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Fluorine in PDB 7mmf: Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60

Enzymatic activity of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60

All present enzymatic activity of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60:
3.4.21.98;

Protein crystallography data

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60, PDB code: 7mmf was solved by J.Zephyr, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.75 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.787, 59.835, 58.702, 90, 90, 90
R / Rfree (%) 16.6 / 20

Other elements in 7mmf:

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60 (pdb code 7mmf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60, PDB code: 7mmf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7mmf

Go back to Fluorine Binding Sites List in 7mmf
Fluorine binding site 1 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:22.1
occ:0.39
 F56 A:ZK41203 0.0 22.1 0.4
H531 A:ZK41203 1.1 24.3 0.6
H541 A:ZK41203 1.3 25.2 0.6
C53 A:ZK41203 1.3 20.2 0.6
C55 A:ZK41203 1.4 20.9 0.4
C54 A:ZK41203 1.5 21.0 0.6
H532 A:ZK41203 2.0 24.3 0.6
F57 A:ZK41203 2.2 23.2 0.4
H542 A:ZK41203 2.2 25.2 0.6
F58 A:ZK41203 2.3 22.9 0.4
O16 A:ZK41203 2.3 18.5 0.4
C17 A:ZK41203 2.4 19.6 0.4
O16 A:ZK41203 2.4 18.5 0.6
C17 A:ZK41203 2.4 19.5 0.6
C52 A:ZK41203 2.7 20.3 0.6
C14 A:ZK41203 2.8 18.9 0.4
O15 A:ZK41203 2.8 19.6 0.4
C14 A:ZK41203 2.9 19.0 0.6
H542 A:ZK41203 2.9 24.6 0.4
O15 A:ZK41203 2.9 19.6 0.6
C54 A:ZK41203 3.0 20.5 0.4
C51 A:ZK41203 3.0 20.4 0.6
H522 A:ZK41203 3.0 24.4 0.6
H541 A:ZK41203 3.1 24.6 0.4
H511 A:ZK41203 3.3 24.6 0.6
H521 A:ZK41203 3.4 24.4 0.6
C55 A:ZK41203 3.7 22.1 0.6
C51 A:ZK41203 3.8 22.1 0.4
H512 A:ZK41203 3.9 24.6 0.6
H512 A:ZK41203 4.0 26.6 0.4
F58 A:ZK41203 4.1 18.7 0.6
N13 A:ZK41203 4.1 17.7 0.4
F57 A:ZK41203 4.1 22.9 0.6
N13 A:ZK41203 4.1 17.6 0.6
H511 A:ZK41203 4.2 26.6 0.4
C53 A:ZK41203 4.5 21.1 0.4
H111 A:ZK41203 4.5 20.2 0.4
H131 A:ZK41203 4.6 21.3 0.4
H131 A:ZK41203 4.6 21.1 0.6
H111 A:ZK41203 4.6 20.0 0.6
H333 A:ZK41203 4.7 21.3 0.4
F56 A:ZK41203 4.7 21.7 0.6
H333 A:ZK41203 4.7 21.3 0.6
C52 A:ZK41203 4.8 21.9 0.4
H041 A:ZK41203 4.9 20.7 0.4
H041 A:ZK41203 4.9 20.8 0.6
C11 A:ZK41203 4.9 16.8 0.4
C11 A:ZK41203 5.0 16.6 0.6
H531 A:ZK41203 5.0 25.4 0.4

