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Fluorine in PDB 7mmg: Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58

Enzymatic activity of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58

All present enzymatic activity of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58:
3.4.21.98;

Protein crystallography data

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58, PDB code: 7mmg 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) 42.51 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.854, 50.987, 77.068, 90, 92.84, 90
R / Rfree (%) 19.9 / 24.8

Other elements in 7mmg:

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58 (pdb code 7mmg). 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 NR02-58, PDB code: 7mmg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7mmg

Go back to Fluorine Binding Sites List in 7mmg
Fluorine binding site 1 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58


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 NR02-58 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:26.2
occ:0.96
 F55 A:ZK71202 0.0 26.2 1.0
C51 A:ZK71202 1.4 23.4 1.0
F56 A:ZK71202 2.2 27.2 1.0
F57 A:ZK71202 2.2 27.9 1.0
C17 A:ZK71202 2.3 20.3 1.0
H541 A:ZK71202 2.7 25.3 1.0
O15 A:ZK71202 2.8 17.7 1.0
HG22 A:VAL1158 2.8 34.6 1.0
C54 A:ZK71202 3.0 21.0 1.0
HH21 A:ARG1123 3.3 33.9 0.4
H542 A:ZK71202 3.5 25.3 1.0
C52 A:ZK71202 3.7 18.7 1.0
CG2 A:VAL1158 3.7 28.8 1.0
HH22 A:ARG1123 3.7 33.9 0.4
NH2 A:ARG1123 3.7 28.1 0.4
H522 A:ZK71202 3.8 22.5 1.0
C53 A:ZK71202 4.0 23.9 1.0
HG21 A:VAL1158 4.1 34.6 1.0
HG23 A:VAL1158 4.1 34.6 1.0
C14 A:ZK71202 4.1 16.5 1.0
HG13 A:VAL1158 4.1 36.2 1.0
HA A:VAL1158 4.1 27.7 1.0
H532 A:ZK71202 4.2 28.8 1.0
HH22 A:ARG1123 4.3 32.4 0.6
H521 A:ZK71202 4.4 22.5 1.0
CB A:VAL1158 4.6 25.6 1.0
NH2 A:ARG1123 4.6 26.9 0.6
H131 A:ZK71202 4.7 18.5 1.0
CZ A:ARG1123 4.7 29.1 0.4
CA A:VAL1158 4.8 23.0 1.0
CG1 A:VAL1158 4.8 30.1 1.0
O16 A:ZK71202 4.8 16.9 1.0
H531 A:ZK71202 4.9 28.8 1.0
HE A:ARG1123 4.9 27.4 0.4
N13 A:ZK71202 4.9 15.8 1.0
HH21 A:ARG1123 4.9 32.4 0.6
HH12 A:ARG1123 4.9 37.2 0.6
O A:ALA1157 5.0 17.6 1.0

Fluorine binding site 2 out of 6 in 7mmg

Go back to Fluorine Binding Sites List in 7mmg
Fluorine binding site 2 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58


