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Fluorine in PDB 4wef: Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid

Protein crystallography data

The structure of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid, PDB code: 4wef was solved by V.A.Streltsov, P.Pilling, S.Barrett, J.Mckimm-Breschkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.46 / 2.50
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 218.668, 218.668, 109.769, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 25.8

Other elements in 4wef:

The structure of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid (pdb code 4wef). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid, PDB code: 4wef:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 4wef

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Fluorine binding site 1 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:29.8
occ:0.70
 F1 A:FSI609 0.0 29.8 0.7
C3 A:DF4610 0.4 18.9 0.3
F1 A:DF4610 1.2 19.0 0.3
C2 A:DF4610 1.4 18.6 0.3
C3 A:FSI609 1.4 26.5 0.7
C4 A:DF4610 1.9 18.9 0.3
C2 A:FSI609 2.3 25.5 0.7
C1 A:DF4610 2.3 18.3 0.3
C4 A:FSI609 2.4 26.3 0.7
C1 A:FSI609 2.5 23.1 0.7
O6 A:DF4610 2.6 18.4 0.3
O1B A:FSI609 2.6 21.8 0.7
O1B A:DF4610 2.7 18.3 0.3
C5 A:DF4610 2.7 18.9 0.3
O4 A:DF4610 2.8 18.3 0.3
O6 A:FSI609 2.8 24.6 0.7
C5 A:FSI609 2.8 26.7 0.7
O4 A:FSI609 2.9 24.5 0.7
C6 A:DF4610 3.1 18.6 0.3
O A:HOH701 3.2 29.9 1.0
O A:HOH789 3.3 25.7 1.0
C6 A:FSI609 3.3 25.4 0.7
O1A A:FSI609 3.5 23.6 0.7
O A:HOH752 3.5 41.0 1.0
OH A:TYR530 3.5 30.5 1.0
NH1 A:ARG192 3.5 32.3 1.0
O1A A:DF4610 3.5 19.2 0.3
O A:HOH717 3.7 30.6 1.0
O7 A:FSI609 3.9 22.7 0.7
NH2 A:ARG192 3.9 27.8 1.0
N5 A:DF4610 4.0 19.5 0.3
CZ A:ARG192 4.1 30.3 1.0
N5 A:FSI609 4.2 28.6 0.7
C7 A:FSI609 4.3 24.3 0.7
CZ A:TYR530 4.4 29.5 1.0
C7 A:DF4610 4.4 18.2 0.3
O7 A:DF4610 4.5 17.8 0.3
O10 A:FSI609 4.8 29.8 0.7
C10 A:FSI609 4.9 30.5 0.7
C10 A:DF4610 4.9 20.0 0.3
O10 A:DF4610 5.0 20.1 0.3

Fluorine binding site 2 out of 10 in 4wef

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Fluorine binding site 2 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F610

b:19.0
occ:0.30
 F1 A:DF4610 0.0 19.0 0.3
F1 A:FSI609 1.2 29.8 0.7
C3 A:DF4610 1.4 18.9 0.3
C2 A:DF4610 2.3 18.6 0.3
O A:HOH701 2.4 29.9 1.0
C3 A:FSI609 2.4 26.5 0.7
C4 A:DF4610 2.4 18.9 0.3
O4 A:DF4610 2.8 18.3 0.3
O A:HOH752 3.0 41.0 1.0
O A:HOH789 3.1 25.7 1.0
C1 A:DF4610 3.1 18.3 0.3
O4 A:FSI609 3.1 24.5 0.7
C4 A:FSI609 3.1 26.3 0.7
O1B A:DF4610 3.1 18.3 0.3
C5 A:DF4610 3.1 18.9 0.3
O A:HOH717 3.2 30.6 1.0
NH1 A:ARG192 3.3 32.3 1.0
C5 A:FSI609 3.4 26.7 0.7
O6 A:DF4610 3.4 18.4 0.3
C2 A:FSI609 3.4 25.5 0.7
O1B A:FSI609 3.4 21.8 0.7
C1 A:FSI609 3.5 23.1 0.7
O6 A:FSI609 3.8 24.6 0.7
C6 A:DF4610 3.9 18.6 0.3
C6 A:FSI609 4.2 25.4 0.7
CZ A:ARG192 4.3 30.3 1.0
O1A A:DF4610 4.3 19.2 0.3
O7 A:FSI609 4.3 22.7 0.7
O1A A:FSI609 4.4 23.6 0.7
NH2 A:ARG192 4.4 27.8 1.0
N5 A:DF4610 4.4 19.5 0.3
OAC A:SFJ612 4.4 87.9 1.0
N5 A:FSI609 4.5 28.6 0.7
O10 A:FSI609 4.6 29.8 0.7
OH A:TYR530 4.7 30.5 1.0
O7 A:DF4610 4.8 17.8 0.3
O10 A:DF4610 4.8 20.1 0.3
C7 A:FSI609 4.9 24.3 0.7
C10 A:FSI609 5.0 30.5 0.7
OAE A:SFJ612 5.0 69.9 1.0

