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Manganese in PDB 4avl: Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Dtmp

Protein crystallography data

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

Resolution Low / High (Å) 41.80 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.890, 121.240, 129.020, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.5

Manganese Binding Sites:

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

Manganese binding site 1 out of 8 in 4avl

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


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 Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1198

b:23.1
occ:1.00
 OE2 A:GLU119 2.0 25.9 1.0
OD2 A:ASP108 2.1 21.3 1.0
O A:ILE120 2.1 26.5 1.0
O2P A:TMP1200 2.2 23.5 1.0
O1P A:TMP1200 2.2 28.9 1.0
NE2 A:HIS41 2.3 22.8 1.0
P A:TMP1200 2.7 28.2 1.0
CG A:ASP108 3.0 19.7 1.0
CD A:GLU119 3.2 27.7 1.0
CE1 A:HIS41 3.2 21.5 1.0
CD2 A:HIS41 3.3 25.4 1.0
C A:ILE120 3.3 24.6 1.0
OD1 A:ASP108 3.3 22.3 1.0
MN A:MN1199 3.7 21.9 1.0
OE1 A:GLU119 3.7 27.4 1.0
N A:ILE120 3.7 23.8 1.0
O3P A:TMP1200 3.8 25.2 1.0
O A:HOH2063 3.9 22.0 1.0
NZ A:LYS134 3.9 36.5 1.0
O5' A:TMP1200 4.0 28.0 1.0
CA A:ILE120 4.0 23.6 1.0
C5' A:TMP1200 4.2 28.1 1.0
CB A:ILE120 4.2 23.4 1.0
O A:HOH2070 4.3 32.3 1.0
ND1 A:HIS41 4.3 22.4 1.0
CG A:GLU119 4.3 27.2 1.0
CB A:ASP108 4.3 19.9 1.0
CG A:HIS41 4.4 22.6 1.0
N A:GLY121 4.4 27.1 1.0
CE A:LYS134 4.5 39.3 1.0
OE1 A:GLU80 4.6 23.3 1.0
C A:GLU119 4.7 23.7 1.0
CA A:GLY121 4.7 27.5 1.0
CA A:GLU119 4.9 23.7 1.0
CG2 A:ILE120 5.0 24.9 1.0

Manganese binding site 2 out of 8 in 4avl

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


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 Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1199

b:21.9
occ:1.00
 OE1 A:GLU80 2.1 23.3 1.0
O A:HOH2043 2.1 18.7 1.0
O2P A:TMP1200 2.1 23.5 1.0
O A:HOH2044 2.1 24.1 1.0
O A:HOH2063 2.1 22.0 1.0
OD1 A:ASP108 2.1 22.3 1.0
CD A:GLU80 3.2 20.3 1.0
CG A:ASP108 3.2 19.7 1.0
P A:TMP1200 3.4 28.2 1.0
OD2 A:ASP108 3.7 21.3 1.0
MN A:MN1198 3.7 23.1 1.0
CE1 A:HIS41 3.9 21.5 1.0
OE2 A:GLU80 4.0 26.0 1.0
O3P A:TMP1200 4.0 25.2 1.0
O5' A:TMP1200 4.0 28.0 1.0
CG A:GLU80 4.1 22.1 1.0
O A:HOH2062 4.1 37.9 1.0
CB A:GLU80 4.3 20.9 1.0
O A:PRO107 4.3 19.3 1.0
OE1 A:GLU119 4.3 27.4 1.0
NE2 A:HIS41 4.3 22.8 1.0
O A:LEU106 4.4 22.5 1.0
CB A:ASP108 4.4 19.9 1.0
C5' A:TMP1200 4.4 28.1 1.0
C A:PRO107 4.5 19.0 1.0
CA A:ASP108 4.5 19.1 1.0
OE2 A:GLU119 4.5 25.9 1.0
O1P A:TMP1200 4.5 28.9 1.0
N A:ASP108 4.6 19.6 1.0
CD A:GLU119 4.9 27.7 1.0
CA A:GLU80 5.0 20.0 1.0

