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Manganese in PDB 4e5g: Crystal Structure of Avian Influenza Virus Pan Bound to Compound 2

Protein crystallography data

The structure of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 2, PDB code: 4e5g 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) 44.84 / 2.65
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.892, 133.659, 126.778, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 28.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 2 (pdb code 4e5g). 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 2, PDB code: 4e5g:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4e5g

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


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

b:57.0
occ:1.00
 OD1 A:ASP108 2.1 34.9 1.0
OE1 A:GLU80 2.3 40.9 1.0
O14 A:XI7305 2.4 54.9 1.0
O8 A:XI7305 2.5 53.8 1.0
CG A:ASP108 3.2 34.6 1.0
CD A:GLU80 3.5 40.5 1.0
C7 A:XI7305 3.5 54.3 1.0
C9 A:XI7305 3.7 53.5 1.0
OD2 A:ASP108 3.7 34.2 1.0
O A:PRO107 3.7 37.5 1.0
O A:LEU106 3.8 40.4 1.0
MN A:MN304 3.8 37.5 1.0
OE1 A:GLU119 3.9 45.6 1.0
C8 A:XI7305 4.0 53.8 1.0
C A:PRO107 4.1 37.7 1.0
OE2 A:GLU119 4.2 40.3 1.0
CE1 A:HIS41 4.2 29.9 1.0
CB A:ASP108 4.3 35.4 1.0
OE2 A:GLU80 4.3 40.6 1.0
CA A:ASP108 4.3 35.7 1.0
CG A:GLU80 4.3 39.0 1.0
N A:ASP108 4.4 36.6 1.0
CD A:GLU119 4.5 41.8 1.0
CB A:GLU80 4.5 39.6 1.0
C A:LEU106 4.7 40.6 1.0
NE2 A:HIS41 4.7 30.0 1.0
C1 A:XI7305 4.8 55.3 1.0
CA A:PRO107 4.8 38.4 1.0
C10 A:XI7305 4.9 53.3 1.0

Manganese binding site 2 out of 8 in 4e5g

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


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

b:37.5
occ:1.00
 OE2 A:GLU119 1.9 40.3 1.0
O A:ILE120 2.2 39.5 1.0
OD2 A:ASP108 2.2 34.2 1.0
O11 A:XI7305 2.3 53.2 1.0
O8 A:XI7305 2.3 53.8 1.0
NE2 A:HIS41 2.4 30.0 1.0
C10 A:XI7305 3.0 53.3 1.0
C9 A:XI7305 3.0 53.5 1.0
CE1 A:HIS41 3.1 29.9 1.0
CD A:GLU119 3.1 41.8 1.0
CG A:ASP108 3.1 34.6 1.0
OD1 A:ASP108 3.3 34.9 1.0
C A:ILE120 3.3 39.5 1.0
CD2 A:HIS41 3.4 30.7 1.0
N A:ILE120 3.7 39.3 1.0
OE1 A:GLU119 3.8 45.6 1.0
MN A:MN303 3.8 57.0 1.0
CA A:ILE120 4.0 39.1 1.0
CG A:GLU119 4.2 40.5 1.0
ND1 A:HIS41 4.2 29.0 1.0
NZ A:LYS134 4.2 56.6 1.0
O10 A:XI7305 4.2 53.4 1.0
O A:HOH401 4.3 27.9 1.0
C8 A:XI7305 4.3 53.8 1.0
CG A:HIS41 4.4 30.5 1.0
N A:GLY121 4.4 39.9 1.0
CB A:ASP108 4.5 35.4 1.0
CB A:ILE120 4.5 39.0 1.0
OE1 A:GLU80 4.7 40.9 1.0
CA A:GLY121 4.7 40.2 1.0
C A:GLU119 4.7 39.3 1.0
CE A:LYS134 4.8 56.7 1.0
O14 A:XI7305 4.8 54.9 1.0

Manganese binding site 3 out of 8 in 4e5g

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Manganese binding site 3 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 2


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

b:60.0
occ:1.00
 O14 B:XI7305 2.0 55.1 1.0
OD1 B:ASP108 2.1 42.5 1.0
OE1 B:GLU80 2.3 40.3 1.0
O8 B:XI7305 2.3 50.3 1.0
C7 B:XI7305 3.1 54.2 1.0
CG B:ASP108 3.2 41.6 1.0
C9 B:XI7305 3.3 51.6 1.0
CD B:GLU80 3.4 40.5 1.0
OD2 B:ASP108 3.6 42.2 1.0
C8 B:XI7305 3.7 52.9 1.0
O B:PRO107 3.8 42.7 1.0
O B:LEU106 3.8 45.6 1.0
OE2 B:GLU119 3.8 41.0 1.0
MN B:MN304 3.8 38.9 1.0
C B:PRO107 4.1 42.9 1.0
OE2 B:GLU80 4.1 39.8 1.0
CE1 B:HIS41 4.2 30.4 1.0
OE1 B:GLU119 4.2 38.1 1.0
CG B:GLU80 4.3 39.2 1.0
CB B:ASP108 4.3 41.6 1.0
CA B:ASP108 4.3 41.8 1.0
C1 B:XI7305 4.4 55.9 1.0
N B:ASP108 4.4 42.4 1.0
CB B:GLU80 4.5 39.7 1.0
CD B:GLU119 4.5 39.1 1.0
C10 B:XI7305 4.7 51.8 1.0
C6 B:XI7305 4.7 56.4 1.0
NE2 B:HIS41 4.7 30.8 1.0
C B:LEU106 4.7 45.7 1.0
CA B:PRO107 4.9 43.5 1.0
CA B:GLU80 4.9 39.7 1.0
O11 B:XI7305 5.0 52.1 1.0

