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Manganese in PDB 4e5f: Crystal Structure of Avian Influenza Virus Pan Bound to Compound 1

Protein crystallography data

The structure of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 1, PDB code: 4e5f 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) 46.09 / 2.39
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.568, 134.321, 126.712, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 28.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 1 (pdb code 4e5f). 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 1, PDB code: 4e5f:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4e5f

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:44.1
occ:1.00
 O A:ILE120 2.1 34.0 1.0
OE1 A:GLU119 2.2 39.1 1.0
NE2 A:HIS41 2.3 29.5 1.0
OD2 A:ASP108 2.3 34.3 1.0
O13 A:0N7305 2.4 65.1 1.0
O12 A:0N7305 2.4 65.2 1.0
CE1 A:HIS41 3.1 29.7 1.0
C10 A:0N7305 3.1 66.9 1.0
N9 A:0N7305 3.1 66.1 1.0
CG A:ASP108 3.2 35.2 1.0
C A:ILE120 3.3 34.5 1.0
OD1 A:ASP108 3.3 35.1 1.0
CD2 A:HIS41 3.3 29.7 1.0
CD A:GLU119 3.4 40.1 1.0
N A:ILE120 3.8 34.8 1.0
CA A:ILE120 4.0 34.6 1.0
MN A:MN304 4.1 79.9 1.0
OE2 A:GLU119 4.2 42.8 1.0
ND1 A:HIS41 4.2 30.4 1.0
N A:GLY121 4.3 33.9 1.0
CG A:GLU119 4.3 37.6 1.0
O A:HOH401 4.3 37.3 1.0
CG A:HIS41 4.4 30.4 1.0
CB A:ILE120 4.5 34.7 1.0
NZ A:LYS134 4.5 57.1 1.0
C8 A:0N7305 4.5 66.5 1.0
CA A:GLY121 4.6 33.4 1.0
C3 A:0N7305 4.6 68.4 1.0
CB A:ASP108 4.6 35.7 1.0
C A:GLU119 4.7 35.5 1.0
CE A:LYS134 4.8 56.4 1.0
OE2 A:GLU80 4.8 46.3 1.0

Manganese binding site 2 out of 8 in 4e5f

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Manganese binding site 2 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:79.9
occ:1.00
 OD1 A:ASP108 2.2 35.1 1.0
O12 A:0N7305 2.2 65.2 1.0
O11 A:0N7305 2.3 66.3 1.0
OE2 A:GLU80 2.5 46.3 1.0
N9 A:0N7305 3.0 66.1 1.0
C8 A:0N7305 3.0 66.5 1.0
CG A:ASP108 3.3 35.2 1.0
O A:HOH414 3.5 42.7 1.0
O A:LEU106 3.6 39.5 1.0
CD A:GLU80 3.6 45.3 1.0
O A:PRO107 3.7 37.5 1.0
OD2 A:ASP108 3.9 34.3 1.0
C A:PRO107 4.0 37.6 1.0
MN A:MN303 4.1 44.1 1.0
CE1 A:HIS41 4.3 29.7 1.0
CB A:GLU80 4.3 41.5 1.0
C10 A:0N7305 4.3 66.9 1.0
CG A:GLU80 4.3 42.7 1.0
N A:ASP108 4.3 36.4 1.0
CA A:ASP108 4.4 35.8 1.0
CB A:ASP108 4.4 35.7 1.0
OE1 A:GLU119 4.4 39.1 1.0
OE1 A:GLU80 4.4 46.9 1.0
C A:LEU106 4.5 40.1 1.0
C7 A:0N7305 4.5 67.5 1.0
OE2 A:GLU119 4.6 42.8 1.0
CA A:PRO107 4.7 37.8 1.0
O13 A:0N7305 4.8 65.1 1.0
NE2 A:HIS41 4.8 29.5 1.0
CD A:GLU119 4.9 40.1 1.0
CA A:GLU80 4.9 41.6 1.0

Manganese binding site 3 out of 8 in 4e5f

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Manganese binding site 3 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:43.7
occ:1.00
 O B:ILE120 2.1 33.6 1.0
OD2 B:ASP108 2.2 37.6 1.0
O12 B:0N7305 2.2 68.2 1.0
NE2 B:HIS41 2.4 27.8 1.0
OE1 B:GLU119 2.4 41.8 1.0
O13 B:0N7305 2.4 68.1 1.0
N9 B:0N7305 3.1 68.7 1.0
CE1 B:HIS41 3.1 27.7 1.0
C10 B:0N7305 3.1 69.8 1.0
CG B:ASP108 3.2 37.0 1.0
C B:ILE120 3.3 33.4 1.0
CD2 B:HIS41 3.4 27.9 1.0
OD1 B:ASP108 3.5 38.4 1.0
CD B:GLU119 3.6 42.0 1.0
NZ B:LYS134 3.7 58.8 1.0
N B:ILE120 3.7 33.5 1.0
MN B:MN304 3.8 66.0 1.0
CA B:ILE120 4.0 33.2 1.0
ND1 B:HIS41 4.3 30.7 1.0
N B:GLY121 4.3 32.9 1.0
OE2 B:GLU119 4.4 44.8 1.0
C8 B:0N7305 4.4 68.5 1.0
O B:HOH401 4.4 42.8 1.0
CG B:HIS41 4.4 29.1 1.0
CG B:GLU119 4.5 37.7 1.0
CA B:GLY121 4.5 32.5 1.0
CB B:ILE120 4.6 33.5 1.0
CB B:ASP108 4.6 36.8 1.0
C3 B:0N7305 4.6 70.8 1.0
C B:GLU119 4.7 34.1 1.0
CE B:LYS134 4.7 57.8 1.0
O11 B:0N7305 4.9 66.7 1.0

