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Manganese in PDB 4e5h: Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3

Protein crystallography data

The structure of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3, PDB code: 4e5h 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) 46.05 / 2.16
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.101, 134.825, 125.905, 90.00, 90.00, 90.00
R / Rfree (%) 25.6 / 29

Other elements in 4e5h:

The structure of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3 (pdb code 4e5h). 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 3, PDB code: 4e5h:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4e5h

Go back to Manganese Binding Sites List in 4e5h
Manganese binding site 1 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3


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

b:54.4
occ:1.00
 NE2 A:HIS41 2.2 35.6 1.0
O A:ILE120 2.3 35.1 1.0
OE1 A:GLU119 2.3 43.9 1.0
OD2 A:ASP108 2.5 37.0 1.0
CE1 A:HIS41 3.0 36.5 1.0
CD2 A:HIS41 3.2 34.5 1.0
CG A:ASP108 3.2 37.2 1.0
OD1 A:ASP108 3.3 39.0 1.0
CD A:GLU119 3.4 42.4 1.0
C A:ILE120 3.4 36.2 1.0
MN A:MN304 3.8 0.4 1.0
N A:ILE120 3.9 36.2 1.0
NZ A:LYS134 4.1 57.2 1.0
CA A:ILE120 4.1 36.3 1.0
ND1 A:HIS41 4.1 36.3 1.0
OE2 A:GLU119 4.2 44.5 1.0
CG A:HIS41 4.2 34.1 1.0
CG A:GLU119 4.3 38.9 1.0
O A:HOH401 4.4 52.4 1.0
CB A:ILE120 4.5 36.5 1.0
N A:GLY121 4.5 36.0 1.0
CB A:ASP108 4.6 36.3 1.0
CA A:GLY121 4.7 35.2 1.0
C A:GLU119 4.8 36.5 1.0
CE A:LYS134 4.9 56.8 1.0
OE2 A:GLU80 5.0 52.4 1.0

Manganese binding site 2 out of 8 in 4e5h

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


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

b:0.4
occ:1.00
 OD1 A:ASP108 2.4 39.0 1.0
OE2 A:GLU80 2.7 52.4 1.0
CG A:ASP108 3.4 37.2 1.0
O A:LEU106 3.5 39.6 1.0
MN A:MN303 3.8 54.4 1.0
OD2 A:ASP108 3.8 37.0 1.0
CD A:GLU80 3.9 50.8 1.0
OE1 A:GLU119 4.0 43.9 1.0
CE1 A:HIS41 4.1 36.5 1.0
OE2 A:GLU119 4.2 44.5 1.0
O A:PRO107 4.2 36.7 1.0
C A:PRO107 4.3 37.1 1.0
C A:LEU106 4.5 39.7 1.0
CD A:GLU119 4.5 42.4 1.0
CB A:ASP108 4.6 36.3 1.0
N A:ASP108 4.6 36.2 1.0
NE2 A:HIS41 4.6 35.6 1.0
CA A:ASP108 4.6 36.1 1.0
CG A:GLU80 4.8 46.4 1.0
OE1 A:GLU80 4.8 55.6 1.0
CA A:PRO107 4.9 37.4 1.0
CB A:GLU80 4.9 43.4 1.0

Manganese binding site 3 out of 8 in 4e5h

Go back to Manganese Binding Sites List in 4e5h
Manganese binding site 3 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3


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

b:54.2
occ:1.00
 O B:ILE120 2.1 35.1 1.0
OD2 B:ASP108 2.3 36.4 1.0
OE1 B:GLU119 2.4 48.1 1.0
NE2 B:HIS41 2.4 34.2 1.0
CE1 B:HIS41 3.1 33.9 1.0
C B:ILE120 3.2 35.3 1.0
CG B:ASP108 3.2 35.7 1.0
OD1 B:ASP108 3.4 37.6 1.0
CD2 B:HIS41 3.4 33.4 1.0
CD B:GLU119 3.5 46.2 1.0
N B:ILE120 3.7 35.9 1.0
MN B:MN304 3.8 93.8 1.0
NZ B:LYS134 3.9 56.6 1.0
CA B:ILE120 3.9 35.8 1.0
ND1 B:HIS41 4.2 34.9 1.0
N B:GLY121 4.3 35.1 1.0
CG B:GLU119 4.3 41.3 1.0
OE2 B:GLU119 4.4 47.9 1.0
CB B:ILE120 4.4 36.2 1.0
CG B:HIS41 4.4 34.7 1.0
O B:HOH401 4.5 41.7 1.0
CE B:LYS134 4.5 55.9 1.0
CA B:GLY121 4.5 33.9 1.0
CB B:ASP108 4.6 35.9 1.0
C B:GLU119 4.6 36.5 1.0
CA B:GLU119 5.0 36.7 1.0