Manganese binding site 3 out of 8 in 4avl

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


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 Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1197

b:36.3
occ:1.00
 O B:ILE120 2.0 38.3 1.0
O2P B:TMP1199 2.1 42.8 1.0
OD2 B:ASP108 2.2 30.7 1.0
OE2 B:GLU119 2.2 37.8 1.0
NE2 B:HIS41 2.3 35.5 1.0
O1P B:TMP1199 2.4 44.9 1.0
P B:TMP1199 2.8 45.2 1.0
CG B:ASP108 3.1 32.0 1.0
C B:ILE120 3.1 38.9 1.0
CE1 B:HIS41 3.2 37.7 1.0
CD B:GLU119 3.3 39.7 1.0
CD2 B:HIS41 3.3 36.0 1.0
OD1 B:ASP108 3.3 31.4 1.0
N B:ILE120 3.6 36.8 1.0
MN B:MN1198 3.8 35.6 1.0
OE1 B:GLU119 3.8 36.7 1.0
CA B:ILE120 3.8 37.9 1.0
O3P B:TMP1199 3.9 43.0 1.0
O B:HOH2032 4.0 35.3 1.0
CB B:ILE120 4.1 36.2 1.0
O5' B:TMP1199 4.1 41.4 1.0
NZ B:LYS134 4.2 49.4 1.0
N B:GLY121 4.2 39.7 1.0
C5' B:TMP1199 4.2 41.8 1.0
ND1 B:HIS41 4.4 34.1 1.0
O B:HOH2036 4.4 33.9 1.0
CG B:HIS41 4.4 34.6 1.0
CB B:ASP108 4.5 30.0 1.0
CG B:GLU119 4.5 39.8 1.0
C B:GLU119 4.5 39.3 1.0
CA B:GLY121 4.5 40.2 1.0
CE B:LYS134 4.7 52.2 1.0
CG2 B:ILE120 4.8 37.1 1.0
CA B:GLU119 4.9 38.2 1.0

Manganese binding site 4 out of 8 in 4avl

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


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 Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1198

b:35.6
occ:1.00
 O B:HOH2027 1.7 34.8 1.0
OD1 B:ASP108 2.0 31.4 1.0
O B:HOH2026 2.1 35.0 1.0
O2P B:TMP1199 2.1 42.8 1.0
O B:HOH2032 2.2 35.3 1.0
OE2 B:GLU80 2.3 37.8 1.0
CG B:ASP108 3.1 32.0 1.0
P B:TMP1199 3.4 45.2 1.0
CD B:GLU80 3.4 37.1 1.0
OD2 B:ASP108 3.7 30.7 1.0
CE1 B:HIS41 3.7 37.7 1.0
MN B:MN1197 3.8 36.3 1.0
O3P B:TMP1199 4.0 43.0 1.0
O5' B:TMP1199 4.0 41.4 1.0
O B:HOH2010 4.2 50.8 1.0
OE1 B:GLU119 4.2 36.7 1.0
OE1 B:GLU80 4.3 38.1 1.0
NE2 B:HIS41 4.3 35.5 1.0
CG B:GLU80 4.3 34.0 1.0
CB B:ASP108 4.3 30.0 1.0
O B:PRO107 4.3 33.0 1.0
CA B:ASP108 4.4 30.3 1.0
O B:LEU106 4.5 35.7 1.0
C5' B:TMP1199 4.5 41.8 1.0
C B:PRO107 4.5 32.5 1.0
O1P B:TMP1199 4.6 44.9 1.0
N B:ASP108 4.6 32.6 1.0
CB B:GLU80 4.6 32.6 1.0
OE2 B:GLU119 4.6 37.8 1.0
CD B:GLU119 4.8 39.7 1.0
ND1 B:HIS41 4.8 34.1 1.0