Fluorine binding site 3 out of 10 in 4wef

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Fluorine binding site 3 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F611

b:53.5
occ:1.00
 FAI A:SFJ611 0.0 53.5 1.0
CAS A:SFJ611 1.4 53.5 1.0
CAR A:SFJ611 2.4 51.3 1.0
CAV A:SFJ611 2.4 55.5 1.0
FAJ A:SFJ611 2.7 54.4 1.0
CAT A:SFJ611 2.8 49.5 1.0
OAH A:SFJ611 2.9 46.5 1.0
OAM A:SFJ611 3.0 54.8 1.0
OG1 A:THR263 3.1 31.2 1.0
OD1 A:ASP264 3.1 31.4 1.0
CG A:ASP264 3.3 29.9 1.0
N A:THR263 3.4 29.3 1.0
O A:HOH728 3.5 24.6 1.0
CAU A:SFJ611 3.5 45.9 1.0
OD2 A:ASP264 3.5 29.7 1.0
N A:ASP264 3.6 27.9 1.0
O A:LEU261 3.7 29.3 1.0
CAO A:SFJ611 3.8 57.2 1.0
C A:THR263 3.8 28.2 1.0
CA A:THR263 3.9 29.0 1.0
CB A:ASN262 4.0 39.2 1.0
CB A:THR263 4.1 30.1 1.0
NAL A:SFJ611 4.1 50.1 1.0
OAC A:SFJ611 4.2 55.7 1.0
CB A:ASP264 4.2 29.2 1.0
CA A:ASP264 4.4 27.8 1.0
C A:ASN262 4.4 33.6 1.0
OAG A:SFJ611 4.6 36.0 1.0
O A:THR263 4.6 31.0 1.0
CAQ A:SFJ611 4.6 42.5 1.0
CA A:ASN262 4.7 36.4 1.0
CAN A:SFJ611 4.8 52.4 1.0
OAE A:SFJ611 4.8 48.2 1.0
C A:LEU261 4.8 30.2 1.0
O A:HOH903 4.8 41.5 1.0
OAB A:SFJ611 4.9 45.3 1.0
CG2 A:THR263 5.0 29.8 1.0

Fluorine binding site 4 out of 10 in 4wef

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Fluorine binding site 4 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F611