Manganese binding site 4 out of 8 in 4e5g

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


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

b:38.9
occ:1.00
 OE1 B:GLU119 2.0 38.1 1.0
O B:ILE120 2.0 41.0 1.0
O8 B:XI7305 2.3 50.3 1.0
O11 B:XI7305 2.3 52.1 1.0
OD2 B:ASP108 2.3 42.2 1.0
NE2 B:HIS41 2.3 30.8 1.0
C9 B:XI7305 3.0 51.6 1.0
C10 B:XI7305 3.0 51.8 1.0
CE1 B:HIS41 3.1 30.4 1.0
CD B:GLU119 3.1 39.1 1.0
CG B:ASP108 3.2 41.6 1.0
C B:ILE120 3.2 41.0 1.0
CD2 B:HIS41 3.4 31.2 1.0
OD1 B:ASP108 3.4 42.5 1.0
NZ B:LYS134 3.5 62.3 1.0
N B:ILE120 3.7 40.1 1.0
OE2 B:GLU119 3.7 41.0 1.0
MN B:MN303 3.8 60.0 1.0
CA B:ILE120 3.9 40.4 1.0
ND1 B:HIS41 4.2 30.2 1.0
O10 B:XI7305 4.2 52.2 1.0
CG B:GLU119 4.3 39.2 1.0
N B:GLY121 4.3 41.6 1.0
C8 B:XI7305 4.3 52.9 1.0
CG B:HIS41 4.4 30.7 1.0
CB B:ILE120 4.5 40.4 1.0
CB B:ASP108 4.5 41.6 1.0
CA B:GLY121 4.6 42.2 1.0
OE1 B:GLU80 4.6 40.3 1.0
C B:GLU119 4.7 39.8 1.0
O14 B:XI7305 4.8 55.1 1.0
CE B:LYS134 4.9 62.6 1.0

Manganese binding site 5 out of 8 in 4e5g

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Manganese binding site 5 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 2


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

b:42.6
occ:1.00
 O11 C:XI7305 2.1 43.0 1.0
OD2 C:ASP108 2.1 29.9 1.0
O C:ILE120 2.1 37.2 1.0
OE1 C:GLU119 2.2 36.3 1.0
NE2 C:HIS41 2.4 27.9 1.0
O8 C:XI7305 2.6 44.7 1.0
CG C:ASP108 3.0 33.4 1.0
C10 C:XI7305 3.0 44.5 1.0
OD1 C:ASP108 3.2 30.5 1.0
C9 C:XI7305 3.2 45.3 1.0
C C:ILE120 3.2 37.6 1.0
CD C:GLU119 3.3 38.9 1.0
CD2 C:HIS41 3.3 28.3 1.0
CE1 C:HIS41 3.4 28.0 1.0
N C:ILE120 3.6 37.9 1.0
CA C:ILE120 3.9 37.6 1.0
OE2 C:GLU119 3.9 41.2 1.0
MN C:MN304 3.9 54.0 1.0
O10 C:XI7305 4.2 44.5 1.0
CB C:ILE120 4.3 38.0 1.0
NZ C:LYS134 4.3 63.9 1.0
N C:GLY121 4.3 38.1 1.0
CB C:ASP108 4.4 35.3 1.0
CG C:GLU119 4.4 39.2 1.0
ND1 C:HIS41 4.4 27.8 1.0
CG C:HIS41 4.4 28.6 1.0
C8 C:XI7305 4.5 47.1 1.0
C C:GLU119 4.6 38.1 1.0
OE1 C:GLU80 4.7 40.6 1.0
CA C:GLY121 4.7 38.7 1.0
O C:HOH401 4.7 39.6 1.0
CG2 C:ILE120 4.9 37.1 1.0
CA C:GLU119 5.0 38.4 1.0

