A:XI7303 2.9 24.8 1.0
C9 A:XI7303 3.1 19.3 1.0
CG A:ASP108 3.1 16.5 1.0
C8 A:XI7303 3.4 21.1 1.0
CD A:GLU80 3.5 25.3 1.0
OD2 A:ASP108 3.6 15.6 1.0
MN A:MN302 3.8 18.9 1.0
CE1 A:HIS41 3.9 18.4 1.0
O A:PRO107 4.1 16.0 1.0
C1 A:XI7303 4.2 26.6 1.0
OE1 A:GLU80 4.3 25.8 1.0
CG A:GLU80 4.3 24.0 1.0
CB A:ASP108 4.4 16.3 1.0
C10 A:XI7303 4.4 19.3 1.0
CB A:GLU80 4.5 23.4 1.0
NE2 A:HIS41 4.5 18.6 1.0
C A:PRO107 4.5 15.9 1.0
OE1 A:GLU119 4.5 19.7 1.0
C2 A:XI7303 4.6 29.2 1.0
O A:LEU106 4.6 18.0 1.0
CA A:ASP108 4.6 16.3 1.0
N A:ASP108 4.7 16.0 1.0
O10 A:XI7303 4.8 17.8 1.0
OE2 A:GLU119 4.8 20.4 1.0
CA A:GLU80 4.9 22.3 1.0
ND1 A:HIS41 4.9 17.2 1.0

Manganese binding site 2 out of 8 in 4awf

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Manganese binding site 2 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba


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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:18.9
occ:1.00
 O10 A:XI7303 2.0 17.8 1.0
OD2 A:ASP108 2.0 15.6 1.0
O8 A:XI7303 2.1 17.7 1.0
OE2 A:GLU119 2.1 20.4 1.0
O A:ILE120 2.2 14.2 1.0
NE2 A:HIS41 2.4 18.6 1.0
C10 A:XI7303 2.8 19.3 1.0
C9 A:XI7303 2.8 19.3 1.0
CG A:ASP108 3.1 16.5 1.0
CD A:GLU119 3.2 20.0 1.0
CE1 A:HIS41 3.2 18.4 1.0
OD1 A:ASP108 3.4 15.8 1.0
CD2 A:HIS41 3.4 17.6 1.0
C A:ILE120 3.4 14.8 1.0
OE1 A:GLU119 3.6 19.7 1.0
MN A:MN301 3.8 26.9 1.0
N A:ILE120 3.9 16.2 1.0
O11 A:XI7303 4.0 17.4 1.0
O A:HOH2035 4.2 16.9 1.0
CA A:ILE120 4.2 14.9 1.0
C8 A:XI7303 4.3 21.1 1.0
ND1 A:HIS41 4.3 17.2 1.0
O A:HOH2040 4.4 18.8 1.0
CG A:GLU119 4.4 19.6 1.0
N A:GLY121 4.4 14.2 1.0
CB A:ASP108 4.4 16.3 1.0
CB A:ILE120 4.4 15.5 1.0
CG A:HIS41 4.5 18.3 1.0
NZ A:LYS134 4.5 29.8 1.0
CE A:LYS134 4.5 31.4 1.0
CA A:GLY121 4.6 14.7 1.0
C A:GLU119 4.8 16.7 1.0
O14 A:XI7303 4.9 24.1 1.0

Manganese binding site 3 out of 8 in 4awf

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Manganese binding site 3 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba


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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:31.0
occ:1.00
 O14 B:XI7303 1.9 24.0 1.0
OD1 B:ASP108 2.1 13.8 1.0
O B:HOH2044 2.2 18.2 1.0
O B:HOH2029 2.2 22.9 1.0
O8 B:XI7303 2.2 15.5 1.0
OE2 B:GLU80 2.4 26.1 1.0
C7 B:XI7303 2.9 22.5 1.0
C9 B:XI7303 3.1 17.1 1.0
CG B:ASP108 3.1 15.2 1.0
CD B:GLU80 3.4 26.6 1.0
C8 B:XI7303 3.4 19.0 1.0
OD2 B:ASP108 3.6 15.2 1.0
MN B:MN302 3.7 17.6 1.0
CE1 B:HIS41 3.8 20.8 1.0
O B:PRO107 4.1 17.6 1.0
OE1 B:GLU80 4.1 23.9 1.0
C1 B:XI7303 4.2 25.1 1.0
CG B:GLU80 4.3 24.6 1.0
CB B:ASP108 4.3 15.6 1.0
NE2 B:HIS41 4.4 20.4 1.0
CB B:GLU80 4.4 23.3 1.0
C10 B:XI7303 4.5 16.7 1.0
C B:PRO107 4.5 17.8 1.0
O B:LEU106 4.5 17.5 1.0
CA B:ASP108 4.5 15.9 1.0
OE1 B:GLU119 4.5 13.4 1.0
C2 B:XI7303 4.6 28.0 1.0
N B:ASP108 4.7 17.0 1.0
OE2 B:GLU119 4.7 14.1 1.0
O10 B:XI7303 4.8 16.2 1.0
CA B:GLU80 4.9 21.3 1.0
ND1 B:HIS41 5.0 20.7 1.0

