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Manganese in PDB 4e5i: Crystal Structure of Avian Influenza Virus Pan Bound to Compound 4

Protein crystallography data

The structure of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 4, PDB code: 4e5i 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) 46.14 / 2.94
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.332, 134.828, 126.544, 90.00, 90.00, 90.00
R / Rfree (%) 32 / 36.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 4 (pdb code 4e5i). 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 4, PDB code: 4e5i:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4e5i

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


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

b:98.4
occ:1.00
 O13 A:0N9305 2.2 67.3 1.0
OD1 A:ASP108 2.2 75.1 1.0
O16 A:0N9305 2.6 65.5 1.0
OE2 A:GLU80 3.0 71.6 1.0
CG A:ASP108 3.2 75.1 1.0
C2 A:0N9305 3.4 67.2 1.0
OD2 A:ASP108 3.5 74.7 1.0
CE1 A:HIS41 3.5 62.0 1.0
C14 A:0N9305 3.7 66.3 1.0
MN A:MN304 3.9 80.4 1.0
O A:LEU106 4.0 77.5 1.0
C3 A:0N9305 4.0 66.9 1.0
CD A:GLU80 4.0 71.6 1.0
O A:PRO107 4.2 76.7 1.0
NE2 A:HIS41 4.2 62.0 1.0
OE2 A:GLU119 4.4 76.1 1.0
ND1 A:HIS41 4.5 61.6 1.0
OE1 A:GLU119 4.5 76.1 1.0
CB A:ASP108 4.6 75.5 1.0
C A:PRO107 4.6 76.5 1.0
C1 A:0N9305 4.6 67.5 1.0
CB A:GLU80 4.8 70.9 1.0
O15 A:0N9305 4.8 65.4 1.0
OE1 A:GLU80 4.8 72.4 1.0
CG A:GLU80 4.8 71.0 1.0
O12 A:0N9305 4.9 68.0 1.0
CA A:ASP108 4.9 75.7 1.0
CD A:GLU119 4.9 76.0 1.0
N A:ASP108 4.9 76.1 1.0

Manganese binding site 2 out of 8 in 4e5i

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Manganese binding site 2 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 4


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

b:80.4
occ:1.00
 O A:ILE120 1.9 75.8 1.0
OE1 A:GLU119 2.2 76.1 1.0
NE2 A:HIS41 2.4 62.0 1.0
O12 A:0N9305 2.5 68.0 1.0
OD2 A:ASP108 2.8 74.7 1.0
O13 A:0N9305 3.0 67.3 1.0
C A:ILE120 3.1 76.0 1.0
CE1 A:HIS41 3.2 62.0 1.0
CD2 A:HIS41 3.3 61.3 1.0
CD A:GLU119 3.3 76.0 1.0
C1 A:0N9305 3.3 67.5 1.0
C2 A:0N9305 3.5 67.2 1.0
CG A:ASP108 3.8 75.1 1.0
MN A:MN303 3.9 98.4 1.0
OE2 A:GLU119 4.0 76.1 1.0
N A:ILE120 4.0 75.9 1.0
N A:GLY121 4.0 76.2 1.0
CA A:ILE120 4.1 75.8 1.0
CA A:GLY121 4.1 76.5 1.0
OD1 A:ASP108 4.1 75.1 1.0
ND1 A:HIS41 4.2 61.6 1.0
CG A:HIS41 4.2 60.5 1.0
CG A:GLU119 4.4 76.0 1.0
NZ A:LYS134 4.4 95.2 1.0
N6 A:0N9305 4.6 67.6 1.0
CE A:LYS134 4.6 95.5 1.0
CB A:ILE120 4.7 75.7 1.0
C A:GLU119 4.8 76.1 1.0
C3 A:0N9305 4.9 66.9 1.0

Manganese binding site 3 out of 8 in 4e5i

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Manganese binding site 3 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 4