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 NR02-58 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:27.2
occ:0.96
 F56 A:ZK71202 0.0 27.2 1.0
C51 A:ZK71202 1.4 23.4 1.0
F55 A:ZK71202 2.2 26.2 1.0
C17 A:ZK71202 2.2 20.3 1.0
F57 A:ZK71202 2.3 27.9 1.0
O15 A:ZK71202 2.6 17.7 1.0
H522 A:ZK71202 2.7 22.5 1.0
C52 A:ZK71202 2.9 18.7 1.0
HG22 A:VAL1158 3.0 34.6 1.0
HH21 A:ARG1123 3.3 33.9 0.4
HB3 A:ALA1156 3.4 16.7 1.0
H521 A:ZK71202 3.4 22.5 1.0
HG23 A:VAL1158 3.5 34.6 1.0
C54 A:ZK71202 3.6 21.0 1.0
CG2 A:VAL1158 3.7 28.8 1.0
HE A:ARG1123 3.8 27.4 0.4
HB1 A:ALA1156 3.8 16.7 1.0
H541 A:ZK71202 3.8 25.3 1.0
NH2 A:ARG1123 3.9 28.1 0.4
C14 A:ZK71202 3.9 16.5 1.0
CB A:ALA1168 4.0 18.3 1.0
C53 A:ZK71202 4.0 23.9 1.0
CB A:ALA1156 4.0 14.3 1.0
HG21 A:VAL1158 4.1 34.6 1.0
NH2 A:ARG1123 4.2 26.9 0.6
HH21 A:ARG1123 4.2 32.4 0.6
HH22 A:ARG1123 4.3 32.4 0.6
H532 A:ZK71202 4.3 28.8 1.0
H542 A:ZK71202 4.3 25.3 1.0
NE A:ARG1123 4.3 22.8 0.4
HH22 A:ARG1123 4.3 33.9 0.4
CZ A:ARG1123 4.4 29.1 0.4
CZ A:ARG1123 4.5 22.8 0.6
HA A:VAL1158 4.5 27.7 1.0
C A:ALA1157 4.5 16.2 1.0
O A:ALA1157 4.6 17.6 1.0
O16 A:ZK71202 4.6 16.9 1.0
H131 A:ZK71202 4.6 18.5 1.0
N A:VAL1158 4.6 19.4 1.0
C A:ALA1156 4.7 18.9 1.0
HB2 A:ALA1156 4.7 16.7 1.0
N A:ALA1157 4.7 14.2 1.0
N13 A:ZK71202 4.7 15.8 1.0
NE A:ARG1123 4.8 25.5 0.6
H531 A:ZK71202 4.8 28.8 1.0
O A:ALA1156 4.9 14.0 1.0
HE A:ARG1123 4.9 30.7 0.6
CB A:VAL1158 4.9 25.6 1.0
H A:ALA1157 4.9 16.6 1.0
CA A:VAL1158 4.9 23.0 1.0
H A:VAL1158 4.9 23.4 1.0
NH1 A:ARG1123 4.9 30.9 0.6
HA A:ALA1157 5.0 17.6 1.0
H A:ALA1168 5.0 17.0 1.0

Fluorine binding site 3 out of 6 in 7mmg

Go back to Fluorine Binding Sites List in 7mmg
Fluorine binding site 3 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58


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 NR02-58 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:27.9
occ:0.96
 F57 A:ZK71202 0.0 27.9 1.0
C51 A:ZK71202 1.4 23.4 1.0
F55 A:ZK71202 2.2 26.2 1.0
F56 A:ZK71202 2.3 27.2 1.0
C17 A:ZK71202 2.3 20.3 1.0
H522 A:ZK71202 2.5 22.5 1.0
H541 A:ZK71202 2.5 25.3 1.0
C52 A:ZK71202 2.8 18.7 1.0
C54 A:ZK71202 2.8 21.0 1.0
H532 A:ZK71202 2.8 28.8 1.0
HH21 A:ARG1123 2.8 33.9 0.4
C53 A:ZK71202 3.0 23.9 1.0
HH22 A:ARG1123 3.1 32.4 0.6
HH21 A:ARG1123 3.3 32.4 0.6
NH2 A:ARG1123 3.4 26.9 0.6
O15 A:ZK71202 3.5 17.7 1.0
NH2 A:ARG1123 3.6 28.1 0.4
H521 A:ZK71202 3.7 22.5 1.0
H542 A:ZK71202 3.7 25.3 1.0
HH22 A:ARG1123 3.8 33.9 0.4
H531 A:ZK71202 4.0 28.8 1.0
HE A:ARG1123 4.2 27.4 0.4
CZ A:ARG1123 4.3 22.8 0.6
HG22 A:VAL1158 4.3 34.6 1.0
CZ A:ARG1123 4.6 29.1 0.4
HH12 A:ARG1123 4.7 37.2 0.6
C14 A:ZK71202 4.8 16.5 1.0
NE A:ARG1123 4.8 22.8 0.4
HH12 A:ARG1155 4.8 45.2 1.0
NH1 A:ARG1123 4.8 30.9 0.6
HB3 A:ALA1156 4.9 16.7 1.0
HH11 A:ARG1155 4.9 45.2 1.0
HE A:ARG1123 5.0 30.7 0.6

