Fluorine in PDB 6s0j: Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)-

Protein crystallography data

The structure of Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)-, PDB code: 6s0j was solved by M.Ge, R.W.Molt Jr., H.T.Jenkins, G.M.Blackburn, Y.Jin, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.65 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.943, 69.604, 57.751, 90.00, 94.40, 90.00
R / Rfree (%) 14.5 / 18.9

Other elements in 6s0j:

The structure of Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)- also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)- (pdb code 6s0j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)-, PDB code: 6s0j:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6s0j

Go back to Fluorine Binding Sites List in 6s0j
Fluorine binding site 1 out of 3 in the Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:26.0
occ:1.00
F1 A:KQB701 0.0 26.0 1.0
MG A:MG702 1.8 22.1 1.0
MG1 A:KQB701 1.9 25.2 1.0
O A:HOH817 2.6 23.7 1.0
O A:HOH857 2.6 23.4 1.0
O1 A:KQB701 2.7 26.6 1.0
O3B A:ADP703 2.8 22.7 1.0
O A:HOH967 2.8 27.6 1.0
F2 A:KQB701 2.8 25.7 1.0
O A:HOH871 2.8 27.9 1.0
OE2 A:GLU286 2.8 32.5 1.0
O1B A:ADP703 2.9 23.3 1.0
PB A:ADP703 3.3 22.8 1.0
CD A:GLU286 3.5 31.2 1.0
F3 A:KQB701 3.7 26.2 1.0
OE1 A:GLU286 3.8 38.6 1.0
O A:HOH832 3.8 25.3 1.0
OG1 A:THR201 3.9 24.1 1.0
CA A:GLY415 3.9 30.5 0.5
N A:GLY415 4.0 28.4 0.5
CA A:GLY415 4.1 28.8 0.5
O2B A:ADP703 4.4 23.5 1.0
CE A:LYS200 4.4 23.3 1.0
NZ A:LYS200 4.4 23.3 1.0
O3A A:ADP703 4.6 24.8 1.0
CG A:GLU286 4.6 29.0 1.0
O1A A:ADP703 4.8 28.6 1.0
OD1 A:ASP285 4.8 26.5 1.0
NH2 A:ARG462 5.0 24.2 1.0
CB A:THR201 5.0 24.8 1.0
O A:HOH821 5.0 35.5 1.0

Fluorine binding site 2 out of 3 in 6s0j

Go back to Fluorine Binding Sites List in 6s0j
Fluorine binding site 2 out of 3 in the Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:25.7
occ:1.00
F2 A:KQB701 0.0 25.7 1.0
MG1 A:KQB701 1.9 25.2 1.0
O A:HOH832 2.5 25.3 1.0
NZ A:LYS200 2.7 23.3 1.0
F3 A:KQB701 2.7 26.2 1.0
F1 A:KQB701 2.8 26.0 1.0
O A:HOH857 2.8 23.4 1.0
O3B A:ADP703 2.8 22.7 1.0
CE A:LYS200 3.2 23.3 1.0
CA A:PRO196 3.6 21.7 1.0
PB A:ADP703 3.8 22.8 1.0
CB A:ALA317 3.8 23.6 1.0
O1 A:KQB701 3.9 26.6 1.0
O2B A:ADP703 4.0 23.5 1.0
O A:HOH817 4.1 23.7 1.0
N A:GLY197 4.2 23.2 1.0
OE1 A:GLN455 4.2 21.0 1.0
O1B A:ADP703 4.2 23.3 1.0
CB A:PRO196 4.3 22.5 1.0
MG A:MG702 4.3 22.1 1.0
N A:PRO196 4.3 22.7 1.0
OE1 A:GLU286 4.3 38.6 1.0
N A:ALA317 4.4 21.6 1.0
OE2 A:GLU286 4.4 32.5 1.0
NE2 A:GLN455 4.5 19.4 1.0
O A:HIS195 4.5 24.1 1.0
C A:PRO196 4.5 22.7 1.0
CD A:LYS200 4.7 23.9 1.0
C A:HIS195 4.7 23.0 1.0
CA A:ALA317 4.7 22.0 1.0
CG A:PRO196 4.8 22.8 1.0
O A:LEU194 4.8 24.2 1.0
CD A:GLU286 4.8 31.2 1.0
CD A:GLN455 4.8 19.0 1.0
NH2 A:ARG459 4.9 22.6 1.0

Fluorine binding site 3 out of 3 in 6s0j

Go back to Fluorine Binding Sites List in 6s0j
Fluorine binding site 3 out of 3 in the Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Zika Virus NS3 Helicase in Complex with Adp-MGF3(H2O)- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:26.2
occ:1.00
F3 A:KQB701 0.0 26.2 1.0
MG1 A:KQB701 1.9 25.2 1.0
O1 A:KQB701 2.6 26.6 1.0
O A:HOH857 2.7 23.4 1.0
F2 A:KQB701 2.7 25.7 1.0
NH1 A:ARG462 2.8 22.2 1.0
NH2 A:ARG459 2.9 22.6 1.0
O3B A:ADP703 2.9 22.7 1.0
CB A:PRO196 3.2 22.5 1.0
CA A:PRO196 3.2 21.7 1.0
N A:GLY197 3.4 23.2 1.0
NH1 A:ARG459 3.7 23.0 1.0
CZ A:ARG462 3.7 23.2 1.0
C A:PRO196 3.7 22.7 1.0
CZ A:ARG459 3.7 22.4 1.0
F1 A:KQB701 3.7 26.0 1.0
NH2 A:ARG462 3.7 24.2 1.0
OE1 A:GLN455 4.0 21.0 1.0
CG A:PRO196 4.3 22.8 1.0
O A:GLY458 4.4 18.8 1.0
PB A:ADP703 4.4 22.8 1.0
CA A:GLY197 4.5 23.9 1.0
N A:PRO196 4.5 22.7 1.0
O A:HOH832 4.7 25.3 1.0
O A:PRO196 4.8 23.6 1.0
N A:GLY415 4.8 28.4 0.5
NZ A:LYS200 4.9 23.3 1.0
NE A:ARG462 4.9 23.2 1.0
NE A:ARG459 4.9 21.1 1.0
C A:GLY458 5.0 17.0 1.0

Reference:

M.Ge, R.W.Molt Jr., H.T.Jenkins, G.M.Blackburn, Y.Jin, A.A.Antson. New Mfx Transition State Analog Reveals the Molecular Mechanism of Atp Hydrolysis By the Zika Virus NS3 Helicase To Be Published.
Page generated: Sun Dec 13 13:11:29 2020

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