b:54.4
occ:1.00
 FAJ A:SFJ611 0.0 54.4 1.0
CAV A:SFJ611 1.4 55.5 1.0
OAM A:SFJ611 2.3 54.8 1.0
CAO A:SFJ611 2.4 57.2 1.0
CAS A:SFJ611 2.4 53.5 1.0
FAI A:SFJ611 2.7 53.5 1.0
OAE A:SFJ611 3.0 48.2 1.0
OAC A:SFJ611 3.2 55.7 1.0
OG1 A:THR263 3.3 31.2 1.0
CB A:ASN262 3.3 39.2 1.0
CAU A:SFJ611 3.6 45.9 1.0
N A:THR263 3.7 29.3 1.0
CAR A:SFJ611 3.7 51.3 1.0
CAT A:SFJ611 4.1 49.5 1.0
CG A:ASN262 4.2 43.7 1.0
CB A:THR263 4.2 30.1 1.0
CG2 A:THR263 4.2 29.8 1.0
OD1 A:ASN262 4.4 49.6 1.0
CA A:ASN262 4.5 36.4 1.0
C A:ASN262 4.5 33.6 1.0
CA A:THR263 4.5 29.0 1.0
O A:HOH992 4.6 29.0 1.0
CAQ A:SFJ611 4.6 42.5 1.0
CAP A:SFJ611 4.7 41.5 1.0
OAF A:SFJ611 4.8 39.3 1.0
OAH A:SFJ611 4.9 46.5 1.0
OAG A:SFJ611 4.9 36.0 1.0
O A:LEU261 5.0 29.3 1.0

Fluorine binding site 5 out of 10 in 4wef

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Fluorine binding site 5 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F612

b:91.5
occ:1.00
 FAI A:SFJ612 0.0 91.5 1.0
CAS A:SFJ612 1.4 84.9 1.0
OAH A:SFJ612 2.3 69.2 1.0
CAR A:SFJ612 2.4 80.4 1.0
CAV A:SFJ612 2.5 80.6 1.0
NE2 A:GLN215 2.6 45.8 1.0
FAJ A:SFJ612 2.7 64.2 1.0
OAM A:SFJ612 3.3 76.0 1.0
CAT A:SFJ612 3.5 81.8 1.0
CD A:GLN215 3.6 43.3 1.0
CAO A:SFJ612 3.7 76.7 1.0
CAU A:SFJ612 3.9 76.2 1.0
OAC A:SFJ612 4.0 87.9 1.0
OE1 A:GLN215 4.1 46.6 1.0
O A:HOH810 4.5 29.7 1.0
CG A:GLN215 4.5 38.5 1.0
OAE A:SFJ612 4.7 69.9 1.0
NAL A:SFJ612 4.7 86.0 1.0

Fluorine binding site 6 out of 10 in 4wef

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Fluorine binding site 6 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F612

b:64.2
occ:1.00
 FAJ A:SFJ612 0.0 64.2 1.0
CAV A:SFJ612 1.4 80.6 1.0
OAM A:SFJ612 2.2 76.0 1.0
CAO A:SFJ612 2.4 76.7 1.0
CAS A:SFJ612 2.5 84.9 1.0
FAI A:SFJ612 2.7 91.5 1.0
OAC A:SFJ612 3.0 87.9 1.0
OAE A:SFJ612 3.2 69.9 1.0
NE2 A:GLN215 3.5 45.8 1.0
CAU A:SFJ612 3.6 76.2 1.0
CB A:CYS214 3.8 30.6 1.0
CAR A:SFJ612 3.8 80.4 1.0
SG A:CYS214 4.0 34.3 1.0
CAT A:SFJ612 4.2 81.8 1.0
CAP A:SFJ612 4.4 66.6 1.0
CAQ A:SFJ612 4.5 74.5 1.0
O A:HOH810 4.5 29.7 1.0
OAH A:SFJ612 4.6 69.2 1.0
OAF A:SFJ612 4.6 54.5 1.0
OAG A:SFJ612 4.7 83.9 1.0
CD A:GLN215 4.8 43.3 1.0
O A:ASN556 4.9 41.9 1.0