Fluorine binding site 2 out of 6 in 7mmf

Go back to Fluorine Binding Sites List in 7mmf
Fluorine binding site 2 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:21.7
occ:0.61
 F56 A:ZK41203 0.0 21.7 0.6
H522 A:ZK41203 0.5 26.4 0.4
C52 A:ZK41203 0.6 21.9 0.4
C55 A:ZK41203 1.4 22.1 0.6
H521 A:ZK41203 1.5 26.4 0.4
C51 A:ZK41203 1.6 22.1 0.4
C53 A:ZK41203 1.8 21.1 0.4
H511 A:ZK41203 2.0 26.6 0.4
H532 A:ZK41203 2.1 25.4 0.4
F58 A:ZK41203 2.2 18.7 0.6
C17 A:ZK41203 2.3 19.5 0.6
F57 A:ZK41203 2.3 22.9 0.6
H512 A:ZK41203 2.3 26.6 0.4
C17 A:ZK41203 2.3 19.6 0.4
H531 A:ZK41203 2.5 25.4 0.4
H512 A:ZK41203 2.5 24.6 0.6
C54 A:ZK41203 2.6 20.5 0.4
O15 A:ZK41203 2.6 19.6 0.4
O15 A:ZK41203 2.6 19.6 0.6
HG22 A:VAL1158 2.8 28.2 1.0
C51 A:ZK41203 2.8 20.4 0.6
H541 A:ZK41203 3.0 24.6 0.4
H511 A:ZK41203 3.2 24.6 0.6
H542 A:ZK41203 3.3 24.6 0.4
HB3 A:ALA1156 3.3 20.6 1.0
C54 A:ZK41203 3.5 21.0 0.6
HB1 A:ALA1156 3.5 20.6 1.0
CG2 A:VAL1158 3.6 23.5 1.0
H542 A:ZK41203 3.6 25.2 0.6
HG23 A:VAL1158 3.6 28.2 1.0
C55 A:ZK41203 3.7 20.9 0.4
C14 A:ZK41203 3.8 18.9 0.4
CB A:ALA1168 3.8 17.1 1.0
C14 A:ZK41203 3.8 19.0 0.6
CB A:ALA1156 3.9 17.2 1.0
NH2 A:ARG1123 3.9 30.0 1.0
HH21 A:ARG1123 4.0 36.0 1.0
HG21 A:VAL1158 4.0 28.2 1.0
C52 A:ZK41203 4.0 20.3 0.6
H541 A:ZK41203 4.0 25.2 0.6
CZ A:ARG1123 4.1 30.0 1.0
HH22 A:ARG1123 4.1 36.0 1.0
F57 A:ZK41203 4.1 23.2 0.4
H521 A:ZK41203 4.2 24.4 0.6
F58 A:ZK41203 4.2 22.9 0.4
HA A:VAL1158 4.3 27.1 1.0
NE A:ARG1123 4.3 27.1 1.0
HE A:ARG1123 4.4 32.6 1.0
O3 A:SO41210 4.4 38.0 1.0
O A:ALA1157 4.4 18.0 1.0
H131 A:ZK41203 4.4 21.3 0.4
C53 A:ZK41203 4.5 20.2 0.6
O16 A:ZK41203 4.5 18.5 0.4
HB2 A:ALA1156 4.5 20.6 1.0
O16 A:ZK41203 4.5 18.5 0.6
NH1 A:ARG1123 4.5 30.5 1.0
O A:HOH1307 4.6 28.9 1.0
N13 A:ZK41203 4.6 17.7 0.4
H131 A:ZK41203 4.6 21.1 0.6
C A:ALA1157 4.6 21.4 1.0
N13 A:ZK41203 4.7 17.6 0.6
HH12 A:ARG1123 4.7 36.6 1.0
C A:ALA1156 4.7 15.8 1.0
F56 A:ZK41203 4.7 22.1 0.4
H522 A:ZK41203 4.8 24.4 0.6
N A:VAL1158 4.8 20.3 1.0
CB A:VAL1158 4.8 21.0 1.0
H A:ALA1168 4.8 20.1 1.0
O A:ALA1156 4.8 13.9 1.0
CA A:VAL1158 4.8 22.6 1.0
N A:ALA1157 4.9 14.9 1.0
HH11 A:ARG1123 5.0 36.6 1.0
CA A:ALA1156 5.0 15.7 1.0