Fluorine binding site 4 out of 6 in 7mmg

Go back to Fluorine Binding Sites List in 7mmg
Fluorine binding site 4 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58


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 NR02-58 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1301

b:29.7
occ:0.94
 F55 B:ZK71301 0.0 29.7 0.9
C51 B:ZK71301 1.4 27.5 0.9
F57 B:ZK71301 2.2 28.1 0.9
F56 B:ZK71301 2.3 26.6 0.9
C17 B:ZK71301 2.3 23.6 0.9
HG22 B:VAL1158 2.4 32.5 1.0
O15 B:ZK71301 2.5 19.1 0.9
H541 B:ZK71301 2.9 26.4 0.9
C54 B:ZK71301 3.1 22.0 0.9
CG2 B:VAL1158 3.3 27.0 1.0
HA B:VAL1158 3.3 27.0 1.0
HG13 B:VAL1158 3.6 32.9 1.0
H542 B:ZK71301 3.6 26.4 0.9
C52 B:ZK71301 3.6 17.4 0.9
HG21 B:VAL1158 3.7 32.5 1.0
H521 B:ZK71301 3.8 20.9 0.9
HG23 B:VAL1158 3.9 32.5 1.0
C14 B:ZK71301 3.9 20.0 0.9
CB B:VAL1158 4.0 19.6 1.0
CA B:VAL1158 4.1 22.5 1.0
C53 B:ZK71301 4.1 23.7 0.9
CG1 B:VAL1158 4.2 27.3 1.0
H522 B:ZK71301 4.3 20.9 0.9
HG11 B:VAL1158 4.3 32.9 1.0
O B:HOH1435 4.4 19.1 1.0
H532 B:ZK71301 4.4 28.5 0.9
H131 B:ZK71301 4.4 20.6 0.9
HH22 B:ARG1123 4.5 32.6 1.0
O B:ALA1157 4.6 19.8 1.0
N B:VAL1158 4.6 24.5 1.0
O16 B:ZK71301 4.7 19.6 0.9
N13 B:ZK71301 4.7 17.1 0.9
HE B:ARG1123 4.9 23.7 1.0
C B:ALA1157 4.9 17.2 1.0
H531 B:ZK71301 4.9 28.5 0.9
H B:SER1159 5.0 36.2 1.0
HB B:VAL1158 5.0 23.6 1.0
NH2 B:ARG1123 5.0 27.1 1.0

Fluorine binding site 5 out of 6 in 7mmg

Go back to Fluorine Binding Sites List in 7mmg
Fluorine binding site 5 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58


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 NR02-58 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1301

b:26.6
occ:0.94
 F56 B:ZK71301 0.0 26.6 0.9
C51 B:ZK71301 1.4 27.5 0.9
F55 B:ZK71301 2.3 29.7 0.9
C17 B:ZK71301 2.3 23.6 0.9
F57 B:ZK71301 2.3 28.1 0.9
H541 B:ZK71301 2.4 26.4 0.9
H521 B:ZK71301 2.5 20.9 0.9
C54 B:ZK71301 2.7 22.0 0.9
C52 B:ZK71301 2.7 17.4 0.9
H532 B:ZK71301 2.8 28.5 0.9
C53 B:ZK71301 3.0 23.7 0.9
HH22 B:ARG1123 3.1 32.6 1.0
O B:HOH1435 3.3 19.1 1.0
NH2 B:ARG1123 3.4 27.1 1.0
O15 B:ZK71301 3.5 19.1 0.9
HH21 B:ARG1123 3.5 32.6 1.0
H542 B:ZK71301 3.6 26.4 0.9
H522 B:ZK71301 3.7 20.9 0.9
HG22 B:VAL1158 3.9 32.5 1.0
H531 B:ZK71301 3.9 28.5 0.9
HH12 B:ARG1155 4.2 29.8 1.0
CZ B:ARG1123 4.3 28.1 1.0
HE B:ARG1123 4.4 23.7 1.0
CG2 B:VAL1158 4.7 27.0 1.0
C14 B:ZK71301 4.7 20.0 0.9
NE B:ARG1123 4.7 19.6 1.0
HG21 B:VAL1158 4.7 32.5 1.0
HB3 B:ALA1156 4.8 16.5 1.0
NH1 B:ARG1155 4.8 24.7 1.0
CB B:ALA1168 4.9 29.4 1.0
HH11 B:ARG1155 4.9 29.8 1.0
O16 B:ZK71301 5.0 19.6 0.9

