Zinc in PDB 5etx: Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue)

The structure of Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue), PDB code: 5etx was solved by D.Soumana, N.K.Yilmaz, A.Ali, K.L.Prachanronarong, C.Aydin, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.53 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.441, 63.232, 92.304, 90.00, 91.65, 90.00
R / Rfree (%)	20 / 25.4

The structure of Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue) (pdb code 5etx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue), PDB code: 5etx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:30.0 occ:1.00 HD1 A:HIS1149 1.2 60.2 1.0 HG A:CYS1145 1.5 35.5 1.0 ND1 A:HIS1149 2.0 50.4 1.0 SG A:CYS1097 2.1 21.7 1.0 H A:CYS1099 2.5 43.9 1.0 SG A:CYS1145 2.7 29.8 1.0 HA A:CYS1097 2.8 39.5 1.0 HB2 A:HIS1149 2.8 26.4 1.0 SG A:CYS1099 3.0 30.0 1.0 H A:THR1098 3.0 34.7 1.0 CE1 A:HIS1149 3.0 46.7 1.0 CG A:HIS1149 3.0 38.3 1.0 CB A:CYS1097 3.2 26.9 1.0 HE1 A:HIS1149 3.2 55.8 1.0 CB A:CYS1099 3.2 30.0 1.0 N A:CYS1099 3.3 36.8 1.0 CA A:CYS1097 3.4 33.1 1.0 HB2 A:CYS1097 3.4 32.0 1.0 CB A:HIS1149 3.4 22.2 1.0 N A:THR1098 3.5 29.1 1.0 HB3 A:CYS1145 3.5 24.1 1.0 CB A:CYS1145 3.6 20.3 1.0 HB2 A:CYS1145 3.7 24.1 1.0 HB3 A:HIS1149 3.7 26.4 1.0 HB1 A:ALA1147 3.8 23.5 1.0 C A:CYS1097 3.8 35.9 1.0 CA A:CYS1099 3.8 34.4 1.0 HB3 A:CYS1097 4.0 32.0 1.0 NE2 A:HIS1149 4.1 46.9 1.0 CD2 A:HIS1149 4.2 31.9 1.0 H A:HIS1149 4.3 33.6 1.0 C A:THR1098 4.4 30.4 1.0 H A:GLY1100 4.4 45.9 1.0 CA A:THR1098 4.5 36.9 1.0 HA A:CYS1099 4.6 41.0 1.0 N A:CYS1097 4.7 45.9 1.0 CB A:ALA1147 4.7 19.8 1.0 CA A:HIS1149 4.7 28.6 1.0 C A:CYS1099 4.7 44.0 1.0 H A:SER1101 4.8 50.9 1.0 N A:GLY1100 4.8 38.5 1.0 H A:ALA1147 4.9 17.4 1.0 HB3 A:ALA1147 4.9 23.5 1.0 HD2 A:PRO1146 4.9 19.1 1.0 O A:CYS1097 4.9 36.0 1.0 HE2 A:HIS1149 4.9 56.0 1.0 O A:HOH1304 4.9 37.2 1.0 N A:HIS1149 4.9 28.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:42.3 occ:1.00 CB B:CYS1099 2.1 31.8 1.0 SG B:CYS1145 2.2 22.3 1.0 H B:CYS1099 2.4 56.9 1.0 ND1 B:HIS1149 3.0 30.0 1.0 N B:CYS1099 3.1 47.6 1.0 CA B:CYS1099 3.2 36.1 1.0 HB2 B:CYS1145 3.2 17.9 1.0 HB3 B:ALA1147 3.3 24.8 1.0 CB B:CYS1145 3.3 15.1 1.0 CB B:CYS1097 3.3 30.0 1.0 HB3 B:CYS1145 3.4 17.9 1.0 HA B:CYS1097 3.5 33.7 1.0 H B:THR1098 3.6 48.8 1.0 HA B:CYS1099 3.7 43.1 1.0 CB B:HIS1149 3.7 30.0 1.0 CG B:HIS1149 3.8 30.0 1.0 CA B:CYS1097 3.9 28.3 1.0 H B:ALA1147 3.9 29.1 1.0 N B:THR1098 4.0 40.9 1.0 HB2 B:ALA1147 4.0 24.8 1.0 CE1 B:HIS1149 4.0 30.0 1.0 CB B:ALA1147 4.1 20.9 1.0 H B:HIS1149 4.2 30.5 1.0 H B:GLY1100 4.3 20.3 1.0 HD2 B:PRO1146 4.3 27.1 1.0 C B:CYS1099 4.3 29.6 1.0 C B:THR1098 4.3 57.0 1.0 C B:CYS1097 4.4 38.8 1.0 H B:SER1101 4.4 36.9 1.0 N B:GLY1100 4.6 17.1 1.0 HB1 B:ALA1147 4.7 24.8 1.0 CA B:CYS1145 4.7 20.6 1.0 N B:ALA1147 4.7 24.5 1.0 HB3 B:SER1101 4.7 16.2 1.0 CA B:THR1098 4.8 51.9 1.0 N B:HIS1149 4.9 25.7 1.0 CA B:HIS1149 4.9 24.2 1.0 HB2 B:SER1101 4.9 16.2 1.0 CD2 B:HIS1149 5.0 30.