Fluorine binding site 7 out of 10 in 4wef

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Fluorine binding site 7 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F610

b:29.2
occ:0.70
 F1 B:FSI610 0.0 29.2 0.7
C3 B:DF4611 0.8 13.9 0.3
F1 B:DF4611 1.2 13.9 0.3
C2 B:DF4611 1.3 13.7 0.3
C3 B:FSI610 1.4 26.2 0.7
C1 B:DF4611 2.2 13.5 0.3
C4 B:DF4611 2.2 13.9 0.3
C2 B:FSI610 2.3 26.2 0.7
C4 B:FSI610 2.3 26.6 0.7
O1A B:DF4611 2.5 13.2 0.3
O1A B:FSI610 2.6 23.6 0.7
O6 B:DF4611 2.6 13.7 0.3
C1 B:FSI610 2.6 25.2 0.7
O4 B:FSI610 2.6 26.8 0.7
O6 B:FSI610 2.7 24.5 0.7
C5 B:DF4611 2.9 13.8 0.3
C5 B:FSI610 2.9 25.9 0.7
O4 B:DF4611 3.1 14.2 0.3
C6 B:DF4611 3.3 13.8 0.3
O B:HOH954 3.3 39.5 1.0
OH B:TYR530 3.3 29.4 1.0
NH2 B:ARG192 3.4 35.0 1.0
C6 B:FSI610 3.4 24.6 0.7
O1B B:DF4611 3.4 13.3 0.3
O1B B:FSI610 3.6 23.4 0.7
O B:HOH763 3.7 34.6 1.0
CZ B:ARG192 4.1 34.8 1.0
CZ B:TYR530 4.1 28.7 1.0
N5 B:FSI610 4.3 28.4 0.7
NH1 B:ARG192 4.3 33.0 1.0
N5 B:DF4611 4.3 14.0 0.3
O7 B:FSI610 4.4 24.4 0.7
C7 B:FSI610 4.5 25.0 0.7
C7 B:DF4611 4.6 14.0 0.3
O7 B:DF4611 4.6 13.9 0.3
CE2 B:TYR530 4.7 27.3 1.0
O10 B:DF4611 4.8 13.8 0.3
CE1 B:TYR530 4.9 28.5 1.0

Fluorine binding site 8 out of 10 in 4wef

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Fluorine binding site 8 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F611

b:13.9
occ:0.30
 F1 B:DF4611 0.0 13.9 0.3
F1 B:FSI610 1.2 29.2 0.7
C3 B:DF4611 1.4 13.9 0.3
O4 B:FSI610 2.2 26.8 0.7
C3 B:FSI610 2.3 26.2 0.7
C4 B:DF4611 2.4 13.9 0.3
C2 B:DF4611 2.4 13.7 0.3
O B:HOH763 2.5 34.6 1.0
C4 B:FSI610 2.6 26.6 0.7
O4 B:DF4611 2.6 14.2 0.3
O B:HOH954 2.6 39.5 1.0
C5 B:DF4611 3.0 13.8 0.3
C5 B:FSI610 3.1 25.9 0.7
C1 B:DF4611 3.4 13.5 0.3
C2 B:FSI610 3.4 26.2 0.7
NH2 B:ARG192 3.4 35.0 1.0
O6 B:DF4611 3.5 13.7 0.3
O1A B:DF4611 3.5 13.2 0.3
O6 B:FSI610 3.6 24.5 0.7
O1A B:FSI610 3.7 23.6 0.7
C1 B:FSI610 3.8 25.2 0.7
C6 B:DF4611 3.9 13.8 0.3
C6 B:FSI610 4.0 24.6 0.7
O10 B:DF4611 4.2 13.8 0.3
N5 B:FSI610 4.2 28.4 0.7
N5 B:DF4611 4.3 14.0 0.3
CZ B:ARG192 4.3 34.8 1.0
OH B:TYR530 4.4 29.4 1.0
O1B B:DF4611 4.6 13.3 0.3
C10 B:DF4611 4.6 14.2 0.3
O10 B:FSI610 4.7 30.8 0.7
O7 B:FSI610 4.8 24.4 0.7
O1B B:FSI610 4.8 23.4 0.7
C10 B:FSI610 4.9 30.5 0.7
NH1 B:ARG192 4.9 33.0 1.0
O7 B:DF4611 4.9 13.9 0.3
O B:HOH717 5.0 33.9 1.0
C7 B:FSI610 5.0 25.0 0.7