Manganese binding site 4 out of 8 in 4awf

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Manganese binding site 4 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba


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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:17.6
occ:1.00
 O8 B:XI7303 2.1 15.5 1.0
O B:ILE120 2.2 15.0 1.0
OD2 B:ASP108 2.2 15.2 1.0
O10 B:XI7303 2.2 16.2 1.0
NE2 B:HIS41 2.3 20.4 1.0
OE2 B:GLU119 2.4 14.1 1.0
C9 B:XI7303 2.9 17.1 1.0
C10 B:XI7303 2.9 16.7 1.0
CG B:ASP108 3.0 15.2 1.0
CE1 B:HIS41 3.1 20.8 1.0
OD1 B:ASP108 3.3 13.8 1.0
CD B:GLU119 3.3 14.4 1.0
CD2 B:HIS41 3.3 20.7 1.0
C B:ILE120 3.4 14.4 1.0
MN B:MN301 3.7 31.0 1.0
OE1 B:GLU119 3.8 13.4 1.0
O B:HOH2044 3.9 18.2 1.0
N B:ILE120 3.9 14.9 1.0
CA B:ILE120 4.1 13.9 1.0
O11 B:XI7303 4.2 16.3 1.0
CB B:ILE120 4.3 14.1 1.0
ND1 B:HIS41 4.3 20.7 1.0
C8 B:XI7303 4.3 19.0 1.0
N B:GLY121 4.4 14.5 1.0
CB B:ASP108 4.4 15.6 1.0
CG B:HIS41 4.4 20.6 1.0
CG B:GLU119 4.5 15.1 1.0
O B:HOH2048 4.6 20.0 1.0
CA B:GLY121 4.7 14.7 1.0
OE2 B:GLU80 4.7 26.1 1.0
O14 B:XI7303 4.8 24.0 1.0
CE B:LYS134 4.8 31.9 1.0
C B:GLU119 4.8 14.8 1.0
NZ B:LYS134 5.0 33.1 1.0
CG2 B:ILE120 5.0 14.3 1.0

Manganese binding site 5 out of 8 in 4awf

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Manganese binding site 5 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba


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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:28.6
occ:1.00
 O14 C:XI7303 2.0 24.9 1.0
OD1 C:ASP108 2.1 19.2 1.0
O8 C:XI7303 2.2 20.4 1.0
O C:HOH2032 2.2 21.4 1.0
OE1 C:GLU80 2.2 20.6 1.0
O C:HOH2020 2.5 15.8 1.0
C7 C:XI7303 3.0 25.0 1.0
C9 C:XI7303 3.1 22.2 1.0
CG C:ASP108 3.1 18.4 1.0
CD C:GLU80 3.4 19.4 1.0
C8 C:XI7303 3.5 22.9 1.0
OD2 C:ASP108 3.5 19.6 1.0
MN C:MN302 3.6 17.8 1.0
CE1 C:HIS41 3.8 19.8 1.0
O C:PRO107 4.1 16.0 1.0
CG C:GLU80 4.2 18.9 1.0
OE2 C:GLU80 4.3 20.8 1.0
C1 C:XI7303 4.3 29.2 1.0
CB C:ASP108 4.3 17.4 1.0
O C:LEU106 4.3 17.0 1.0
OE1 C:GLU119 4.3 16.9 1.0
NE2 C:HIS41 4.4 20.7 1.0
CB C:GLU80 4.4 18.7 1.0
C10 C:XI7303 4.4 22.7 1.0
C C:PRO107 4.5 16.8 1.0
OE2 C:GLU119 4.5 19.2 1.0
CA C:ASP108 4.5 16.6 1.0
C2 C:XI7303 4.7 33.1 1.0
N C:ASP108 4.7 16.7 1.0
O10 C:XI7303 4.8 20.5 1.0
ND1 C:HIS41 4.9 18.3 1.0
CD C:GLU119 4.9 19.0 1.0
CA C:GLU80 4.9 17.4 1.0
O C:HOH2031 4.9 37.2 1.0

Manganese binding site 6 out of 8 in 4awf

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Manganese binding site 6 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba


