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Fluorine in PDB 4h52: Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC

Protein crystallography data

The structure of Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC, PDB code: 4h52 was solved by C.J.Vavricka, Y.Liu, H.Kiyota, N.Sriwilaijaroen, J.Qi, K.Tanaka, Y.Wu, Q.Li, Y.Li, J.Yan, Y.Suzuki, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.82 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 114.698, 139.704, 140.070, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.5

Other elements in 4h52:

The structure of Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC (pdb code 4h52). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC, PDB code: 4h52:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4h52

Go back to Fluorine Binding Sites List in 4h52
Fluorine binding site 1 out of 2 in the Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:23.3
occ:1.00
F1 A:FSI508 0.0 23.3 1.0
C3 A:FSI508 1.4 16.0 1.0
C4 A:FSI508 2.3 14.2 1.0
C2 A:FSI508 2.3 14.3 1.0
O4 A:FSI508 2.7 14.5 1.0
C1 A:FSI508 2.7 20.0 1.0
O1B A:FSI508 2.8 13.8 1.0
C5 A:FSI508 2.8 13.6 1.0
O6 A:FSI508 2.9 12.8 1.0
O A:HOH757 3.0 24.2 1.0
C6 A:FSI508 3.4 12.8 1.0
O A:HOH878 3.5 39.7 1.0
NH1 A:ARG118 3.5 11.1 1.0
OH A:TYR406 3.6 16.5 1.0
OE2 A:GLU119 3.6 18.1 1.0
O1A A:FSI508 3.7 13.4 1.0
O A:HOH925 3.8 29.0 1.0
O A:HOH623 4.1 13.1 1.0
N5 A:FSI508 4.2 14.1 1.0
CZ A:ARG118 4.3 11.4 1.0
O7 A:FSI508 4.4 15.8 1.0
CZ A:TYR406 4.4 15.7 1.0
NH2 A:ARG118 4.5 12.2 1.0
O A:HOH743 4.5 31.2 1.0
C7 A:FSI508 4.5 14.9 1.0
CD A:GLU119 4.6 18.4 1.0
O10 A:FSI508 4.8 16.6 1.0
O A:HOH745 4.9 23.6 1.0
CE2 A:TYR406 5.0 16.0 1.0
C10 A:FSI508 5.0 17.8 1.0

Fluorine binding site 2 out of 2 in 4h52

Go back to Fluorine Binding Sites List in 4h52
Fluorine binding site 2 out of 2 in the Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F508

b:22.3
occ:1.00
F1 B:FSI508 0.0 22.3 1.0
C3 B:FSI508 1.4 17.0 1.0
C4 B:FSI508 2.3 14.6 1.0
C2 B:FSI508 2.3 16.0 1.0
O4 B:FSI508 2.7 15.4 1.0
C1 B:FSI508 2.8 19.7 1.0
C5 B:FSI508 2.8 14.5 1.0
O1B B:FSI508 2.9 14.2 1.0
O6 B:FSI508 2.9 12.8 1.0
O B:HOH751 3.1 24.0 1.0
C6 B:FSI508 3.4 11.3 1.0
O B:HOH982 3.5 43.7 1.0
NH1 B:ARG118 3.6 14.1 1.0
OE2 B:GLU119 3.6 16.8 1.0
OH B:TYR406 3.6 16.1 1.0
O1A B:FSI508 3.8 14.2 1.0
O B:HOH905 3.9 33.4 1.0
O B:HOH636 4.0 13.5 1.0
N5 B:FSI508 4.1 12.8 1.0
CZ B:ARG118 4.3 12.9 1.0
O7 B:FSI508 4.3 17.4 1.0
CZ B:TYR406 4.4 17.5 1.0
NH2 B:ARG118 4.5 12.0 1.0
C7 B:FSI508 4.5 14.4 1.0
O B:HOH758 4.5 29.5 1.0
CD B:GLU119 4.6 18.8 1.0
O10 B:FSI508 4.8 15.9 1.0
C10 B:FSI508 4.9 17.5 1.0
CE2 B:TYR406 5.0 16.2 1.0
O B:HOH745 5.0 22.6 1.0

Reference:

C.J.Vavricka, Y.Liu, H.Kiyota, N.Sriwilaijaroen, J.Qi, K.Tanaka, Y.Wu, Q.Li, Y.Li, J.Yan, Y.Suzuki, G.F.Gao. Influenza Neuraminidase Operates Via A Nucleophilic Mechanism and Can Be Targeted By Covalent Inhibitors Nat Commun V. 4 1491 2013.
ISSN: ESSN 2041-1723
PubMed: 23422659
DOI: 10.1038/NCOMMS2487
Page generated: Sun Dec 13 12:03:40 2020

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