Fluorine binding site 6 out of 6 in 7mmg

Go back to Fluorine Binding Sites List in 7mmg
Fluorine binding site 6 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-58


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 NR02-58 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1301

b:28.1
occ:0.94
 F57 B:ZK71301 0.0 28.1 0.9
C51 B:ZK71301 1.4 27.5 0.9
F55 B:ZK71301 2.2 29.7 0.9
C17 B:ZK71301 2.3 23.6 0.9
F56 B:ZK71301 2.3 26.6 0.9
H521 B:ZK71301 2.5 20.9 0.9
HG22 B:VAL1158 2.6 32.5 1.0
C52 B:ZK71301 2.8 17.4 0.9
O15 B:ZK71301 2.8 19.1 0.9
HB3 B:ALA1156 3.2 16.5 1.0
H522 B:ZK71301 3.3 20.9 0.9
CG2 B:VAL1158 3.4 27.0 1.0
HG23 B:VAL1158 3.4 32.5 1.0
CB B:ALA1168 3.5 29.4 1.0
C54 B:ZK71301 3.7 22.0 0.9
HB1 B:ALA1156 3.7 16.5 1.0
HG21 B:VAL1158 3.8 32.5 1.0
H541 B:ZK71301 3.9 26.4 0.9
CB B:ALA1156 3.9 14.1 1.0
C53 B:ZK71301 3.9 23.7 0.9
C14 B:ZK71301 3.9 20.0 0.9
HA B:VAL1158 4.1 27.0 1.0
HH22 B:ARG1123 4.1 32.6 1.0
H532 B:ZK71301 4.2 28.5 0.9
NH2 B:ARG1123 4.3 27.1 1.0
H542 B:ZK71301 4.3 26.4 0.9
N B:VAL1158 4.4 24.5 1.0
HE B:ARG1123 4.4 23.7 1.0
C B:ALA1157 4.4 17.2 1.0
O B:ALA1157 4.4 19.8 1.0
C B:ALA1156 4.5 13.8 1.0
H131 B:ZK71301 4.5 20.6 0.9
CA B:VAL1158 4.5 22.5 1.0
CZ B:ARG1123 4.5 28.1 1.0
H B:ALA1168 4.5 16.1 1.0
HH12 B:ARG1155 4.5 29.8 1.0
CB B:VAL1158 4.5 19.6 1.0
HB2 B:ALA1156 4.6 16.5 1.0
HH21 B:ARG1123 4.6 32.6 1.0
NE B:ARG1123 4.6 19.6 1.0
O16 B:ZK71301 4.6 19.6 0.9
O B:ALA1156 4.6 13.7 1.0
H B:VAL1158 4.7 29.5 1.0
N13 B:ZK71301 4.7 17.1 0.9
H531 B:ZK71301 4.7 28.5 0.9
CA B:ALA1168 4.8 16.0 1.0
N B:ALA1157 4.8 14.2 1.0
CA B:ALA1156 4.8 13.7 1.0
N B:ALA1168 4.8 13.8 1.0
NH1 B:ARG1155 4.9 24.7 1.0
O B:HOH1435 5.0 19.1 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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