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Zinc in PDB 4u01: Hcv NS3/4A Serine Protease in Complex with 6570

Protein crystallography data

The structure of Hcv NS3/4A Serine Protease in Complex with 6570, PDB code: 4u01 was solved by C.C.Parsy, F.-R.Alexandre, G.Brandt, C.Caillet, D.Chaves, M.Derock, D.Gloux, Y.Griffon, L.B.Lallos, F.Leroy, M.Liuzzi, A.-G.Loi, B.Mayes, L.Moulat, A.Moussa, M.Chiara, V.Roques, E.Rosinovsky, M.Seifer, A.Stewart, J.Wang, D.Standring, D.Surleraux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.23 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 150.034, 174.363, 133.010, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 29

Other elements in 4u01:

The structure of Hcv NS3/4A Serine Protease in Complex with 6570 also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Hcv NS3/4A Serine Protease in Complex with 6570 (pdb code 4u01). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Hcv NS3/4A Serine Protease in Complex with 6570, PDB code: 4u01:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4u01

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Zinc binding site 1 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:89.7
occ:1.00
 SG A:CYS145 2.2 56.4 1.0
SG A:CYS97 2.2 66.9 1.0
SG A:CYS99 2.8 83.4 1.0
CB A:CYS145 3.2 68.3 1.0
CB A:CYS97 3.3 66.8 1.0
OG A:SER147 3.4 83.6 1.0
CB A:CYS99 3.6 88.1 1.0
CA A:CYS97 3.7 68.1 1.0
N A:CYS99 3.8 84.0 1.0
N A:THR98 4.0 76.5 1.0
CB A:HIS149 4.1 70.8 1.0
CA A:CYS99 4.3 88.4 1.0
C A:CYS97 4.3 72.2 1.0
CG A:HIS149 4.5 74.3 1.0
CB A:SER147 4.6 84.7 1.0
CA A:CYS145 4.7 67.5 1.0
CD2 A:HIS149 4.8 76.4 1.0
C A:THR98 4.9 84.8 1.0
N A:CYS97 4.9 64.2 1.0
N A:SER147 5.0 80.5 1.0
N A:GLY100 5.0 85.4 1.0

Zinc binding site 2 out of 9 in 4u01

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Zinc binding site 2 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:0.7
occ:1.00
 SG B:CYS97 2.4 1.0 1.0
SG B:CYS99 2.9 0.7 1.0
CB B:CYS97 3.3 0.9 1.0
N B:CYS99 3.3 0.1 1.0
SG B:CYS145 3.3 0.4 1.0
CB B:CYS99 3.3 0.2 1.0
CA B:CYS97 3.4 0.1 1.0
N B:THR98 3.4 0.5 1.0
C B:CYS97 3.8 0.5 1.0
OG B:SER147 3.8 0.1 1.0
CA B:CYS99 3.9 0.3 1.0
C B:THR98 4.3 0.6 1.0
CB B:CYS145 4.3 0.5 1.0
CB B:HIS149 4.4 0.1 1.0
CA B:THR98 4.4 0.3 1.0
N B:GLY100 4.7 0.5 1.0
N B:CYS97 4.7 0.4 1.0
ND1 B:HIS149 4.8 0.7 1.0
C B:CYS99 4.8 0.8 1.0
CG B:HIS149 4.8 0.4 1.0
O B:CYS97 4.9 0.9 1.0

Zinc binding site 3 out of 9 in 4u01

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Zinc binding site 3 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:0.3
occ:1.00
 SG C:CYS99 1.8 0.3 1.0
SG C:CYS145 2.2 0.3 1.0
SG C:CYS97 2.3 0.8 1.0
CB C:CYS145 3.0 0.3 1.0
CB C:CYS99 3.2 0.2 1.0
CB C:CYS97 3.2 0.7 1.0
N C:CYS99 3.8 0.8 1.0
CA C:CYS97 3.9 0.3 1.0
CA C:CYS99 4.0 0.1 1.0
OG C:SER147 4.2 0.1 1.0
C C:CYS97 4.3 0.6 1.0
N C:THR98 4.4 0.7 1.0
N C:GLY100 4.5 0.4 1.0
CA C:CYS145 4.5 0.3 1.0
CB C:SER101 4.5 1.0 1.0
CB C:HIS149 4.6 0.7 1.0
C C:CYS99 4.7 0.4 1.0
N C:SER101 4.8 0.2 1.0
CD C:PRO146 4.8 0.8 1.0
C C:THR98 4.9 0.5 1.0
C C:CYS145 5.0 0.4 1.0