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

b:78.9
occ:1.00
 O B:ILE120 2.1 78.0 1.0
O13 B:0N9305 2.3 65.5 1.0
OD2 B:ASP108 2.4 77.8 1.0
NE2 B:HIS41 2.5 60.2 1.0
O12 B:0N9305 2.5 66.5 1.0
OE1 B:GLU119 2.5 77.7 1.0
CE1 B:HIS41 3.0 60.3 1.0
C2 B:0N9305 3.1 65.2 1.0
C1 B:0N9305 3.2 65.8 1.0
C B:ILE120 3.2 78.0 1.0
CG B:ASP108 3.4 78.5 1.0
CD2 B:HIS41 3.5 59.7 1.0
MN B:MN304 3.5 96.1 1.0
CD B:GLU119 3.5 77.7 1.0
OD1 B:ASP108 3.7 78.6 1.0
N B:ILE120 3.9 77.7 1.0
OE2 B:GLU119 4.0 77.8 1.0
ND1 B:HIS41 4.1 60.2 1.0
CA B:ILE120 4.1 77.8 1.0
NZ B:LYS134 4.2 0.0 1.0
N B:GLY121 4.2 78.4 1.0
CG B:HIS41 4.3 59.3 1.0
CA B:GLY121 4.4 78.8 1.0
N6 B:0N9305 4.5 65.6 1.0
C3 B:0N9305 4.5 64.8 1.0
CE B:LYS134 4.6 0.8 1.0
CB B:ILE120 4.7 77.7 1.0
CG B:GLU119 4.7 77.7 1.0
CB B:ASP108 4.8 79.0 1.0
O16 B:0N9305 4.8 63.1 1.0
C B:GLU119 4.9 77.7 1.0

Manganese binding site 4 out of 8 in 4e5i

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


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

b:96.1
occ:1.00
 OD1 B:ASP108 2.0 78.6 1.0
O13 B:0N9305 2.3 65.5 1.0
O16 B:0N9305 2.4 63.1 1.0
CG B:ASP108 3.0 78.5 1.0
OE1 B:GLU80 3.1 74.0 1.0
OD2 B:ASP108 3.4 77.8 1.0
C2 B:0N9305 3.5 65.2 1.0
MN B:MN303 3.5 78.9 1.0
C14 B:0N9305 3.5 64.3 1.0
CE1 B:HIS41 3.7 60.3 1.0
O B:LEU106 3.8 80.7 1.0
C3 B:0N9305 4.0 64.8 1.0
CD B:GLU80 4.2 73.0 1.0
OE2 B:GLU119 4.2 77.8 1.0
CB B:ASP108 4.4 79.0 1.0
NE2 B:HIS41 4.4 60.2 1.0
O B:PRO107 4.5 80.0 1.0
OE1 B:GLU119 4.6 77.7 1.0
O15 B:0N9305 4.6 64.0 1.0
C B:PRO107 4.7 80.0 1.0
CA B:ASP108 4.7 79.2 1.0
ND1 B:HIS41 4.7 60.2 1.0
N B:ASP108 4.8 79.6 1.0
CB B:GLU80 4.8 71.9 1.0
C1 B:0N9305 4.8 65.8 1.0
C B:LEU106 4.8 80.9 1.0
CD B:GLU119 4.8 77.7 1.0
CG B:GLU80 5.0 72.2 1.0
OE2 B:GLU80 5.0 73.2 1.0

Manganese binding site 5 out of 8 in 4e5i

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Manganese binding site 5 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 4


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

b:89.1
occ:1.00
 O C:ILE120 2.1 77.0 1.0
OE1 C:GLU119 2.2 77.3 1.0
O12 C:0N9305 2.3 64.8 1.0
OD2 C:ASP108 2.3 74.7 1.0
NE2 C:HIS41 2.4 57.8 1.0
O13 C:0N9305 2.5 64.3 1.0
C1 C:0N9305 3.0 64.6 1.0
CE1 C:HIS41 3.1 57.7 1.0
C2 C:0N9305 3.1 64.2 1.0
CG C:ASP108 3.2 75.6 1.0
C C:ILE120 3.2 77.1 1.0
CD C:GLU119 3.3 77.1 1.0
OD1 C:ASP108 3.4 75.0 1.0
CD2 C:HIS41 3.5 56.9 1.0
MN C:MN304 3.6 93.2 1.0
N C:ILE120 3.7 76.8 1.0
OE2 C:GLU119 3.7 77.5 1.0
CA C:ILE120 4.0 76.8 1.0
ND1 C:HIS41 4.2 57.6 1.0
N C:GLY121 4.3 77.5 1.0
N6 C:0N9305 4.3 65.3 1.0
CG C:HIS41 4.4 56.7 1.0
CA C:GLY121 4.5 78.0 1.0
CG C:GLU119 4.5 76.8 1.0
CB C:ILE120 4.5 76.7 1.0
CB C:ASP108 4.6 76.4 1.0
C3 C:0N9305 4.6 64.2 1.0
C C:GLU119 4.8 76.8 1.0

