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Manganese in PDB 6e0q: The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 4,6-Dihydroxy-2-Methyl-5-Oxocyclohepta-1,3,6-Triene- 1-Carboxylic Acid

Protein crystallography data

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 4,6-Dihydroxy-2-Methyl-5-Oxocyclohepta-1,3,6-Triene- 1-Carboxylic Acid, PDB code: 6e0q was solved by B.L.Dick, C.N.Morrison, S.M.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.03 / 2.35
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 75.090, 75.090, 119.670, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 25.8

Manganese Binding Sites:

The binding sites of Manganese atom in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 4,6-Dihydroxy-2-Methyl-5-Oxocyclohepta-1,3,6-Triene- 1-Carboxylic Acid (pdb code 6e0q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 4,6-Dihydroxy-2-Methyl-5-Oxocyclohepta-1,3,6-Triene- 1-Carboxylic Acid, PDB code: 6e0q:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6e0q

Go back to Manganese Binding Sites List in 6e0q
Manganese binding site 1 out of 2 in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 4,6-Dihydroxy-2-Methyl-5-Oxocyclohepta-1,3,6-Triene- 1-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 4,6-Dihydroxy-2-Methyl-5-Oxocyclohepta-1,3,6-Triene- 1-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:34.4
occ:1.00
OAN A:HKD203 2.1 39.4 1.0
OAM A:HKD203 2.1 32.9 1.0
OE2 A:GLU119 2.1 31.7 1.0
O A:ILE120 2.2 33.2 1.0
OD2 A:ASP108 2.2 31.7 1.0
NE2 A:HIS41 2.3 37.3 1.0
CAL A:HKD203 2.9 34.9 1.0
CAK A:HKD203 2.9 40.6 1.0
CG A:ASP108 3.1 39.3 1.0
CE1 A:HIS41 3.2 34.5 1.0
CD A:GLU119 3.2 31.8 1.0
C A:ILE120 3.3 33.4 1.0
CD2 A:HIS41 3.4 34.5 1.0
OD1 A:ASP108 3.4 34.3 1.0
N A:ILE120 3.6 30.5 1.0
OE1 A:GLU119 3.6 33.1 1.0
MN A:MN202 3.8 38.9 1.0
CA A:ILE120 3.9 33.0 1.0
O A:HOH303 4.0 26.3 1.0
NZ A:LYS134 4.1 40.2 1.0
CB A:ILE120 4.1 34.6 1.0
O A:HOH301 4.2 31.1 1.0
CAH A:HKD203 4.2 34.6 1.0
CAJ A:HKD203 4.2 38.4 1.0
ND1 A:HIS41 4.3 34.9 1.0
CG A:GLU119 4.4 32.4 1.0
N A:GLY121 4.4 29.6 1.0
CG A:HIS41 4.4 33.1 1.0
CB A:ASP108 4.5 36.1 1.0
C A:GLU119 4.7 32.6 1.0
OAI A:HKD203 4.7 38.5 1.0
CA A:GLY121 4.7 31.3 1.0
CE A:LYS134 4.7 39.1 1.0
OE2 A:GLU80 4.8 36.3 1.0
CG2 A:ILE120 4.9 35.4 1.0

Manganese binding site 2 out of 2 in 6e0q

Go back to Manganese Binding Sites List in 6e0q
Manganese binding site 2 out of 2 in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 4,6-Dihydroxy-2-Methyl-5-Oxocyclohepta-1,3,6-Triene- 1-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 4,6-Dihydroxy-2-Methyl-5-Oxocyclohepta-1,3,6-Triene- 1-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:38.9
occ:1.00
OE2 A:GLU80 2.0 36.3 1.0
OD1 A:ASP108 2.1 34.3 1.0
OAI A:HKD203 2.1 38.5 1.0
OAM A:HKD203 2.2 32.9 1.0
O A:HOH301 2.3 31.1 1.0
O A:HOH305 2.4 32.9 1.0
CAL A:HKD203 2.9 34.9 1.0
CAH A:HKD203 2.9 34.6 1.0
CG A:ASP108 3.1 39.3 1.0
CD A:GLU80 3.2 43.0 1.0
OD2 A:ASP108 3.6 31.7 1.0
MN A:MN201 3.8 34.4 1.0
CE1 A:HIS41 3.9 34.5 1.0
CG A:GLU80 4.0 40.6 1.0
O A:LEU106 4.1 38.4 1.0
O A:PRO107 4.1 26.7 1.0
OE1 A:GLU80 4.1 47.7 1.0
CB A:GLU80 4.2 38.8 1.0
C A:PRO107 4.2 30.8 1.0
CA A:ASP108 4.2 37.7 1.0
O1 A:EDO205 4.2 48.2 1.0
CAG A:HKD203 4.2 36.5 1.0
CB A:ASP108 4.2 36.1 1.0
CAK A:HKD203 4.2 40.6 1.0
OE1 A:GLU119 4.3 33.1 1.0
N A:ASP108 4.3 33.8 1.0
NE2 A:HIS41 4.5 37.3 1.0
O2 A:EDO205 4.5 56.2 1.0
OE2 A:GLU119 4.6 31.7 1.0
OAN A:HKD203 4.7 39.4 1.0
O2 A:EDO204 4.8 59.8 1.0
CA A:GLU80 4.8 38.6 1.0
CD A:GLU119 4.9 31.8 1.0
CA A:PRO107 4.9 34.2 1.0
C A:LEU106 5.0 37.2 1.0

Reference:

C.V.Credille, B.L.Dick, C.N.Morrison, R.W.Stokes, R.N.Adamek, N.C.Wu, I.A.Wilson, S.M.Cohen. Structure-Activity Relationships in Metal-Binding Pharmacophores For Influenza Endonuclease. J. Med. Chem. V. 61 10206 2018.
ISSN: ISSN 1520-4804
PubMed: 30351002
DOI: 10.1021/ACS.JMEDCHEM.8B01363
Page generated: Tue Dec 15 04:52:12 2020

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