Manganese binding site 4 out of 8 in 4e5h

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


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

b:93.8
occ:1.00
 OD1 B:ASP108 2.3 37.6 1.0
OE1 B:GLU80 2.8 52.9 1.0
CG B:ASP108 3.3 35.7 1.0
OD2 B:ASP108 3.7 36.4 1.0
MN B:MN303 3.8 54.2 1.0
O B:LEU106 3.8 40.2 1.0
CE1 B:HIS41 3.9 33.9 1.0
CD B:GLU80 4.0 51.4 1.0
OE1 B:GLU119 4.0 48.1 1.0
O B:PRO107 4.1 37.6 1.0
C B:PRO107 4.4 37.9 1.0
CB B:ASP108 4.5 35.9 1.0
NE2 B:HIS41 4.5 34.2 1.0
OE2 B:GLU119 4.6 47.9 1.0
CA B:ASP108 4.6 35.6 1.0
N B:ASP108 4.6 36.7 1.0
CG B:GLU80 4.7 45.8 1.0
CD B:GLU119 4.7 46.2 1.0
C B:LEU106 4.8 40.8 1.0
CB B:GLU80 4.8 42.7 1.0
OE2 B:GLU80 4.9 55.4 1.0
ND1 B:HIS41 4.9 34.9 1.0

Manganese binding site 5 out of 8 in 4e5h

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Manganese binding site 5 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3


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

b:59.3
occ:1.00
 OD2 C:ASP108 2.1 37.9 1.0
O C:ILE120 2.1 35.9 1.0
OE1 C:GLU119 2.2 44.8 1.0
NE2 C:HIS41 2.5 36.4 1.0
CG C:ASP108 3.0 39.6 1.0
CE1 C:HIS41 3.2 35.6 1.0
C C:ILE120 3.2 36.4 1.0
OD1 C:ASP108 3.2 39.7 1.0
CD C:GLU119 3.3 44.3 1.0
CD2 C:HIS41 3.5 36.5 1.0
N C:ILE120 3.5 37.6 1.0
CA C:ILE120 3.8 37.0 1.0
MN C:MN304 3.9 89.1 1.0
OE2 C:GLU119 4.1 43.5 1.0
N C:GLY121 4.3 36.7 1.0
CB C:ILE120 4.3 37.5 1.0
CG C:GLU119 4.3 40.2 1.0
ND1 C:HIS41 4.3 37.4 1.0
CB C:ASP108 4.4 38.4 1.0
C C:GLU119 4.5 37.7 1.0
CG C:HIS41 4.5 35.6 1.0
O C:HOH401 4.6 41.0 1.0
CA C:GLY121 4.6 36.0 1.0
CA C:GLU119 4.8 37.5 1.0
NZ C:LYS134 4.8 63.6 1.0
OE1 C:GLU80 4.9 56.5 1.0
CG2 C:ILE120 4.9 37.9 1.0
CE C:LYS134 5.0 61.9 1.0
SG C:CYS45 5.0 37.6 1.0

Manganese binding site 6 out of 8 in 4e5h

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


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

b:89.1
occ:1.00
 OE1 C:GLU80 2.1 56.5 1.0
OD1 C:ASP108 2.3 39.7 1.0
CG C:ASP108 3.3 39.6 1.0
CD C:GLU80 3.3 50.5 1.0
OD2 C:ASP108 3.8 37.9 1.0
CE1 C:HIS41 3.8 35.6 1.0
MN C:MN303 3.9 59.3 1.0
O C:LEU106 4.0 43.6 1.0
OE2 C:GLU80 4.1 52.9 1.0
O C:PRO107 4.1 39.8 1.0
CG C:GLU80 4.4 46.1 1.0
C C:PRO107 4.4 40.3 1.0
CB C:ASP108 4.5 38.4 1.0
CA C:ASP108 4.5 38.8 1.0
NE2 C:HIS41 4.5 36.4 1.0
OE1 C:GLU119 4.5 44.8 1.0
CB C:GLU80 4.6 43.6 1.0
N C:ASP108 4.6 39.3 1.0
OE2 C:GLU119 4.6 43.5 1.0
ND1 C:HIS41 4.8 37.4 1.0
C C:LEU106 4.9 43.3 1.0