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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:17.8
occ:1.00
 OE2 C:GLU119 2.0 19.2 1.0
OD2 C:ASP108 2.1 19.6 1.0
O C:ILE120 2.1 14.2 1.0
O8 C:XI7303 2.1 20.4 1.0
O10 C:XI7303 2.3 20.5 1.0
NE2 C:HIS41 2.4 20.7 1.0
C9 C:XI7303 2.9 22.2 1.0
C10 C:XI7303 3.0 22.7 1.0
CG C:ASP108 3.1 18.4 1.0
CE1 C:HIS41 3.1 19.8 1.0
CD C:GLU119 3.1 19.0 1.0
C C:ILE120 3.4 15.5 1.0
CD2 C:HIS41 3.4 17.8 1.0
OD1 C:ASP108 3.4 19.2 1.0
MN C:MN301 3.6 28.6 1.0
OE1 C:GLU119 3.6 16.9 1.0
N C:ILE120 3.9 16.4 1.0
O C:HOH2032 4.0 21.4 1.0
CA C:ILE120 4.1 14.9 1.0
O11 C:XI7303 4.2 25.4 1.0
ND1 C:HIS41 4.3 18.3 1.0
CG C:GLU119 4.3 18.2 1.0
CB C:ILE120 4.3 15.4 1.0
C8 C:XI7303 4.3 22.9 1.0
N C:GLY121 4.4 15.1 1.0
CB C:ASP108 4.4 17.4 1.0
O C:HOH2037 4.4 16.2 1.0
CG C:HIS41 4.5 18.5 1.0
CA C:GLY121 4.6 16.1 1.0
CE C:LYS134 4.7 26.9 1.0
OE1 C:GLU80 4.7 20.6 1.0
C C:GLU119 4.8 16.7 1.0
CG2 C:ILE120 4.8 15.3 1.0
NZ C:LYS134 4.8 27.0 1.0
O14 C:XI7303 4.9 24.9 1.0

Manganese binding site 7 out of 8 in 4awf

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Manganese binding site 7 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba


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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:27.2
occ:1.00
 O8 D:XI7303 2.1 20.1 1.0
O D:HOH2035 2.1 20.4 1.0
OD1 D:ASP108 2.1 13.4 1.0
O14 D:XI7303 2.2 24.6 1.0
O D:HOH2036 2.3 11.2 1.0
OE2 D:GLU80 2.5 26.9 1.0
C9 D:XI7303 3.1 21.4 1.0
C7 D:XI7303 3.1 23.5 1.0
CG D:ASP108 3.2 14.6 1.0
CD D:GLU80 3.4 26.8 1.0
C8 D:XI7303 3.6 20.5 1.0
OD2 D:ASP108 3.7 14.1 1.0
MN D:MN302 3.8 19.1 1.0
CE1 D:HIS41 3.8 18.7 1.0
O D:PRO107 4.0 14.0 1.0
OE1 D:GLU80 4.1 23.4 1.0
CG D:GLU80 4.2 25.9 1.0
CB D:GLU80 4.3 25.6 1.0
OE1 D:GLU119 4.4 19.6 1.0
C10 D:XI7303 4.4 22.5 1.0
O D:LEU106 4.4 19.3 1.0
CB D:ASP108 4.4 14.8 1.0
C1 D:XI7303 4.4 26.4 1.0
NE2 D:HIS41 4.4 18.5 1.0
C D:PRO107 4.4 15.9 1.0
CA D:ASP108 4.5 15.0 1.0
O10 D:XI7303 4.6 22.7 1.0
OE2 D:GLU119 4.7 19.4 1.0
N D:ASP108 4.7 16.2 1.0
C2 D:XI7303 4.7 28.8 1.0
ND1 D:HIS41 4.8 18.7 1.0
CA D:GLU80 4.9 22.8 1.0
CD D:GLU119 5.0 19.3 1.0

Manganese binding site 8 out of 8 in 4awf

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Manganese binding site 8 out of 8 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with 2 4-Dioxo-4-Phenylbutanoic Acid Dpba


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 2 4-Dioxo-4-Phenylbutanoic Acid Dpba within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:19.1
occ:1.00
 O10 D:XI7303 1.9 22.7 1.0
OD2 D:ASP108 2.1 14.1 1.0
OE2 D:GLU119 2.1 19.4 1.0
O D:ILE120 2.2 15.6 1.0
NE2 D:HIS41 2.3 18.5 1.0
O8 D:XI7303 2.3 20.1 1.0
C10 D:XI7303 2.7 22.5 1.0
C9 D:XI7303 2.9 21.4 1.0
CG D:ASP108 3.0 14.6 1.0
CE1 D:HIS41 3.0 18.7 1.0
CD D:GLU119 3.2 19.3 1.0
OD1 D:ASP108 3.4 13.4 1.0
C D:ILE120 3.4 17.1 1.0
CD2 D:HIS41 3.4 17.8 1.0
OE1 D:GLU119 3.6 19.6 1.0
MN D:MN301 3.8 27.2 1.0
N D:ILE120 3.8 17.8 1.0
O11 D:XI7303 3.9 20.9 1.0
O D:HOH2035 4.0 20.4 1.0
CA D:ILE120 4.0 17.8 1.0
NZ D:LYS134 4.1 33.0 1.0
CB D:ILE120 4.2 19.9 1.0
ND1 D:HIS41 4.2 18.7 1.0
CG D:GLU119 4.4 18.9 1.0
C8 D:XI7303 4.4 20.5 1.0
CB D:ASP108 4.4 14.8 1.0
CG D:HIS41 4.4 17.9 1.0
N D:GLY121 4.5 17.1 1.0
O D:HOH2039 4.5 15.1 1.0
CA D:GLY121 4.7 16.4 1.0
C D:GLU119 4.7 17.2 1.0
OE2 D:GLU80 4.8 26.9 1.0
CG2 D:ILE120 4.9 19.7 1.0
O14 D:XI7303 5.0 24.6 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 18:45:58 2024

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