Manganese binding site 6 out of 8 in 4e5g

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


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

b:54.0
occ:1.00
 O8 C:XI7305 2.1 44.7 1.0
O14 C:XI7305 2.2 48.9 1.0
OE1 C:GLU80 2.2 40.6 1.0
OD1 C:ASP108 2.3 30.5 1.0
C7 C:XI7305 3.2 49.1 1.0
C9 C:XI7305 3.3 45.3 1.0
CD C:GLU80 3.3 39.6 1.0
CG C:ASP108 3.3 33.4 1.0
C8 C:XI7305 3.7 47.1 1.0
O C:LEU106 3.9 42.6 1.0
OD2 C:ASP108 3.9 29.9 1.0
O C:PRO107 3.9 38.9 1.0
MN C:MN303 3.9 42.6 1.0
OE2 C:GLU80 4.1 37.9 1.0
CE1 C:HIS41 4.2 28.0 1.0
CG C:GLU80 4.2 38.6 1.0
C C:PRO107 4.2 38.9 1.0
CB C:GLU80 4.3 38.4 1.0
CA C:ASP108 4.5 36.2 1.0
CB C:ASP108 4.5 35.3 1.0
OE2 C:GLU119 4.5 41.2 1.0
C10 C:XI7305 4.5 44.5 1.0
C1 C:XI7305 4.5 51.2 1.0
N C:ASP108 4.5 37.5 1.0
NE2 C:HIS41 4.6 27.9 1.0
OE1 C:GLU119 4.6 36.3 1.0
O11 C:XI7305 4.7 43.0 1.0
C C:LEU106 4.8 42.8 1.0
C6 C:XI7305 4.9 51.3 1.0
CA C:GLU80 4.9 38.5 1.0
CA C:PRO107 5.0 40.0 1.0

Manganese binding site 7 out of 8 in 4e5g

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Manganese binding site 7 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 2


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

b:44.8
occ:1.00
 OD2 D:ASP108 2.0 38.5 1.0
OE1 D:GLU119 2.1 41.1 1.0
O D:ILE120 2.2 41.3 1.0
O11 D:XI7305 2.3 53.5 1.0
NE2 D:HIS41 2.4 33.1 1.0
O8 D:XI7305 2.7 55.4 1.0
CG D:ASP108 2.9 40.7 1.0
CE1 D:HIS41 3.1 33.4 1.0
CD D:GLU119 3.1 42.2 1.0
OD1 D:ASP108 3.2 40.3 1.0
C10 D:XI7305 3.2 55.0 1.0
C D:ILE120 3.3 41.0 1.0
C9 D:XI7305 3.4 55.5 1.0
CD2 D:HIS41 3.5 33.7 1.0
N D:ILE120 3.6 41.1 1.0
OE2 D:GLU119 3.7 44.8 1.0
MN D:MN304 3.7 56.6 1.0
CA D:ILE120 3.9 40.6 1.0
NZ D:LYS134 4.2 61.5 1.0
ND1 D:HIS41 4.3 32.1 1.0
CB D:ASP108 4.3 41.7 1.0
CG D:GLU119 4.3 41.9 1.0
CB D:ILE120 4.3 40.6 1.0
O10 D:XI7305 4.4 55.4 1.0
N D:GLY121 4.4 41.2 1.0
CG D:HIS41 4.5 32.3 1.0
C D:GLU119 4.6 41.3 1.0
O D:HOH401 4.7 38.0 1.0
C8 D:XI7305 4.7 56.9 1.0
OE1 D:GLU80 4.8 46.2 1.0
CA D:GLY121 4.8 41.2 1.0
CA D:GLU119 5.0 41.4 1.0
CE D:LYS134 5.0 61.2 1.0

Manganese binding site 8 out of 8 in 4e5g

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


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

b:56.6
occ:1.00
 OD1 D:ASP108 2.1 40.3 1.0
O8 D:XI7305 2.2 55.4 1.0
OE1 D:GLU80 2.5 46.2 1.0
O14 D:XI7305 2.5 57.9 1.0
CG D:ASP108 3.2 40.7 1.0
C9 D:XI7305 3.4 55.5 1.0
CD D:GLU80 3.5 46.1 1.0
C7 D:XI7305 3.6 58.6 1.0
OD2 D:ASP108 3.7 38.5 1.0
MN D:MN303 3.7 44.8 1.0
O D:PRO107 3.9 44.6 1.0
C8 D:XI7305 4.0 56.9 1.0
CE1 D:HIS41 4.0 33.4 1.0
OE2 D:GLU119 4.1 44.8 1.0
O D:LEU106 4.1 48.3 1.0
C D:PRO107 4.3 44.7 1.0
CG D:GLU80 4.3 43.7 1.0
CB D:GLU80 4.3 43.1 1.0
OE2 D:GLU80 4.3 44.5 1.0
CB D:ASP108 4.3 41.7 1.0
OE1 D:GLU119 4.4 41.1 1.0
CA D:ASP108 4.4 41.9 1.0
N D:ASP108 4.5 43.3 1.0
NE2 D:HIS41 4.6 33.1 1.0
C10 D:XI7305 4.6 55.0 1.0
CD D:GLU119 4.7 42.2 1.0
O11 D:XI7305 4.7 53.5 1.0
C1 D:XI7305 4.9 60.7 1.0
CA D:GLU80 4.9 43.0 1.0
C D:LEU106 5.0 48.1 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 19:09:59 2024

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