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Manganese in PDB 4e5e: Crystal Structure of Avian Influenza Virus Pan Apo

Protein crystallography data

The structure of Crystal Structure of Avian Influenza Virus Pan Apo, PDB code: 4e5e was solved by R.M.Dubois, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.95 / 2.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.393, 133.875, 126.352, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Avian Influenza Virus Pan Apo (pdb code 4e5e). 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 Apo, PDB code: 4e5e:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4e5e

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Manganese binding site 1 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Apo


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

b:39.9
occ:1.00
 O A:ILE120 2.1 23.7 1.0
OD2 A:ASP108 2.2 23.3 1.0
NE2 A:HIS41 2.3 23.2 1.0
OE1 A:GLU119 2.3 32.0 1.0
O A:HOH405 2.4 27.1 1.0
MN A:MN304 3.1 98.8 1.0
CG A:ASP108 3.1 22.8 1.0
CE1 A:HIS41 3.1 23.1 1.0
OD1 A:ASP108 3.2 22.0 1.0
CD2 A:HIS41 3.2 22.3 1.0
C A:ILE120 3.3 24.2 1.0
CD A:GLU119 3.3 30.1 1.0
N A:ILE120 3.7 24.3 1.0
OE2 A:GLU119 3.8 30.2 1.0
CA A:ILE120 4.0 24.5 1.0
ND1 A:HIS41 4.2 24.0 1.0
CG A:HIS41 4.3 23.4 1.0
NZ A:LYS134 4.3 40.0 1.0
N A:GLY121 4.3 24.1 1.0
O A:HOH401 4.4 29.2 1.0
CB A:ILE120 4.4 24.6 1.0
CB A:ASP108 4.5 23.8 1.0
CG A:GLU119 4.5 26.9 1.0
C A:GLU119 4.6 24.6 1.0
CA A:GLY121 4.6 24.1 1.0
SG A:CYS45 4.8 24.9 1.0
CA A:GLU119 4.9 24.5 1.0

Manganese binding site 2 out of 8 in 4e5e

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Manganese binding site 2 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Apo


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

b:98.8
occ:1.00
 OD1 A:ASP108 2.3 22.0 1.0
MN A:MN303 3.1 39.9 1.0
O A:HOH417 3.2 35.1 1.0
CG A:ASP108 3.2 22.8 1.0
OD2 A:ASP108 3.5 23.3 1.0
CE1 A:HIS41 3.5 23.1 1.0
OE2 A:GLU80 3.8 35.2 1.0
O A:HOH455 3.8 44.2 1.0
NE2 A:HIS41 3.8 23.2 1.0
OE2 A:GLU119 3.8 30.2 1.0
OE1 A:GLU119 3.9 32.0 1.0
O A:LEU106 4.1 28.0 1.0
O A:HOH405 4.2 27.1 1.0
CD A:GLU119 4.3 30.1 1.0
CD A:GLU80 4.5 33.4 1.0
CB A:ASP108 4.5 23.8 1.0
O A:PRO107 4.6 24.4 1.0
ND1 A:HIS41 4.6 24.0 1.0
C A:PRO107 4.7 25.1 1.0
N A:ASP108 4.8 24.1 1.0
CA A:ASP108 4.8 24.1 1.0

Manganese binding site 3 out of 8 in 4e5e

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Manganese binding site 3 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Apo