Manganese binding site 5 out of 8 in 4avl

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


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 Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1197

b:31.6
occ:1.00
 OD2 C:ASP108 2.0 27.6 1.0
O C:ILE120 2.1 35.8 1.0
O1P C:TMP1199 2.2 35.7 1.0
OE2 C:GLU119 2.2 36.5 1.0
NE2 C:HIS41 2.3 32.6 1.0
O2P C:TMP1199 2.4 33.4 1.0
P C:TMP1199 2.7 37.6 1.0
CG C:ASP108 3.0 30.2 1.0
CE1 C:HIS41 3.1 33.0 1.0
CD C:GLU119 3.2 34.0 1.0
C C:ILE120 3.3 36.6 1.0
CD2 C:HIS41 3.3 32.2 1.0
OD1 C:ASP108 3.4 28.7 1.0
OE1 C:GLU119 3.7 31.6 1.0
N C:ILE120 3.8 32.7 1.0
MN C:MN1198 3.8 30.8 1.0
O3P C:TMP1199 3.8 33.3 1.0
CA C:ILE120 4.0 35.5 1.0
NZ C:LYS134 4.0 39.7 1.0
O5' C:TMP1199 4.0 36.4 1.0
O C:HOH2030 4.0 27.2 1.0
O C:HOH2034 4.1 34.8 1.0
C5' C:TMP1199 4.2 36.5 1.0
ND1 C:HIS41 4.3 31.1 1.0
CB C:ILE120 4.3 34.4 1.0
N C:GLY121 4.4 36.9 1.0
CB C:ASP108 4.4 29.1 1.0
CG C:GLU119 4.4 33.6 1.0
CG C:HIS41 4.4 32.2 1.0
CE C:LYS134 4.6 41.3 1.0
CA C:GLY121 4.6 37.6 1.0
C C:GLU119 4.7 33.0 1.0
OE2 C:GLU80 4.9 39.5 1.0
CA C:GLU119 5.0 32.2 1.0

Manganese binding site 6 out of 8 in 4avl

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


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 Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1198

b:30.8
occ:1.00
 O C:HOH2023 2.0 29.8 1.0
O C:HOH2024 2.1 33.3 1.0
O2P C:TMP1199 2.1 33.4 1.0
OD1 C:ASP108 2.1 28.7 1.0
O C:HOH2030 2.1 27.2 1.0
OE2 C:GLU80 2.4 39.5 1.0
CG C:ASP108 3.1 30.2 1.0
CD C:GLU80 3.4 38.1 1.0
P C:TMP1199 3.5 37.6 1.0
OD2 C:ASP108 3.7 27.6 1.0
MN C:MN1197 3.8 31.6 1.0
O3P C:TMP1199 3.9 33.3 1.0
CE1 C:HIS41 3.9 33.0 1.0
O5' C:TMP1199 4.2 36.4 1.0
OE1 C:GLU80 4.2 42.5 1.0
O C:PRO107 4.3 29.3 1.0
O C:LEU106 4.3 35.4 1.0
O C:HOH2022 4.3 41.5 1.0
O C:HOH2008 4.3 41.8 1.0
OE1 C:GLU119 4.3 31.6 1.0
CG C:GLU80 4.4 34.4 1.0
CB C:ASP108 4.4 29.1 1.0
CA C:ASP108 4.5 28.7 1.0
C C:PRO107 4.5 30.4 1.0
C5' C:TMP1199 4.5 36.5 1.0
NE2 C:HIS41 4.5 32.6 1.0
O1P C:TMP1199 4.6 35.7 1.0
N C:ASP108 4.6 29.5 1.0
CB C:GLU80 4.6 30.4 1.0
OE2 C:GLU119 4.7 36.5 1.0
O C:HOH2007 4.7 38.6 1.0
O C:HOH2043 4.7 51.6 1.0
CD C:GLU119 4.9 34.0 1.0