Manganese binding site 4 out of 8 in 4e5f

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Manganese binding site 4 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn304

b:66.0
occ:1.00
 OD1 B:ASP108 2.1 38.4 1.0
O12 B:0N7305 2.2 68.2 1.0
O11 B:0N7305 2.5 66.7 1.0
OE1 B:GLU80 2.6 43.2 1.0
N9 B:0N7305 3.0 68.7 1.0
CG B:ASP108 3.1 37.0 1.0
C8 B:0N7305 3.1 68.5 1.0
OD2 B:ASP108 3.6 37.6 1.0
CD B:GLU80 3.6 42.9 1.0
MN B:MN303 3.8 43.7 1.0
O B:PRO107 3.9 39.0 1.0
O B:LEU106 4.0 42.8 1.0
CE1 B:HIS41 4.0 27.7 1.0
C B:PRO107 4.2 39.3 1.0
OE1 B:GLU119 4.2 41.8 1.0
CB B:ASP108 4.2 36.8 1.0
CA B:ASP108 4.3 36.9 1.0
C10 B:0N7305 4.3 69.8 1.0
N B:ASP108 4.4 38.0 1.0
CG B:GLU80 4.4 42.2 1.0
OE2 B:GLU80 4.5 45.2 1.0
CB B:GLU80 4.5 42.0 1.0
OE2 B:GLU119 4.5 44.8 1.0
NE2 B:HIS41 4.6 27.8 1.0
C7 B:0N7305 4.6 69.8 1.0
O13 B:0N7305 4.8 68.1 1.0
CD B:GLU119 4.8 42.0 1.0
C B:LEU106 4.8 43.0 1.0
CA B:PRO107 5.0 40.5 1.0

Manganese binding site 5 out of 8 in 4e5f

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Manganese binding site 5 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:47.6
occ:1.00
 O C:ILE120 2.1 34.7 1.0
OD2 C:ASP108 2.2 34.0 1.0
O13 C:0N7305 2.3 56.4 1.0
NE2 C:HIS41 2.3 30.9 1.0
OE1 C:GLU119 2.4 37.5 1.0
O12 C:0N7305 2.5 59.4 1.0
CE1 C:HIS41 3.0 29.9 1.0
CG C:ASP108 3.1 37.2 1.0
C10 C:0N7305 3.1 59.9 1.0
N9 C:0N7305 3.2 59.3 1.0
C C:ILE120 3.2 34.8 1.0
OD1 C:ASP108 3.3 36.8 1.0
CD2 C:HIS41 3.3 30.4 1.0
CD C:GLU119 3.6 39.1 1.0
N C:ILE120 3.7 35.1 1.0
CA C:ILE120 4.0 34.7 1.0
MN C:MN304 4.0 69.5 1.0
ND1 C:HIS41 4.1 32.4 1.0
OE2 C:GLU119 4.3 41.0 1.0
O C:HOH401 4.3 40.9 1.0
N C:GLY121 4.3 34.9 1.0
CG C:HIS41 4.3 30.9 1.0
CB C:ILE120 4.4 35.1 1.0
NZ C:LYS134 4.4 60.2 1.0
CB C:ASP108 4.5 37.8 1.0
C3 C:0N7305 4.5 62.1 1.0
CA C:GLY121 4.5 34.6 1.0
C8 C:0N7305 4.6 60.2 1.0
CG C:GLU119 4.6 36.9 1.0
C C:GLU119 4.7 35.1 1.0
OE1 C:GLU80 4.8 48.9 1.0
CG2 C:ILE120 5.0 35.1 1.0