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

b:36.0
occ:1.00
 O B:ILE120 2.1 24.1 1.0
OD2 B:ASP108 2.2 25.8 1.0
NE2 B:HIS41 2.3 22.3 1.0
O B:HOH405 2.3 29.5 1.0
OE1 B:GLU119 2.3 34.1 1.0
MN B:MN304 2.7 88.7 1.0
CE1 B:HIS41 3.1 22.2 1.0
CG B:ASP108 3.2 25.4 1.0
C B:ILE120 3.2 24.4 1.0
CD2 B:HIS41 3.3 22.8 1.0
CD B:GLU119 3.3 32.7 1.0
OD1 B:ASP108 3.4 26.8 1.0
N B:ILE120 3.6 24.8 1.0
OE2 B:GLU119 3.8 34.0 1.0
CA B:ILE120 3.9 24.9 1.0
NZ B:LYS134 4.1 42.2 1.0
ND1 B:HIS41 4.3 23.7 1.0
N B:GLY121 4.3 24.2 1.0
O B:HOH401 4.3 26.9 1.0
CG B:HIS41 4.4 23.2 1.0
CB B:ILE120 4.4 25.3 1.0
CG B:GLU119 4.4 28.9 1.0
CA B:GLY121 4.5 23.8 1.0
CB B:ASP108 4.5 24.9 1.0
C B:GLU119 4.6 25.5 1.0
CE B:LYS134 4.7 41.7 1.0
CA B:GLU119 4.9 25.7 1.0
SG B:CYS45 5.0 23.6 1.0

Manganese binding site 4 out of 8 in 4e5e

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Manganese binding site 4 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Apo


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

b:88.7
occ:1.00
 OD1 B:ASP108 2.6 26.8 1.0
MN B:MN303 2.7 36.0 1.0
OD2 B:ASP108 3.2 25.8 1.0
CG B:ASP108 3.3 25.4 1.0
OE1 B:GLU119 3.3 34.1 1.0
CE1 B:HIS41 3.5 22.2 1.0
OE2 B:GLU119 3.6 34.0 1.0
NE2 B:HIS41 3.7 22.3 1.0
O B:HOH405 3.8 29.5 1.0
CD B:GLU119 3.8 32.7 1.0
O B:HOH466 3.8 47.3 1.0
OE1 B:GLU80 3.9 34.6 1.0
O B:HOH418 4.0 35.7 1.0
O B:LEU106 4.2 28.6 1.0
ND1 B:HIS41 4.6 23.7 1.0
CB B:ASP108 4.7 24.9 1.0
CD B:GLU80 4.7 33.1 1.0
O B:ILE120 4.8 24.1 1.0
CD2 B:HIS41 4.9 22.8 1.0
NZ B:LYS134 4.9 42.2 1.0
O B:PRO107 4.9 25.1 1.0
C B:PRO107 5.0 25.8 1.0

Manganese binding site 5 out of 8 in 4e5e

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Manganese binding site 5 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Apo


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

b:40.2
occ:1.00
 OD2 C:ASP108 2.1 24.8 1.0
O C:ILE120 2.2 23.2 1.0
OE1 C:GLU119 2.2 33.6 1.0
O C:HOH405 2.3 32.9 1.0
NE2 C:HIS41 2.3 23.4 1.0
CG C:ASP108 3.0 25.8 1.0
MN C:MN304 3.1 98.1 1.0
CE1 C:HIS41 3.1 22.9 1.0
CD C:GLU119 3.1 32.2 1.0
OD1 C:ASP108 3.2 25.8 1.0
C C:ILE120 3.2 23.1 1.0
CD2 C:HIS41 3.4 23.3 1.0
OE2 C:GLU119 3.5 33.4 1.0
N C:ILE120 3.5 24.0 1.0
CA C:ILE120 3.9 23.4 1.0
ND1 C:HIS41 4.3 24.5 1.0
NZ C:LYS134 4.3 39.6 1.0
N C:GLY121 4.3 23.1 1.0
CG C:GLU119 4.3 28.3 1.0
CB C:ILE120 4.4 23.9 1.0
CB C:ASP108 4.4 25.2 1.0
CG C:HIS41 4.4 23.6 1.0
C C:GLU119 4.5 24.8 1.0
O C:HOH401 4.6 29.9 1.0
CA C:GLY121 4.6 22.9 1.0
CA C:GLU119 4.8 25.3 1.0
SG C:CYS45 4.8 25.6 1.0

Manganese binding site 6 out of 8 in 4e5e

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Manganese binding site 6 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Apo