Manganese binding site 7 out of 8 in 4avl

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


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 Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1198

b:23.7
occ:1.00
 OD2 D:ASP108 2.0 20.9 1.0
O D:ILE120 2.0 25.6 1.0
OE2 D:GLU119 2.1 26.0 1.0
O1P D:TMP1200 2.2 28.8 1.0
NE2 D:HIS41 2.2 23.4 1.0
O2P D:TMP1200 2.4 22.5 1.0
P D:TMP1200 2.7 27.8 1.0
CG D:ASP108 3.0 19.3 1.0
CE1 D:HIS41 3.0 20.4 1.0
CD D:GLU119 3.2 25.4 1.0
C D:ILE120 3.2 23.0 1.0
CD2 D:HIS41 3.3 23.4 1.0
OD1 D:ASP108 3.3 20.3 1.0
N D:ILE120 3.7 22.6 1.0
OE1 D:GLU119 3.7 24.8 1.0
O3P D:TMP1200 3.8 25.8 1.0
MN D:MN1199 3.8 21.0 1.0
CA D:ILE120 3.9 22.0 1.0
NZ D:LYS134 4.0 35.7 1.0
O5' D:TMP1200 4.0 28.1 1.0
O D:HOH2043 4.1 19.0 1.0
C5' D:TMP1200 4.2 25.2 1.0
CB D:ILE120 4.2 22.0 1.0
ND1 D:HIS41 4.2 20.6 1.0
CG D:GLU119 4.3 26.4 1.0
O D:HOH2051 4.3 27.3 1.0
N D:GLY121 4.3 25.8 1.0
CG D:HIS41 4.4 20.2 1.0
CB D:ASP108 4.4 20.3 1.0
CE D:LYS134 4.5 40.2 1.0
C D:GLU119 4.6 22.8 1.0
CA D:GLY121 4.7 27.8 1.0
OE1 D:GLU80 4.7 23.8 1.0
CA D:GLU119 4.9 23.2 1.0

Manganese binding site 8 out of 8 in 4avl

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


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 Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1199

b:21.0
occ:1.00
 O D:HOH2028 1.9 19.1 1.0
O2P D:TMP1200 2.0 22.5 1.0
OE1 D:GLU80 2.0 23.8 1.0
OD1 D:ASP108 2.1 20.3 1.0
O D:HOH2010 2.1 22.3 1.0
O D:HOH2043 2.1 19.0 1.0
CD D:GLU80 3.2 25.4 1.0
CG D:ASP108 3.2 19.3 1.0
P D:TMP1200 3.4 27.8 1.0
OD2 D:ASP108 3.7 20.9 1.0
MN D:MN1198 3.8 23.7 1.0
CE1 D:HIS41 3.9 20.4 1.0
OE2 D:GLU80 3.9 31.5 1.0
O3P D:TMP1200 4.0 25.8 1.0
O5' D:TMP1200 4.1 28.1 1.0
O D:HOH2044 4.1 30.8 1.0
CG D:GLU80 4.1 23.1 1.0
OH D:TYR24 4.1 45.5 1.0
OE1 D:GLU119 4.2 24.8 1.0
O D:PRO107 4.3 18.9 1.0
O D:LEU106 4.3 26.5 1.0
CB D:GLU80 4.3 21.2 1.0
O D:HOH2066 4.3 39.7 1.0
CB D:ASP108 4.4 20.3 1.0
CA D:ASP108 4.5 18.9 1.0
OE2 D:GLU119 4.5 26.0 1.0
NE2 D:HIS41 4.5 23.4 1.0
C D:PRO107 4.5 18.4 1.0
C5' D:TMP1200 4.5 25.2 1.0
N D:ASP108 4.6 18.6 1.0
O1P D:TMP1200 4.6 28.8 1.0
CD D:GLU119 4.8 25.4 1.0
CA D:GLU80 4.8 20.0 1.0
ND1 D:HIS41 5.0 20.6 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 18:45:04 2024

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