Fluorine binding site 9 out of 10 in 4wef

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Fluorine binding site 9 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F612

b:60.4
occ:1.00
 FAI B:SFJ612 0.0 60.4 1.0
CAS B:SFJ612 1.4 66.6 1.0
FAJ B:SFJ612 2.2 81.0 1.0
CAV B:SFJ612 2.4 66.8 1.0
CAR B:SFJ612 2.5 68.7 1.0
OAH B:SFJ612 2.7 74.8 1.0
NZ B:LYS358 3.0 53.2 1.0
OAC B:SFJ612 3.4 64.0 1.0
CAO B:SFJ612 3.4 65.3 1.0
OAM B:SFJ612 3.5 64.0 1.0
CAT B:SFJ612 3.7 68.5 1.0
CB B:ASP362 3.8 45.0 1.0
CG B:ASP362 4.0 49.0 1.0
CE B:LYS358 4.2 57.2 1.0
CAU B:SFJ612 4.2 65.6 1.0
CD B:LYS358 4.2 55.6 1.0
O B:PRO470 4.3 38.0 1.0
OD1 B:ASP362 4.3 49.0 1.0
CA B:ASP362 4.4 42.8 1.0
OD2 B:ASP362 4.4 54.7 1.0
C B:PRO470 4.5 40.2 1.0
OAE B:SFJ612 4.5 51.9 1.0
CA B:ASP471 4.6 37.6 1.0
N B:ASP471 4.6 36.9 1.0
O B:ASP362 4.6 39.5 1.0
CB B:PRO470 4.7 41.4 1.0
C B:ASP362 4.8 43.1 1.0
NAL B:SFJ612 4.9 69.3 1.0
OE1 B:GLN365 4.9 56.3 1.0

Fluorine binding site 10 out of 10 in 4wef

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Fluorine binding site 10 out of 10 in the Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of the Hemagglutinin-Neuraminidase From Human Parainfluenza Virus Type III: Complex with Difluorosialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F612

b:81.0
occ:1.00
 FAJ B:SFJ612 0.0 81.0 1.0
CAV B:SFJ612 1.3 66.8 1.0
FAI B:SFJ612 2.2 60.4 1.0
CAS B:SFJ612 2.2 66.6 1.0
CAO B:SFJ612 2.2 65.3 1.0
OAM B:SFJ612 2.4 64.0 1.0
OAC B:SFJ612 2.9 64.0 1.0
OAE B:SFJ612 2.9 51.9 1.0
OE1 B:GLN365 3.2 56.3 1.0
CAR B:SFJ612 3.5 68.7 1.0
CAU B:SFJ612 3.6 65.6 1.0
CB B:GLN365 3.9 47.6 1.0
CAT B:SFJ612 3.9 68.5 1.0
O B:ASP362 4.0 39.5 1.0
CD B:GLN365 4.1 54.9 1.0
CA B:ASP362 4.2 42.8 1.0
OAH B:SFJ612 4.2 74.8 1.0
CB B:ASP362 4.3 45.0 1.0
OD1 B:ASP362 4.3 49.0 1.0
CG B:ASP362 4.5 49.0 1.0
C B:ASP362 4.5 43.1 1.0
CG B:GLN365 4.6 52.5 1.0
CAQ B:SFJ612 4.9 67.3 1.0
O B:HOH934 4.9 22.9 1.0

Reference:

V.A.Streltsov, P.Pilling, S.Barrett, J.L.Mckimm-Breschkin. Catalytic Mechanism and Novel Receptor Binding Sites of Human Parainfluenza Virus Type 3 Hemagglutinin-Neuraminidase (HPIV3 Hn) Antiviral Res. V. 123 216 2015.
ISSN: ISSN 0166-3542
PubMed: 26364554
DOI: 10.1016/J.ANTIVIRAL.2015.08.014
Page generated: Thu Aug 1 06:19:35 2024

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