Zinc binding site 4 out of 9 in 4u01

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Zinc binding site 4 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:87.4
occ:1.00
 SG D:CYS97 2.3 93.7 1.0
SG D:CYS145 2.5 86.2 1.0
SG D:CYS99 2.9 0.7 1.0
CB D:CYS97 3.2 85.1 1.0
OG D:SER147 3.5 99.7 1.0
CB D:CYS99 3.6 0.1 1.0
CB D:CYS145 3.7 85.1 1.0
CA D:CYS97 3.7 87.5 1.0
N D:CYS99 3.9 1.0 1.0
N D:THR98 4.0 99.1 1.0
C D:CYS97 4.3 92.8 1.0
CB D:SER147 4.3 0.3 1.0
CB D:HIS149 4.3 82.5 1.0
CA D:CYS99 4.4 0.7 1.0
CG D:HIS149 4.7 88.6 1.0
ND1 D:HIS149 4.7 93.1 1.0
N D:CYS97 5.0 82.8 1.0
C D:THR98 5.0 0.7 1.0

Zinc binding site 5 out of 9 in 4u01

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Zinc binding site 5 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:0.9
occ:1.00
 SG E:CYS97 2.0 0.5 1.0
SG E:CYS145 2.5 0.6 1.0
CB E:CYS97 2.9 0.1 1.0
SG E:CYS99 3.2 0.9 1.0
CA E:CYS97 3.4 0.8 1.0
CB E:CYS145 3.5 0.1 1.0
OG E:SER147 3.6 0.4 1.0
CB E:CYS99 3.8 0.9 1.0
CB E:HIS149 4.0 0.8 1.0
N E:CYS99 4.0 0.6 1.0
N E:THR98 4.1 0.1 1.0
C E:CYS97 4.1 0.1 1.0
CG E:HIS149 4.5 0.7 1.0
ND1 E:HIS149 4.5 0.6 1.0
CA E:CYS99 4.5 0.8 1.0
CB E:SER147 4.7 0.3 1.0
N E:CYS97 4.7 0.4 1.0
CA E:CYS145 4.9 0.8 1.0

Zinc binding site 6 out of 9 in 4u01

Go back to Zinc Binding Sites List in 4u01
Zinc binding site 6 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn302

b:93.4
occ:1.00
 SG F:CYS97 1.9 76.1 1.0
SG F:CYS145 2.1 75.1 1.0
SG F:CYS99 2.9 91.5 1.0
CB F:CYS97 3.0 72.3 1.0
CB F:CYS145 3.3 72.3 1.0
CA F:CYS97 3.6 76.0 1.0
OG F:SER147 3.8 90.2 1.0
CB F:CYS99 3.8 94.1 1.0
N F:CYS99 3.8 91.0 1.0
N F:THR98 4.0 86.1 1.0
C F:CYS97 4.2 80.9 1.0
CA F:CYS99 4.3 94.2 1.0
CB F:HIS149 4.3 75.1 1.0
N F:GLY100 4.5 86.5 1.0
CA F:CYS145 4.7 70.7 1.0
CG F:HIS149 4.8 81.2 1.0
C F:CYS99 4.8 91.9 1.0
ND1 F:HIS149 4.9 84.8 1.0
C F:THR98 4.9 93.8 1.0
N F:CYS97 5.0 73.2 1.0
CB F:SER147 5.0 91.8 1.0