Fluorine binding site 3 out of 6 in 7mmf

Go back to Fluorine Binding Sites List in 7mmf
Fluorine binding site 3 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:23.2
occ:0.39
 F57 A:ZK41203 0.0 23.2 0.4
H542 A:ZK41203 1.1 25.2 0.6
H541 A:ZK41203 1.2 25.2 0.6
C55 A:ZK41203 1.4 20.9 0.4
C54 A:ZK41203 1.4 21.0 0.6
F56 A:ZK41203 2.2 22.1 0.4
F58 A:ZK41203 2.2 22.9 0.4
C17 A:ZK41203 2.4 19.6 0.4
C17 A:ZK41203 2.4 19.5 0.6
F58 A:ZK41203 2.6 18.7 0.6
C53 A:ZK41203 2.7 20.2 0.6
H511 A:ZK41203 2.7 26.6 0.4
O15 A:ZK41203 2.8 19.6 0.4
C51 A:ZK41203 2.8 22.1 0.4
C55 A:ZK41203 2.9 22.1 0.6
O15 A:ZK41203 2.9 19.6 0.6
H532 A:ZK41203 2.9 24.3 0.6
H512 A:ZK41203 2.9 26.6 0.4
H531 A:ZK41203 3.1 24.3 0.6
F57 A:ZK41203 3.3 22.9 0.6
C54 A:ZK41203 3.6 20.5 0.4
C14 A:ZK41203 3.6 18.9 0.4
H542 A:ZK41203 3.7 24.6 0.4
C14 A:ZK41203 3.7 19.0 0.6
C51 A:ZK41203 3.8 20.4 0.6
O16 A:ZK41203 3.9 18.5 0.4
C52 A:ZK41203 3.9 20.3 0.6
O16 A:ZK41203 3.9 18.5 0.6
H541 A:ZK41203 4.1 24.6 0.4
F56 A:ZK41203 4.1 21.7 0.6
C52 A:ZK41203 4.1 21.9 0.4
H521 A:ZK41203 4.3 24.4 0.6
O A:HOH1402 4.3 31.6 1.0
H512 A:ZK41203 4.4 24.6 0.6
H511 A:ZK41203 4.4 24.6 0.6
H522 A:ZK41203 4.5 26.4 0.4
C53 A:ZK41203 4.6 21.1 0.4
H522 A:ZK41203 4.7 24.4 0.6
N13 A:ZK41203 4.7 17.7 0.4
N13 A:ZK41203 4.7 17.6 0.6
H131 A:ZK41203 4.8 21.3 0.4
H521 A:ZK41203 4.8 26.4 0.4
H131 A:ZK41203 4.8 21.1 0.6

Fluorine binding site 4 out of 6 in 7mmf

Go back to Fluorine Binding Sites List in 7mmf
Fluorine binding site 4 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:22.9
occ:0.61
 F57 A:ZK41203 0.0 22.9 0.6
H512 A:ZK41203 0.5 26.6 0.4
C51 A:ZK41203 1.2 22.1 0.4
C55 A:ZK41203 1.4 22.1 0.6
C52 A:ZK41203 1.8 21.9 0.4
H511 A:ZK41203 2.0 26.6 0.4
H521 A:ZK41203 2.0 26.4 0.4
C17 A:ZK41203 2.3 19.6 0.4
F56 A:ZK41203 2.3 21.7 0.6
F58 A:ZK41203 2.3 18.7 0.6
C53 A:ZK41203 2.4 21.1 0.4
H542 A:ZK41203 2.4 25.2 0.6
C17 A:ZK41203 2.4 19.5 0.6
H531 A:ZK41203 2.4 25.4 0.4
C54 A:ZK41203 2.6 20.5 0.4
F58 A:ZK41203 2.6 22.9 0.4
H512 A:ZK41203 2.6 24.6 0.6
H542 A:ZK41203 2.7 24.6 0.4
HH22 A:ARG1123 2.7 36.0 1.0
H522 A:ZK41203 2.7 26.4 0.4
C54 A:ZK41203 2.8 21.0 0.6
HH21 A:ARG1123 2.8 36.0 1.0
C55 A:ZK41203 2.9 20.9 0.4
NH2 A:ARG1123 2.9 30.0 1.0
C51 A:ZK41203 2.9 20.4 0.6
H521 A:ZK41203 3.2 24.4 0.6
F57 A:ZK41203 3.3 23.2 0.4
H532 A:ZK41203 3.3 25.4 0.4
C52 A:ZK41203 3.4 20.3 0.6
O15 A:ZK41203 3.4 19.6 0.4
O3 A:SO41210 3.5 38.0 1.0
H541 A:ZK41203 3.5 24.6 0.4
C53 A:ZK41203 3.6 20.2 0.6
O15 A:ZK41203 3.6 19.6 0.6
H541 A:ZK41203 3.6 25.2 0.6
H532 A:ZK41203 3.7 24.3 0.6
CZ A:ARG1123 3.7 30.0 1.0
H511 A:ZK41203 3.8 24.6 0.6
F56 A:ZK41203 4.1 22.1 0.4
HG22 A:VAL1158 4.2 28.2 1.0
O A:HOH1301 4.2 34.8 1.0
HH12 A:ARG1123 4.2 36.6 1.0
H522 A:ZK41203 4.3 24.4 0.6
NH1 A:ARG1123 4.4 30.5 1.0
HE A:ARG1123 4.4 32.6 1.0
NE A:ARG1123 4.5 27.1 1.0
H531 A:ZK41203 4.5 24.3 0.6
C14 A:ZK41203 4.7 18.9 0.4
C14 A:ZK41203 4.8 19.0 0.6
O A:HOH1307 4.8 28.9 1.0
S A:SO41210 4.8 45.1 1.0
O2 A:SO41210 5.0 49.1 1.0