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

b:98.1
occ:1.00
 OD1 C:ASP108 2.4 25.8 1.0
O C:HOH455 2.8 44.3 1.0
O C:HOH416 2.9 38.6 1.0
MN C:MN303 3.1 40.2 1.0
CG C:ASP108 3.2 25.8 1.0
OD2 C:ASP108 3.4 24.8 1.0
CE1 C:HIS41 3.6 22.9 1.0
OE2 C:GLU119 3.6 33.4 1.0
O C:HOH456 3.8 48.6 1.0
OE1 C:GLU80 3.9 35.4 1.0
O C:LEU106 4.0 30.0 1.0
NE2 C:HIS41 4.0 23.4 1.0
O C:HOH405 4.0 32.9 1.0
OE1 C:GLU119 4.0 33.6 1.0
CD C:GLU119 4.2 32.2 1.0
O C:PRO107 4.5 26.3 1.0
CB C:ASP108 4.5 25.2 1.0
C C:PRO107 4.6 26.8 1.0
CD C:GLU80 4.6 35.0 1.0
ND1 C:HIS41 4.7 24.5 1.0
N C:ASP108 4.8 25.9 1.0
CA C:ASP108 4.8 25.9 1.0
C C:LEU106 5.0 29.6 1.0

Manganese binding site 7 out of 8 in 4e5e

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Manganese binding site 7 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Apo


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

b:38.1
occ:1.00
 OD2 D:ASP108 2.1 25.7 1.0
O D:ILE120 2.1 25.0 1.0
NE2 D:HIS41 2.4 23.2 1.0
OE1 D:GLU119 2.4 34.2 1.0
O D:HOH405 2.5 25.4 1.0
MN D:MN304 2.9 0.4 1.0
CG D:ASP108 3.1 24.8 1.0
CE1 D:HIS41 3.1 23.0 1.0
C D:ILE120 3.2 24.9 1.0
OD1 D:ASP108 3.4 22.7 1.0
CD D:GLU119 3.4 32.9 1.0
CD2 D:HIS41 3.4 23.7 1.0
N D:ILE120 3.6 25.2 1.0
CA D:ILE120 3.9 24.9 1.0
OE2 D:GLU119 4.0 35.1 1.0
ND1 D:HIS41 4.3 24.4 1.0
N D:GLY121 4.3 24.7 1.0
NZ D:LYS134 4.3 41.8 1.0
CB D:ASP108 4.4 24.7 1.0
CB D:ILE120 4.4 25.2 1.0
CG D:HIS41 4.5 23.0 1.0
CG D:GLU119 4.5 29.1 1.0
CA D:GLY121 4.5 23.7 1.0
C D:GLU119 4.5 25.5 1.0
O D:HOH401 4.6 26.3 1.0
CE D:LYS134 4.8 40.6 1.0
CA D:GLU119 4.9 25.9 1.0

Manganese binding site 8 out of 8 in 4e5e

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Manganese binding site 8 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Apo


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

b:0.4
occ:1.00
 OD1 D:ASP108 2.5 22.7 1.0
MN D:MN303 2.9 38.1 1.0
CG D:ASP108 3.2 24.8 1.0
O D:HOH457 3.2 47.3 1.0
OD2 D:ASP108 3.2 25.7 1.0
OE1 D:GLU119 3.3 34.2 1.0
OE2 D:GLU119 3.4 35.1 1.0
O D:HOH416 3.5 34.5 1.0
CD D:GLU119 3.8 32.9 1.0
CE1 D:HIS41 3.8 23.0 1.0
O D:LEU106 3.8 30.9 1.0
O D:HOH405 4.1 25.4 1.0
NE2 D:HIS41 4.1 23.2 1.0
OE1 D:GLU80 4.4 34.8 1.0
CB D:ASP108 4.6 24.7 1.0
C D:PRO107 4.7 26.6 1.0
O D:PRO107 4.7 25.6 1.0
N D:ASP108 4.8 25.6 1.0
CA D:ASP108 4.9 25.4 1.0
C D:LEU106 4.9 30.1 1.0
ND1 D:HIS41 5.0 24.4 1.0
O D:ILE120 5.0 25.0 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 19:08:24 2024

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