Manganese binding site 6 out of 8 in 4e5f

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn304

b:69.5
occ:1.00
 O12 C:0N7305 2.0 59.4 1.0
OD1 C:ASP108 2.2 36.8 1.0
O11 C:0N7305 2.4 59.5 1.0
OE1 C:GLU80 2.5 48.9 1.0
N9 C:0N7305 2.9 59.3 1.0
C8 C:0N7305 3.0 60.2 1.0
CG C:ASP108 3.3 37.2 1.0
CD C:GLU80 3.5 46.8 1.0
O C:PRO107 3.8 40.2 1.0
OD2 C:ASP108 3.9 34.0 1.0
O C:LEU106 3.9 43.7 1.0
MN C:MN303 4.0 47.6 1.0
CE1 C:HIS41 4.0 29.9 1.0
C10 C:0N7305 4.2 59.9 1.0
C C:PRO107 4.2 40.2 1.0
CB C:GLU80 4.2 42.8 1.0
CG C:GLU80 4.3 44.2 1.0
OE2 C:GLU80 4.3 49.4 1.0
CA C:ASP108 4.3 38.5 1.0
CB C:ASP108 4.4 37.8 1.0
N C:ASP108 4.5 39.2 1.0
C7 C:0N7305 4.5 61.2 1.0
O13 C:0N7305 4.7 56.4 1.0
NE2 C:HIS41 4.7 30.9 1.0
OE1 C:GLU119 4.7 37.5 1.0
C C:LEU106 4.8 43.5 1.0
CA C:GLU80 4.8 42.7 1.0
OE2 C:GLU119 4.9 41.0 1.0
CA C:PRO107 5.0 41.1 1.0

Manganese binding site 7 out of 8 in 4e5f

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Manganese binding site 7 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn303

b:46.8
occ:1.00
 O D:ILE120 2.1 35.3 1.0
OD2 D:ASP108 2.1 38.2 1.0
OE1 D:GLU119 2.3 40.5 1.0
NE2 D:HIS41 2.3 29.2 1.0
O13 D:0N7305 2.4 80.7 1.0
O12 D:0N7305 2.5 81.8 1.0
CG D:ASP108 3.0 37.8 1.0
CE1 D:HIS41 3.0 28.4 1.0
C10 D:0N7305 3.2 82.8 1.0
C D:ILE120 3.2 35.1 1.0
OD1 D:ASP108 3.2 37.9 1.0
N9 D:0N7305 3.2 82.4 1.0
CD D:GLU119 3.3 41.4 1.0
CD2 D:HIS41 3.4 31.5 1.0
N D:ILE120 3.6 35.5 1.0
CA D:ILE120 3.8 35.0 1.0
OE2 D:GLU119 3.9 45.2 1.0
MN D:MN304 4.0 75.1 1.0
ND1 D:HIS41 4.2 30.7 1.0
CB D:ILE120 4.3 35.2 1.0
N D:GLY121 4.3 35.3 1.0
O D:HOH401 4.3 41.9 1.0
CB D:ASP108 4.4 38.0 1.0
NZ D:LYS134 4.4 54.4 1.0
CG D:HIS41 4.4 30.8 1.0
CG D:GLU119 4.5 39.0 1.0
C D:GLU119 4.6 35.9 1.0
C8 D:0N7305 4.6 82.7 1.0
CA D:GLY121 4.6 34.6 1.0
C3 D:0N7305 4.7 84.1 1.0
CG2 D:ILE120 4.9 35.1 1.0
OE2 D:GLU80 4.9 45.2 1.0
CA D:GLU119 5.0 36.5 1.0

Manganese binding site 8 out of 8 in 4e5f

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn304

b:75.1
occ:1.00
 OD1 D:ASP108 2.2 37.9 1.0
O12 D:0N7305 2.2 81.8 1.0
OE2 D:GLU80 2.6 45.2 1.0
O11 D:0N7305 2.7 81.7 1.0
N9 D:0N7305 3.1 82.4 1.0
CG D:ASP108 3.3 37.8 1.0
C8 D:0N7305 3.3 82.7 1.0
CD D:GLU80 3.5 44.5 1.0
O D:PRO107 3.7 39.5 1.0
O D:LEU106 3.7 43.6 1.0
O D:HOH418 3.8 47.0 1.0
OD2 D:ASP108 3.8 38.2 1.0
MN D:MN303 4.0 46.8 1.0
C D:PRO107 4.0 40.1 1.0
CE1 D:HIS41 4.2 28.4 1.0
OE1 D:GLU80 4.3 46.2 1.0
CA D:ASP108 4.3 38.3 1.0
OE2 D:GLU119 4.3 45.2 1.0
CG D:GLU80 4.3 43.8 1.0
N D:ASP108 4.3 39.1 1.0
CB D:ASP108 4.4 38.0 1.0
CB D:GLU80 4.4 43.5 1.0
C10 D:0N7305 4.4 82.8 1.0
C D:LEU106 4.6 43.3 1.0
OE1 D:GLU119 4.7 40.5 1.0
C7 D:0N7305 4.8 83.5 1.0
NE2 D:HIS41 4.9 29.2 1.0
O13 D:0N7305 4.9 80.7 1.0
CA D:PRO107 4.9 41.0 1.0
CA D:GLU80 4.9 43.5 1.0
CD D:GLU119 4.9 41.4 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 19:08:25 2024

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