Fluorine binding site 5 out of 6 in 7mmf

Go back to Fluorine Binding Sites List in 7mmf
Fluorine binding site 5 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:22.9
occ:0.39
 F58 A:ZK41203 0.0 22.9 0.4
H532 A:ZK41203 1.2 24.3 0.6
H542 A:ZK41203 1.3 25.2 0.6
C55 A:ZK41203 1.4 20.9 0.4
C53 A:ZK41203 1.5 20.2 0.6
C54 A:ZK41203 1.6 21.0 0.6
F57 A:ZK41203 2.2 23.2 0.4
H542 A:ZK41203 2.3 24.6 0.4
F56 A:ZK41203 2.3 22.1 0.4
C17 A:ZK41203 2.3 19.6 0.4
H531 A:ZK41203 2.4 24.3 0.6
H541 A:ZK41203 2.4 25.2 0.6
C52 A:ZK41203 2.4 20.3 0.6
H521 A:ZK41203 2.4 24.4 0.6
C17 A:ZK41203 2.5 19.5 0.6
H512 A:ZK41203 2.6 26.6 0.4
F57 A:ZK41203 2.6 22.9 0.6
C54 A:ZK41203 2.7 20.5 0.4
C51 A:ZK41203 2.9 20.4 0.6
C51 A:ZK41203 3.0 22.1 0.4
C55 A:ZK41203 3.0 22.1 0.6
H522 A:ZK41203 3.2 24.4 0.6
H512 A:ZK41203 3.3 24.6 0.6
H541 A:ZK41203 3.4 24.6 0.4
H511 A:ZK41203 3.5 26.6 0.4
F58 A:ZK41203 3.6 18.7 0.6
O15 A:ZK41203 3.6 19.6 0.4
O15 A:ZK41203 3.7 19.6 0.6
H511 A:ZK41203 3.7 24.6 0.6
C53 A:ZK41203 3.8 21.1 0.4
H531 A:ZK41203 3.9 25.4 0.4
C52 A:ZK41203 4.0 21.9 0.4
O16 A:ZK41203 4.1 18.5 0.4
O16 A:ZK41203 4.2 18.5 0.6
F56 A:ZK41203 4.2 21.7 0.6
C14 A:ZK41203 4.3 18.9 0.4
C14 A:ZK41203 4.4 19.0 0.6
H521 A:ZK41203 4.5 26.4 0.4
O A:HOH1301 4.6 34.8 1.0
H532 A:ZK41203 4.7 25.4 0.4
H522 A:ZK41203 4.7 26.4 0.4
HH22 A:ARG1123 4.9 36.0 1.0

