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Manganese in PDB 4e5l: Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6

Protein crystallography data

The structure of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6, PDB code: 4e5l was solved by R.M.Dubois, P.J.Slavish, T.R.Webb, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.19 / 2.47
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.475, 133.493, 126.400, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 (pdb code 4e5l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6, PDB code: 4e5l:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4e5l

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Manganese binding site 1 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:68.9
occ:1.00
 OD1 A:ASP108 2.2 35.6 1.0
O3 A:DBH305 2.3 69.5 1.0
O17 A:DBH305 2.3 71.8 1.0
O A:HOH414 2.3 47.9 1.0
OE1 A:GLU80 3.1 20.0 1.0
CG A:ASP108 3.3 33.4 1.0
C21 A:DBH305 3.3 71.6 1.0
C3 A:DBH305 3.4 70.5 1.0
MN A:MN302 3.8 42.6 1.0
CE1 A:HIS41 3.8 26.0 1.0
C18 A:DBH305 3.9 71.1 1.0
OD2 A:ASP108 3.9 34.5 1.0
CD A:GLU80 3.9 20.0 1.0
O A:LEU106 4.0 38.6 1.0
O A:PRO107 4.1 35.4 1.0
NE2 A:HIS41 4.3 25.0 1.0
O9 A:DBH305 4.4 71.8 1.0
OE1 A:GLU119 4.4 35.8 1.0
C A:PRO107 4.4 35.6 1.0
CB A:GLU80 4.4 20.0 1.0
CB A:ASP108 4.5 33.5 1.0
CA A:ASP108 4.5 33.5 1.0
CG A:GLU80 4.5 20.0 1.0
OE2 A:GLU119 4.6 40.0 1.0
N A:ASP108 4.6 34.3 1.0
OE2 A:GLU80 4.6 20.0 1.0
C6 A:DBH305 4.6 70.3 1.0
ND1 A:HIS41 4.9 27.5 1.0
C A:LEU106 4.9 38.6 1.0
O6 A:DBH305 4.9 68.6 1.0
CD A:GLU119 4.9 37.3 1.0

Manganese binding site 2 out of 8 in 4e5l

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Manganese binding site 2 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:42.6
occ:1.00
 OE1 A:GLU119 2.2 35.8 1.0
O A:ILE120 2.2 33.0 1.0
O6 A:DBH305 2.4 68.6 1.0
OD2 A:ASP108 2.4 34.5 1.0
NE2 A:HIS41 2.4 25.0 1.0
O3 A:DBH305 2.5 69.5 1.0
CG A:ASP108 3.2 33.4 1.0
C6 A:DBH305 3.2 70.3 1.0
CD2 A:HIS41 3.3 25.9 1.0
CE1 A:HIS41 3.3 26.0 1.0
C3 A:DBH305 3.3 70.5 1.0
OD1 A:ASP108 3.3 35.6 1.0
C A:ILE120 3.3 33.4 1.0
CD A:GLU119 3.3 37.3 1.0
MN A:MN301 3.8 68.9 1.0
N A:ILE120 3.8 33.4 1.0
CA A:ILE120 4.0 33.2 1.0
OE2 A:GLU119 4.1 40.0 1.0
NZ A:LYS134 4.1 50.2 1.0
ND1 A:HIS41 4.3 27.5 1.0
O A:HOH402 4.4 33.8 1.0
N A:GLY121 4.4 33.2 1.0
CG A:GLU119 4.4 35.7 1.0
CG A:HIS41 4.4 27.2 1.0
CB A:ILE120 4.5 33.2 1.0
C9 A:DBH305 4.6 69.7 1.0
CA A:GLY121 4.6 33.0 1.0
CB A:ASP108 4.6 33.5 1.0
C18 A:DBH305 4.7 71.1 1.0
C A:GLU119 4.7 33.8 1.0
CE A:LYS134 4.9 50.4 1.0
O17 A:DBH305 5.0 71.8 1.0

Manganese binding site 3 out of 8 in 4e5l

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Manganese binding site 3 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:63.4
occ:1.00
 OD1 B:ASP108 2.1 36.3 1.0
O17 B:DBH305 2.2 64.6 1.0
O3 B:DBH305 2.2 62.9 1.0
O B:HOH411 2.5 44.7 1.0
OE1 B:GLU80 2.7 20.0 1.0
CG B:ASP108 3.1 34.1 1.0
C21 B:DBH305 3.2 65.0 1.0
C3 B:DBH305 3.3 63.6 1.0
MN B:MN302 3.5 38.8 1.0
OD2 B:ASP108 3.6 36.1 1.0
CE1 B:HIS41 3.7 26.0 1.0
C18 B:DBH305 3.7 64.3 1.0
CD B:GLU80 3.9 20.0 1.0
O B:LEU106 4.0 38.5 1.0
OE1 B:GLU119 4.0 41.3 1.0
O B:PRO107 4.1 34.0 1.0
NE2 B:HIS41 4.2 23.4 1.0
OE2 B:GLU119 4.3 41.5 1.0
O9 B:DBH305 4.3 65.9 1.0
CB B:ASP108 4.3 33.5 1.0
C B:PRO107 4.3 34.5 1.0
CA B:ASP108 4.4 33.3 1.0
CB B:GLU80 4.5 20.0 1.0
N B:ASP108 4.5 33.8 1.0
C6 B:DBH305 4.5 63.9 1.0
CG B:GLU80 4.6 20.0 1.0
CD B:GLU119 4.6 39.9 1.0
ND1 B:HIS41 4.7 27.1 1.0
OE2 B:GLU80 4.8 20.0 1.0
O6 B:DBH305 4.9 60.6 1.0
C B:LEU106 5.0 38.3 1.0