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1201 b:37.0 occ:1.00 HD1 C:HIS1149 2.0 40.3 1.0 CB C:CYS1099 2.1 25.0 1.0 SG C:CYS1097 2.2 28.2 1.0 SG C:CYS1145 2.2 33.6 1.0 H C:CYS1099 2.2 36.1 1.0 HB2 C:HIS1149 2.7 16.2 1.0 ND1 C:HIS1149 2.8 33.8 1.0 N C:CYS1099 2.9 30.3 1.0 HA C:CYS1097 3.0 27.8 1.0 CA C:CYS1099 3.1 30.5 1.0 CB C:CYS1145 3.1 27.8 1.0 HB3 C:CYS1145 3.1 33.1 1.0 HB2 C:CYS1145 3.2 33.1 1.0 H C:THR1098 3.3 43.5 1.0 CB C:CYS1097 3.3 13.6 1.0 HB3 C:ALA1147 3.4 22.6 1.0 HB2 C:CYS1097 3.5 16.1 1.0 CB C:HIS1149 3.5 13.7 1.0 CG C:HIS1149 3.5 27.7 1.0 CA C:CYS1097 3.5 23.4 1.0 HA C:CYS1099 3.6 36.3 1.0 N C:THR1098 3.7 36.5 1.0 CE1 C:HIS1149 3.8 37.0 1.0 HB3 C:HIS1149 3.9 16.2 1.0 C C:CYS1097 4.0 29.3 1.0 HE1 C:HIS1149 4.1 44.2 1.0 H C:GLY1100 4.1 31.4 1.0 H C:ALA1147 4.1 40.5 1.0 C C:THR1098 4.1 31.3 1.0 H C:HIS1149 4.1 37.6 1.0 HB3 C:CYS1097 4.1 16.1 1.0 C C:CYS1099 4.2 34.2 1.0 H C:SER1101 4.3 42.3 1.0 HB2 C:ALA1147 4.3 22.6 1.0 CB C:ALA1147 4.3 19.0 1.0 HD2 C:PRO1146 4.4 25.3 1.0 N C:GLY1100 4.4 26.4 1.0 CA C:THR1098 4.6 31.1 1.0 CA C:CYS1145 4.6 30.4 1.0 HB3 C:SER1101 4.6 23.3 1.0 CA C:HIS1149 4.7 19.8 1.0 HG1 C:THR1098 4.7 42.5 1.0 CD2 C:HIS1149 4.7 20.0 1.0 N C:HIS1149 4.8 31.5 1.0 HG22 C:VAL1151 4.8 21.2 1.0 N C:CYS1097 4.8 22.5 1.0 H C:CYS1145 4.9 43.0 1.0 NE2 C:HIS1149 4.9 24.6 1.0 HB1 C:ALA1147 4.9 22.6 1.0 N C:ALA1147 4.9 34.0 1.0 HB2 C:SER1101 5.0 23.3 1.0 HG23 C:VAL1151 5.0 21.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Hcv NS3/4A Protease A156T Variant in Complex with 5172-Linear (Mk-5172 Linear Analogue) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1201 b:30.0 occ:1.00 H D:CYS1099 1.9 40.2 1.0 CB D:CYS1099 2.1 30.0 1.0 SG D:CYS1145 2.5 31.8 1.0 N D:CYS1099 2.6 33.7 1.0 HA D:CYS1097 2.7 22.8 1.0 CA D:CYS1099 2.9 30.8 1.0 H D:THR1098 3.0 46.0 1.0 CB D:CYS1097 3.1 16.5 1.0 CA D:CYS1097 3.3 19.2 1.0 HB3 D:CYS1145 3.3 28.2 1.0 CB D:CYS1145 3.4 23.7 1.0 HB2 D:CYS1145 3.4 28.2 1.0 ND1 D:HIS1149 3.4 40.1 1.0 N D:THR1098 3.4 38.5 1.0 SG D:CYS1099 3.5 30.0 1.0 HA D:CYS1099 3.5 36.7 1.0 HB3 D:ALA1147 3.6 31.0 1.0 C D:CYS1097 3.8 29.9 1.0 H D:GLY1100 3.8 50.8 1.0 C D:THR1098 3.8 40.3 1.0 CB D:HIS1149 3.9 22.2 1.0 C D:CYS1099 4.0 39.9 1.0 CG D:HIS1149 4.1 24.2 1.0 N D:GLY1100 4.2 42.6 1.0 H D:SER1101 4.2 41.1 1.0 CA D:THR1098 4.3 43.1 1.0 HB2 D:ALA1147 4.5 31.0 1.0 H D:ALA1147 4.5 25.0 1.0 CB D:ALA1147 4.5 26.1 1.0 H D:HIS1149 4.5 30.6 1.0 CE1 D:HIS1149 4.5 61.5 1.0 N D:CYS1097 4.6 27.4 1.0 HD2 D:PRO1146 4.6 14.1 1.0 HB3 D:SER1101 4.7 41.7 1.0 O D:CYS1097 4.8 35.4 1.0 O D:THR1098 4.8 50.9 1.0 CA D:CYS1145 4.9 19.3 1.0 HA D:THR1098 5.0 51.5 1.0 OG1 D:THR1098 5.0 23.5 1.0

D.I.Soumana, N.Kurt Yilmaz, K.L.Prachanronarong, C.Aydin, A.Ali, C.A.Schiffer. Structural and Thermodynamic Effects of Macrocyclization in Hcv NS3/4A Inhibitor Mk-5172. Acs Chem.Biol. V. 11 900 2016.
ISSN: ESSN 1554-8937
PubMed: 26682473
DOI: 10.1021/ACSCHEMBIO.5B00647