Fluorine binding site 6 out of 6 in 7mmf

Go back to Fluorine Binding Sites List in 7mmf
Fluorine binding site 6 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:18.7
occ:0.61
 F58 A:ZK41203 0.0 18.7 0.6
H511 A:ZK41203 0.4 26.6 0.4
C51 A:ZK41203 1.3 22.1 0.4
C55 A:ZK41203 1.4 22.1 0.6
H512 A:ZK41203 1.9 26.6 0.4
F56 A:ZK41203 2.2 21.7 0.6
C52 A:ZK41203 2.3 21.9 0.4
C17 A:ZK41203 2.3 19.5 0.6
F57 A:ZK41203 2.3 22.9 0.6
C17 A:ZK41203 2.3 19.6 0.4
H522 A:ZK41203 2.4 26.4 0.4
H542 A:ZK41203 2.5 25.2 0.6
O15 A:ZK41203 2.5 19.6 0.4
F57 A:ZK41203 2.6 23.2 0.4
O15 A:ZK41203 2.6 19.6 0.6
C54 A:ZK41203 2.7 21.0 0.6
H521 A:ZK41203 2.8 26.4 0.4
HG22 A:VAL1158 2.8 28.2 1.0
C55 A:ZK41203 2.9 20.9 0.4
H541 A:ZK41203 3.0 25.2 0.6
C54 A:ZK41203 3.4 20.5 0.4
C53 A:ZK41203 3.5 21.1 0.4
F58 A:ZK41203 3.6 22.9 0.4
HA A:VAL1158 3.7 27.1 1.0
HG13 A:VAL1158 3.7 32.6 1.0
CG2 A:VAL1158 3.7 23.5 1.0
C51 A:ZK41203 3.8 20.4 0.6
C14 A:ZK41203 3.9 18.9 0.4
HH22 A:ARG1123 3.9 36.0 1.0
H512 A:ZK41203 3.9 24.6 0.6
C14 A:ZK41203 4.0 19.0 0.6
H542 A:ZK41203 4.0 24.6 0.4
O A:HOH1402 4.0 31.6 1.0
H541 A:ZK41203 4.1 24.6 0.4
H531 A:ZK41203 4.1 25.4 0.4
F56 A:ZK41203 4.1 22.1 0.4
HG21 A:VAL1158 4.1 28.2 1.0
H532 A:ZK41203 4.1 25.4 0.4
NH2 A:ARG1123 4.2 30.0 1.0
C53 A:ZK41203 4.2 20.2 0.6
HH12 A:ARG1123 4.3 36.6 1.0
HG23 A:VAL1158 4.3 28.2 1.0
H511 A:ZK41203 4.4 24.6 0.6
CB A:VAL1158 4.4 21.0 1.0
CG1 A:VAL1158 4.4 27.1 1.0
CA A:VAL1158 4.4 22.6 1.0
H131 A:ZK41203 4.4 21.3 0.4
H131 A:ZK41203 4.5 21.1 0.6
CZ A:ARG1123 4.5 30.0 1.0
NH1 A:ARG1123 4.5 30.5 1.0
HH21 A:ARG1123 4.5 36.0 1.0
O A:ALA1157 4.6 18.0 1.0
C52 A:ZK41203 4.6 20.3 0.6
H532 A:ZK41203 4.6 24.3 0.6
N13 A:ZK41203 4.7 17.7 0.4
O16 A:ZK41203 4.7 18.5 0.4
HG11 A:VAL1158 4.7 32.6 1.0
O16 A:ZK41203 4.7 18.5 0.6
N13 A:ZK41203 4.7 17.6 0.6
H521 A:ZK41203 4.8 24.4 0.6
H531 A:ZK41203 4.9 24.3 0.6
N A:VAL1158 5.0 20.3 1.0

Reference:

J.Zephyr, D.Nageswara Rao, S.V.Vo, M.Henes, K.Kosovrasti, A.N.Matthew, A.K.Hedger, J.Timm, E.T.Chan, A.Ali, N.Kurt Yilmaz, C.A.Schiffer. Deciphering the Molecular Mechanism of Hcv Protease Inhibitor Fluorination As A General Approach to Avoid Drug Resistance. J.Mol.Biol. V. 434 67503 2022.
ISSN: ESSN 1089-8638
PubMed: 35183560
DOI: 10.1016/J.JMB.2022.167503
Page generated: Fri Aug 2 09:40:51 2024

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