Manganese binding site 4 out of 8 in 4e5l

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Manganese binding site 4 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:38.8
occ:1.00
 O B:ILE120 2.2 33.8 1.0
O3 B:DBH305 2.2 62.9 1.0
OE1 B:GLU119 2.3 41.3 1.0
NE2 B:HIS41 2.3 23.4 1.0
OD2 B:ASP108 2.3 36.1 1.0
O6 B:DBH305 2.4 60.6 1.0
CE1 B:HIS41 3.0 26.0 1.0
C3 B:DBH305 3.1 63.6 1.0
CG B:ASP108 3.2 34.1 1.0
C6 B:DBH305 3.2 63.9 1.0
OD1 B:ASP108 3.3 36.3 1.0
C B:ILE120 3.3 33.9 1.0
CD2 B:HIS41 3.4 24.7 1.0
CD B:GLU119 3.4 39.9 1.0
MN B:MN301 3.5 63.4 1.0
N B:ILE120 3.7 34.2 1.0
CA B:ILE120 4.0 34.1 1.0
OE2 B:GLU119 4.1 41.5 1.0
ND1 B:HIS41 4.2 27.1 1.0
NZ B:LYS134 4.2 57.8 1.0
CG B:HIS41 4.4 26.6 1.0
N B:GLY121 4.4 33.3 1.0
CG B:GLU119 4.4 36.8 1.0
O B:HOH402 4.4 39.6 1.0
C18 B:DBH305 4.5 64.3 1.0
CB B:ILE120 4.5 34.7 1.0
C9 B:DBH305 4.6 63.5 1.0
CB B:ASP108 4.6 33.5 1.0
CA B:GLY121 4.7 32.0 1.0
C B:GLU119 4.7 34.5 1.0
CE B:LYS134 4.7 56.5 1.0
O17 B:DBH305 4.8 64.6 1.0
CA B:GLU119 5.0 34.6 1.0

Manganese binding site 5 out of 8 in 4e5l

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Manganese binding site 5 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:43.6
occ:1.00
 OD2 C:ASP108 2.1 30.5 1.0
O C:ILE120 2.2 34.8 1.0
OE1 C:GLU119 2.3 40.5 1.0
NE2 C:HIS41 2.3 29.0 1.0
O3 C:DBH305 2.5 76.9 1.0
O6 C:DBH305 2.5 75.5 1.0
CG C:ASP108 3.0 32.9 1.0
CE1 C:HIS41 3.1 27.4 1.0
OD1 C:ASP108 3.2 32.8 1.0
CD C:GLU119 3.3 41.8 1.0
C C:ILE120 3.3 34.8 1.0
C3 C:DBH305 3.4 77.6 1.0
C6 C:DBH305 3.4 77.5 1.0
CD2 C:HIS41 3.4 27.1 1.0
MN C:MN302 3.6 64.2 1.0
N C:ILE120 3.7 35.6 1.0
OE2 C:GLU119 3.8 44.5 1.0
CA C:ILE120 4.0 35.0 1.0
ND1 C:HIS41 4.2 29.4 1.0
NZ C:LYS134 4.3 55.1 1.0
CG C:HIS41 4.4 28.3 1.0
N C:GLY121 4.4 35.0 1.0
CB C:ASP108 4.4 34.5 1.0
CB C:ILE120 4.5 35.2 1.0
CG C:GLU119 4.5 39.1 1.0
O C:HOH401 4.5 37.8 1.0
C C:GLU119 4.7 35.8 1.0
C18 C:DBH305 4.7 78.3 1.0
CA C:GLY121 4.7 34.3 1.0
C9 C:DBH305 4.7 77.5 1.0
OE1 C:GLU80 4.9 20.0 1.0
O9 C:DBH305 5.0 78.4 1.0