Manganese binding site 6 out of 8 in 4e5i

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


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

b:93.2
occ:1.00
 OD1 C:ASP108 2.0 75.0 1.0
O13 C:0N9305 2.1 64.3 1.0
O15 C:0N9305 2.4 62.6 1.0
OE1 C:GLU80 2.8 70.3 1.0
CG C:ASP108 3.1 75.6 1.0
C2 C:0N9305 3.3 64.2 1.0
C14 C:0N9305 3.4 63.7 1.0
MN C:MN303 3.6 89.1 1.0
OD2 C:ASP108 3.7 74.7 1.0
O C:PRO107 3.7 78.2 1.0
CE1 C:HIS41 3.8 57.7 1.0
C3 C:0N9305 3.8 64.2 1.0
CD C:GLU80 3.9 70.5 1.0
O C:LEU106 3.9 79.5 1.0
C C:PRO107 4.2 78.1 1.0
OE2 C:GLU119 4.2 77.5 1.0
CB C:ASP108 4.3 76.4 1.0
NE2 C:HIS41 4.4 57.8 1.0
CA C:ASP108 4.4 76.8 1.0
N C:ASP108 4.5 77.5 1.0
OE2 C:GLU80 4.5 71.2 1.0
O16 C:0N9305 4.5 63.8 1.0
C1 C:0N9305 4.5 64.6 1.0
OE1 C:GLU119 4.6 77.3 1.0
O12 C:0N9305 4.8 64.8 1.0
ND1 C:HIS41 4.8 57.6 1.0
CD C:GLU119 4.8 77.1 1.0
C C:LEU106 4.9 79.6 1.0
CG C:GLU80 4.9 69.5 1.0
CB C:GLU80 4.9 69.2 1.0

Manganese binding site 7 out of 8 in 4e5i

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Manganese binding site 7 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 4


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

b:89.5
occ:1.00
 OE1 D:GLU119 1.9 75.5 1.0
O D:ILE120 2.0 75.6 1.0
OD2 D:ASP108 2.2 80.5 1.0
O12 D:0N9305 2.5 69.3 1.0
O13 D:0N9305 2.7 70.5 1.0
NE2 D:HIS41 3.0 59.0 1.0
C D:ILE120 3.1 75.7 1.0
CD D:GLU119 3.1 75.7 1.0
CG D:ASP108 3.1 80.1 1.0
C1 D:0N9305 3.2 69.9 1.0
C2 D:0N9305 3.3 70.3 1.0
N D:ILE120 3.3 75.3 1.0
OD1 D:ASP108 3.4 80.3 1.0
CE1 D:HIS41 3.7 59.4 1.0
CA D:ILE120 3.7 75.3 1.0
CG D:GLU119 3.9 75.5 1.0
OE2 D:GLU119 4.0 75.9 1.0
CD2 D:HIS41 4.0 58.6 1.0
MN D:MN304 4.0 96.2 1.0
N D:GLY121 4.1 76.0 1.0
C D:GLU119 4.3 75.4 1.0
CB D:ILE120 4.4 75.1 1.0
CB D:ASP108 4.5 80.1 1.0
N6 D:0N9305 4.5 70.3 1.0
CA D:GLY121 4.5 76.8 1.0
NZ D:LYS134 4.5 96.8 1.0
CA D:GLU119 4.6 75.5 1.0
C3 D:0N9305 4.7 70.5 1.0
ND1 D:HIS41 4.8 59.3 1.0
CB D:GLU119 4.9 75.5 1.0
CG D:HIS41 5.0 58.3 1.0

Manganese binding site 8 out of 8 in 4e5i

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


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

b:96.2
occ:1.00
 OD1 D:ASP108 1.9 80.3 1.0
O15 D:0N9305 2.4 70.2 1.0
O13 D:0N9305 2.4 70.5 1.0
O D:PRO107 3.1 81.0 1.0
CG D:ASP108 3.1 80.1 1.0
OE1 D:GLU80 3.2 74.2 1.0
O D:LEU106 3.3 82.4 1.0
C14 D:0N9305 3.5 70.3 1.0
C2 D:0N9305 3.5 70.3 1.0
C D:PRO107 3.6 81.1 1.0
OD2 D:ASP108 3.7 80.5 1.0
C3 D:0N9305 4.0 70.5 1.0
OE1 D:GLU119 4.0 75.5 1.0
MN D:MN303 4.0 89.5 1.0
C D:LEU106 4.1 82.4 1.0
N D:ASP108 4.2 80.5 1.0
OE2 D:GLU119 4.2 75.9 1.0
CA D:ASP108 4.2 80.1 1.0
CB D:ASP108 4.3 80.1 1.0
CD D:GLU80 4.4 74.3 1.0
CA D:PRO107 4.4 81.4 1.0
CD D:GLU119 4.5 75.7 1.0
CE1 D:HIS41 4.6 59.4 1.0
O16 D:0N9305 4.6 69.9 1.0
N D:PRO107 4.6 81.8 1.0
CB D:LEU106 4.7 83.0 1.0
C1 D:0N9305 4.8 69.9 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 19:10:49 2024

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