Manganese binding site 7 out of 8 in 4e5h

Go back to Manganese Binding Sites List in 4e5h
Manganese binding site 7 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3


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

b:59.9
occ:1.00
 O25 D:0N8305 1.9 87.2 1.0
OD2 D:ASP108 2.1 38.2 1.0
O D:ILE120 2.2 36.6 1.0
O28 D:0N8305 2.3 88.7 1.0
NE2 D:HIS41 2.4 34.4 1.0
OE1 D:GLU119 2.6 49.4 1.0
C24 D:0N8305 2.8 88.8 1.0
C23 D:0N8305 2.9 89.8 1.0
CG D:ASP108 3.0 37.9 1.0
CE1 D:HIS41 3.2 33.7 1.0
OD1 D:ASP108 3.2 37.8 1.0
C D:ILE120 3.4 36.5 1.0
CD2 D:HIS41 3.4 35.4 1.0
N D:ILE120 3.7 37.7 1.0
CD D:GLU119 3.8 47.6 1.0
MN D:MN304 3.8 0.7 1.0
O26 D:0N8305 4.0 88.5 1.0
CA D:ILE120 4.0 36.9 1.0
C22 D:0N8305 4.3 92.0 1.0
NZ D:LYS134 4.3 50.8 1.0
ND1 D:HIS41 4.3 36.8 1.0
CB D:ILE120 4.4 37.6 1.0
CB D:ASP108 4.4 36.9 1.0
N D:GLY121 4.5 36.1 1.0
CG D:HIS41 4.5 34.2 1.0
O D:HOH401 4.5 44.0 1.0
O27 D:0N8305 4.6 94.1 1.0
CG D:GLU119 4.6 43.6 1.0
C D:GLU119 4.6 38.4 1.0
OE2 D:GLU119 4.6 48.1 1.0
CA D:GLY121 4.7 34.0 1.0
CE D:LYS134 4.8 52.5 1.0
C14 D:0N8305 4.8 94.2 1.0
CA D:GLU119 5.0 38.8 1.0

Manganese binding site 8 out of 8 in 4e5h

Go back to Manganese Binding Sites List in 4e5h
Manganese binding site 8 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 3


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

b:0.7
occ:1.00
 O27 D:0N8305 1.9 94.1 1.0
OD1 D:ASP108 2.3 37.8 1.0
O28 D:0N8305 2.3 88.7 1.0
C14 D:0N8305 3.0 94.2 1.0
OE1 D:GLU80 3.1 55.2 1.0
CG D:ASP108 3.1 37.9 1.0
C23 D:0N8305 3.4 89.8 1.0
O D:LEU106 3.5 41.4 1.0
OD2 D:ASP108 3.6 38.2 1.0
O D:PRO107 3.7 36.0 1.0
C12 D:0N8305 3.8 95.7 1.0
C22 D:0N8305 3.8 92.0 1.0
MN D:MN303 3.8 59.9 1.0
C D:PRO107 4.0 37.4 1.0
C11 D:0N8305 4.0 95.6 1.0
CD D:GLU80 4.1 52.0 1.0
OE1 D:GLU119 4.2 49.4 1.0
CE1 D:HIS41 4.2 33.7 1.0
CA D:ASP108 4.2 36.9 1.0
N D:ASP108 4.3 36.7 1.0
CB D:ASP108 4.3 36.9 1.0
C D:LEU106 4.5 40.9 1.0
OE2 D:GLU119 4.6 48.1 1.0
CB D:GLU80 4.6 45.5 1.0
C24 D:0N8305 4.7 88.8 1.0
NE2 D:HIS41 4.7 34.4 1.0
C15 D:0N8305 4.7 96.5 1.0
CG D:GLU80 4.7 48.9 1.0
CA D:PRO107 4.8 38.0 1.0
CD D:GLU119 4.8 47.6 1.0
OE2 D:GLU80 4.9 55.5 1.0
O25 D:0N8305 4.9 87.2 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 19:10:36 2024

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