Manganese binding site 6 out of 8 in 4e5l

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Manganese binding site 6 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:64.2
occ:1.00
 OE1 C:GLU80 2.1 20.0 1.0
OD1 C:ASP108 2.1 32.8 1.0
O3 C:DBH305 2.1 76.9 1.0
O9 C:DBH305 2.1 78.4 1.0
O C:HOH416 2.5 45.4 1.0
C21 C:DBH305 3.1 78.5 1.0
CG C:ASP108 3.2 32.9 1.0
C3 C:DBH305 3.3 77.6 1.0
CD C:GLU80 3.3 20.0 1.0
OD2 C:ASP108 3.6 30.5 1.0
MN C:MN301 3.6 43.6 1.0
C18 C:DBH305 3.6 78.3 1.0
CE1 C:HIS41 3.6 27.4 1.0
O C:PRO107 4.0 36.6 1.0
CG C:GLU80 4.1 20.0 1.0
OE2 C:GLU80 4.2 20.0 1.0
O17 C:DBH305 4.2 79.0 1.0
O C:LEU106 4.2 41.0 1.0
NE2 C:HIS41 4.3 29.0 1.0
CB C:GLU80 4.3 20.0 1.0
CB C:ASP108 4.4 34.5 1.0
CA C:ASP108 4.4 35.2 1.0
C C:PRO107 4.4 37.1 1.0
C6 C:DBH305 4.5 77.5 1.0
OE2 C:GLU119 4.6 44.5 1.0
N C:ASP108 4.6 36.2 1.0
ND1 C:HIS41 4.7 29.4 1.0
OE1 C:GLU119 4.7 40.5 1.0
O6 C:DBH305 4.8 75.5 1.0
CA C:GLU80 5.0 40.7 1.0

Manganese binding site 7 out of 8 in 4e5l

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Manganese binding site 7 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:43.5
occ:1.00
 O D:ILE120 2.2 32.5 1.0
OE1 D:GLU119 2.2 39.2 1.0
O3 D:DBH305 2.3 80.0 1.0
OD2 D:ASP108 2.3 39.5 1.0
NE2 D:HIS41 2.3 26.1 1.0
O6 D:DBH305 2.7 76.7 1.0
CG D:ASP108 3.0 38.4 1.0
CE1 D:HIS41 3.1 26.2 1.0
OD1 D:ASP108 3.1 39.3 1.0
CD D:GLU119 3.2 39.5 1.0
C3 D:DBH305 3.2 79.9 1.0
C D:ILE120 3.3 32.1 1.0
CD2 D:HIS41 3.4 28.4 1.0
C6 D:DBH305 3.4 79.5 1.0
N D:ILE120 3.6 33.2 1.0
MN D:MN302 3.7 74.9 1.0
OE2 D:GLU119 3.7 42.7 1.0
CA D:ILE120 3.9 32.3 1.0
ND1 D:HIS41 4.2 29.3 1.0
CB D:ILE120 4.3 32.5 1.0
N D:GLY121 4.4 31.6 1.0
CG D:HIS41 4.4 28.6 1.0
CB D:ASP108 4.4 38.3 1.0
CG D:GLU119 4.4 36.3 1.0
O D:HOH402 4.6 35.2 1.0
C18 D:DBH305 4.6 80.5 1.0
NZ D:LYS134 4.6 55.4 1.0
C D:GLU119 4.6 33.8 1.0
CE D:LYS134 4.7 55.7 1.0
CA D:GLY121 4.7 31.1 1.0
C9 D:DBH305 4.8 79.7 1.0
O9 D:DBH305 4.8 81.0 1.0
CG2 D:ILE120 4.9 32.1 1.0
CA D:GLU119 5.0 34.4 1.0

Manganese binding site 8 out of 8 in 4e5l

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Manganese binding site 8 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:74.9
occ:1.00
 O9 D:DBH305 2.3 81.0 1.0
OD1 D:ASP108 2.3 39.3 1.0
O3 D:DBH305 2.5 80.0 1.0
O D:HOH413 2.6 30.1 1.0
OE1 D:GLU80 2.9 20.0 1.0
CG D:ASP108 3.1 38.4 1.0
C21 D:DBH305 3.2 80.4 1.0
OD2 D:ASP108 3.5 39.5 1.0
C3 D:DBH305 3.6 79.9 1.0
OE2 D:GLU119 3.6 42.7 1.0
O D:LEU106 3.7 43.5 1.0
MN D:MN301 3.7 43.5 1.0
O D:PRO107 3.8 39.9 1.0
C18 D:DBH305 3.9 80.5 1.0
O17 D:DBH305 4.0 80.0 1.0
C D:PRO107 4.0 40.6 1.0
CE1 D:HIS41 4.1 26.2 1.0
CD D:GLU80 4.2 20.0 1.0
N D:ASP108 4.2 39.4 1.0
OE1 D:GLU119 4.2 39.2 1.0
CB D:ASP108 4.2 38.3 1.0
CA D:ASP108 4.2 38.3 1.0
CD D:GLU119 4.4 39.5 1.0
C D:LEU106 4.6 43.5 1.0
NE2 D:HIS41 4.6 26.1 1.0
CA D:PRO107 4.8 41.1 1.0
C6 D:DBH305 4.8 79.5 1.0

Reference:

R.M.Dubois, P.J.Slavish, B.M.Baughman, M.K.Yun, J.Bao, R.J.Webby, T.R.Webb, S.W.White. Structural and Biochemical Basis For Development of Influenza Virus Inhibitors Targeting the Pa Endonuclease. Plos Pathog. V. 8 02830 2012.
ISSN: ISSN 1553-7366
PubMed: 22876176
DOI: 10.1371/JOURNAL.PPAT.1002830
Page generated: Sat Oct 5 19:13:41 2024

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