Zinc binding site 7 out of 9 in 4u01

Go back to Zinc Binding Sites List in 4u01
Zinc binding site 7 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn302

b:0.6
occ:1.00
 SG G:CYS97 1.6 0.4 1.0
CB G:CYS97 2.8 0.9 1.0
SG G:CYS99 3.1 0.8 1.0
SG G:CYS145 3.1 0.3 1.0
CA G:CYS97 3.3 0.2 1.0
N G:THR98 3.5 0.9 1.0
C G:CYS97 3.8 0.9 1.0
N G:CYS99 3.8 0.5 1.0
CB G:CYS145 3.9 0.5 1.0
CB G:CYS99 4.0 0.7 1.0
OG G:SER147 4.0 0.1 1.0
CB G:HIS149 4.2 0.9 1.0
CA G:CYS99 4.5 0.3 1.0
N G:CYS97 4.6 0.9 1.0
CA G:THR98 4.6 0.6 1.0
C G:THR98 4.7 0.7 1.0
N G:GLY100 4.8 0.5 1.0
CG G:HIS149 4.8 0.6 1.0
ND1 G:HIS149 4.8 0.8 1.0
O G:CYS97 4.9 0.3 1.0

Zinc binding site 8 out of 9 in 4u01

Go back to Zinc Binding Sites List in 4u01
Zinc binding site 8 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn302

b:0.2
occ:1.00
 SG H:CYS97 1.9 99.8 1.0
SG H:CYS99 2.6 0.3 1.0
SG H:CYS145 3.3 91.0 1.0
CB H:CYS97 3.3 95.2 1.0
CB H:CYS99 3.4 0.0 1.0
N H:CYS99 3.5 0.5 1.0
CA H:CYS97 3.7 98.2 1.0
N H:THR98 3.7 0.4 1.0
C H:CYS97 4.0 0.2 1.0
CB H:CYS145 4.0 92.6 1.0
CA H:CYS99 4.0 0.9 1.0
OG H:SER147 4.2 0.1 1.0
C H:THR98 4.4 0.0 1.0
N H:GLY100 4.4 0.2 1.0
CA H:THR98 4.6 0.5 1.0
CB H:HIS149 4.7 95.0 1.0
C H:CYS99 4.8 0.2 1.0
O H:CYS97 4.8 0.7 1.0

Zinc binding site 9 out of 9 in 4u01

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Zinc binding site 9 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn302

b:1.0
occ:1.00
 SG J:CYS97 2.0 0.1 1.0
SG J:CYS99 2.1 0.7 1.0
CB J:CYS145 3.0 0.9 1.0
CB J:SER101 3.1 0.6 1.0
N J:SER101 3.2 0.7 1.0
SG J:CYS145 3.3 0.4 1.0
N J:GLY100 3.6 1.0 1.0
CB J:CYS99 3.6 0.4 1.0
CA J:SER101 3.7 0.1 1.0
CB J:CYS97 3.7 0.7 1.0
CA J:CYS99 4.2 1.0 1.0
C J:CYS99 4.2 0.2 1.0
N J:CYS99 4.2 0.8 1.0
C J:GLY100 4.2 0.5 1.0
OG J:SER101 4.4 0.3 1.0
CA J:GLY100 4.4 0.0 1.0
CA J:CYS145 4.5 0.3 1.0
CD J:PRO146 4.5 0.8 1.0
O J:SER101 4.5 0.0 1.0
C J:SER101 4.6 0.1 1.0
CA J:CYS97 4.8 0.1 1.0
CG1 J:VAL151 5.0 0.2 1.0

Reference:

C.C.Parsy, F.R.Alexandre, V.Bidau, F.Bonnaterre, G.Brandt, C.Caillet, S.Cappelle, D.Chaves, T.Convard, M.Derock, D.Gloux, Y.Griffon, L.B.Lallos, F.Leroy, M.Liuzzi, A.G.Loi, L.Moulat, M.Chiara, H.Rahali, V.Roques, E.Rosinovsky, S.Savin, M.Seifer, D.Standring, D.Surleraux. Discovery and Structural Diversity of the Hepatitis C Virus NS3/4A Serine Protease Inhibitor Series Leading to Clinical Candidate IDX320. Bioorg.Med.Chem.Lett. V. 25 5427 2015.
ISSN: ESSN 1464-3405
PubMed: 26410074
DOI: 10.1016/J.BMCL.2015.09.009
Page generated: Sun Oct 27 08:40:37 2024

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