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Manganese in PDB 6fsb: Influenza B/Memphis/13/03 Endonuclease with I38T Mutation

Protein crystallography data

The structure of Influenza B/Memphis/13/03 Endonuclease with I38T Mutation, PDB code: 6fsb was solved by S.Cusack, V.Speranzini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.10 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.980, 61.450, 92.630, 90.00, 95.47, 90.00
R / Rfree (%) 19.7 / 23.6

Other elements in 6fsb:

The structure of Influenza B/Memphis/13/03 Endonuclease with I38T Mutation also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Influenza B/Memphis/13/03 Endonuclease with I38T Mutation (pdb code 6fsb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Influenza B/Memphis/13/03 Endonuclease with I38T Mutation, PDB code: 6fsb:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6fsb

Go back to Manganese Binding Sites List in 6fsb
Manganese binding site 1 out of 2 in the Influenza B/Memphis/13/03 Endonuclease with I38T Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Influenza B/Memphis/13/03 Endonuclease with I38T Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:33.8
occ:0.31
O A:HOH351 2.2 48.2 1.0
OE2 A:GLU120 2.2 60.8 1.0
OD2 A:ASP109 2.2 25.4 1.0
O A:VAL121 2.3 22.2 1.0
NE2 A:HIS41 2.5 23.8 1.0
CG A:ASP109 3.1 30.2 1.0
CE1 A:HIS41 3.1 36.5 1.0
CD A:GLU120 3.2 40.4 1.0
OD1 A:ASP109 3.3 22.9 1.0
C A:VAL121 3.5 22.3 1.0
CD2 A:HIS41 3.6 29.1 1.0
N A:VAL121 3.7 17.4 1.0
MN A:MN202 3.8 77.4 0.7
OE1 A:GLU120 3.9 39.3 1.0
CG A:GLU120 4.0 34.7 1.0
CA A:VAL121 4.2 21.2 1.0
NZ A:LYS135 4.2 53.8 1.0
ND1 A:HIS41 4.3 37.8 1.0
CB A:ASP109 4.5 26.9 1.0
N A:GLY122 4.5 17.5 1.0
CG A:HIS41 4.6 27.7 1.0
CB A:VAL121 4.6 19.8 1.0
C A:GLU120 4.7 18.5 1.0
CA A:GLY122 4.8 21.6 1.0
OE2 A:GLU193 4.8 31.3 1.0
CE A:LYS135 4.8 53.3 1.0
CA A:GLU120 4.9 17.5 1.0
CB A:GLU120 5.0 23.8 1.0

Manganese binding site 2 out of 2 in 6fsb

Go back to Manganese Binding Sites List in 6fsb
Manganese binding site 2 out of 2 in the Influenza B/Memphis/13/03 Endonuclease with I38T Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Influenza B/Memphis/13/03 Endonuclease with I38T Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:77.4
occ:0.71
O A:HOH351 2.2 48.2 1.0
OD1 A:ASP109 2.4 22.9 1.0
O A:HOH331 2.7 27.5 1.0
OE1 A:GLU81 3.3 52.4 1.0
CG A:ASP109 3.4 30.2 1.0
O A:LEU107 3.5 24.7 1.0
MN A:MN201 3.8 33.8 0.3
OD2 A:ASP109 3.8 25.4 1.0
O A:ALA108 3.9 21.2 1.0
OE2 A:GLU120 4.1 60.8 1.0
OE1 A:GLU120 4.1 39.3 1.0
C A:ALA108 4.1 17.6 1.0
N A:ASP109 4.2 19.7 1.0
NH1 A:ARG85 4.3 49.2 1.0
C A:LEU107 4.4 22.7 1.0
CE1 A:HIS41 4.4 36.5 1.0
CA A:ASP109 4.5 18.9 1.0
CD A:GLU120 4.5 40.4 1.0
NH2 A:ARG85 4.5 60.1 1.0
CB A:ASP109 4.5 26.9 1.0
CD A:GLU81 4.5 50.5 1.0
CZ A:ARG85 4.8 66.4 1.0
CA A:ALA108 4.9 23.7 1.0
CG A:LEU107 4.9 25.4 1.0
CB A:LEU107 5.0 22.3 1.0
NE2 A:HIS41 5.0 23.8 1.0
N A:ALA108 5.0 18.7 1.0

Reference:

S.Omoto, V.Speranzini, T.Hashimoto, T.Noshi, H.Yamaguchi, M.Kawai, K.Kawaguchi, T.Uehara, T.Shishido, A.Naito, S.Cusack. Characterization of Influenza Virus Variants Induced By Treatment with the Endonuclease Inhibitor Baloxavir Marboxil. Sci Rep V. 8 9633 2018.
ISSN: ESSN 2045-2322
PubMed: 29941893
DOI: 10.1038/S41598-018-27890-4
Page generated: Sun Oct 6 04:38:23 2024

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