Zinc in PDB 6c2m: Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Mk-5172

The structure of Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Mk-5172, PDB code: 6c2m was solved by A.N.Matthew, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.73 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.635, 103.326, 73.962, 90.00, 112.01, 90.00
R / Rfree (%)	18.1 / 22.4

The binding sites of Zinc atom in the Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Mk-5172 (pdb code 6c2m). 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 Variant Y56H in Complex with Mk-5172, PDB code: 6c2m:
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 Variant Y56H in Complex with Mk-5172


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 Variant Y56H in Complex with Mk-5172 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:24.9 occ:1.00 SG A:CYS1097 2.3 21.7 1.0 O A:HOH1333 2.3 10.6 1.0 SG A:CYS1145 2.3 20.8 1.0 SG A:CYS1099 2.4 23.6 1.0 H A:CYS1099 2.8 26.5 1.0 HB2 A:CYS1145 2.9 21.0 1.0 CB A:CYS1145 3.0 17.5 1.0 HB3 A:CYS1145 3.0 21.0 1.0 HB2 A:CYS1097 3.2 22.5 1.0 HB3 A:CYS1099 3.2 31.0 1.0 CB A:CYS1097 3.2 18.7 1.0 HB2 A:HIS1149 3.3 14.7 1.0 HA A:CYS1097 3.3 23.1 1.0 CB A:CYS1099 3.4 25.8 1.0 H A:THR1098 3.4 31.0 1.0 HB3 A:ALA1147 3.6 23.9 1.0 N A:CYS1099 3.6 22.0 1.0 CA A:CYS1097 3.7 19.2 1.0 N A:THR1098 3.9 25.8 1.0 CA A:CYS1099 4.1 29.8 1.0 HD2 A:PRO1146 4.1 30.9 1.0 HB3 A:CYS1097 4.1 22.5 1.0 H A:ALA1147 4.1 24.6 1.0 C A:CYS1097 4.2 26.8 1.0 HB2 A:CYS1099 4.2 31.0 1.0 CB A:HIS1149 4.3 12.2 1.0 H A:GLY1100 4.3 25.4 1.0 H A:SER1101 4.4 28.3 1.0 HB2 A:ALA1147 4.4 23.9 1.0 CB A:ALA1147 4.4 19.8 1.0 H A:HIS1149 4.5 21.9 1.0 CA A:CYS1145 4.5 19.8 1.0 ND1 A:HIS1149 4.5 34.0 1.0 CG A:HIS1149 4.6 21.7 1.0 HG22 A:VAL1151 4.6 20.3 1.0 HB3 A:SER1101 4.6 27.9 1.0 HB3 A:HIS1149 4.7 14.7 1.0 C A:THR1098 4.7 22.7 1.0 N A:GLY1100 4.7 21.2 1.0 C A:CYS1099 4.7 24.8 1.0 H A:CYS1145 4.8 23.6 1.0 CD A:PRO1146 4.8 25.7 1.0 HA A:CYS1099 4.9 35.9 1.0 CA A:THR1098 4.9 24.9 1.0 HD3 A:PRO1146 4.9 30.9 1.0 N A:ALA1147 4.9 20.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Mk-5172


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 Variant Y56H in Complex with Mk-5172 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:27.0 occ:1.00 SG B:CYS1145 2.2 20.3 1.0 SG B:CYS1097 2.2 22.4 1.0 SG B:CYS1099 2.4 33.0 1.0 HB2 B:CYS1145 2.9 30.2 1.0 H B:CYS1099 2.9 44.1 1.0 CB B:CYS1145 3.0 25.2 1.0 HB3 B:CYS1145 3.0 30.2 1.0 HB2 B:HIS1149 3.1 32.5 1.0 HB2 B:CYS1097 3.2 32.0 1.0 CB B:CYS1097 3.3 26.7 1.0 HA B:CYS1097 3.4 33.5 1.0 HD2 B:HIS1149 3.4 45.4 1.0 HB3 B:ALA1147 3.5 41.2 1.0 H B:THR1098 3.5 38.1 1.0 HB3 B:CYS1099 3.6 31.8 1.0 CB B:CYS1099 3.6 26.5 1.0 N B:CYS1099 3.8 36.7 1.0 CA B:CYS1097 3.8 27.9 1.0 CD2 B:HIS1149 3.9 37.8 1.0 H B:ALA1147 4.0 39.2 1.0 CB B:HIS1149 4.0 27.0 1.0 N B:THR1098 4.0 31.7 1.0 HD2 B:PRO1146 4.1 44.5 1.0 HB3 B:CYS1097 4.1 32.0 1.0 H B:SER1101 4.2 47.0 1.0 CG B:HIS1149 4.2 30.8 1.0 CA B:CYS1099 4.2 32.0 1.0 H B:GLY1100 4.3 36.4 1.0 C B:CYS1097 4.3 26.2 1.0 HB2 B:ALA1147 4.3 41.2 1.0 CB B:ALA1147 4.3 34.3 1.0 HB3 B:SER1101 4.3 51.6 1.0 H B:HIS1149 4.4 30.9 1.0 HB3 B:HIS1149 4.4 32.5 1.0 HB2 B:CYS1099 4.4 31.8 1.0 CA B:CYS1145 4.4 20.8 1.0 N B:GLY1100 4.7 30.3 1.0 N B:ALA1147 4.8 32.6 1.0 H B:CYS1145 4.8 20.0 1.0 C B:CYS1099 4.8 28.5 1.0 C B:THR1098 4.9 40.9 1.0 CD B:PRO1146 4.9 37.1 1.0 HB2 B:SER1101 4.9 51.6 1.0 HB1 B:ALA1147 5.0 41.2 1.0 HA B:CYS1145 5.0 25.0 1.0 C B:CYS1145 5.0 34.6 1.0 N B:SER1101 5.0 39.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Mk-5172


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 Variant Y56H in Complex with Mk-5172 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1202 b:24.6 occ:1.00 SG C:CYS1099 2.3 27.3 1.0 SG C:CYS1145 2.4 25.6 1.0 SG C:CYS1097 2.4 25.2 1.0 H C:CYS1099 3.0 28.1 1.0 HB2 C:CYS1145 3.0 34.8 1.0 O C:HOH1339 3.1 32.3 1.0 CB C:CYS1145 3.1 28.9 1.0 HB3 C:CYS1099 3.1 40.6 1.0 HB3 C:CYS1145 3.2 34.8 1.0 HB2 C:CYS1097 3.2 25.4 1.0 CB C:CYS1099 3.3 33.8 1.0 CB C:CYS1097 3.4 21.2 1.0 HB2 C:HIS1149 3.4 28.4 1.0 HA C:CYS1097 3.5 17.2 1.0 N C:CYS1099 3.7 23.4 1.0 HB3 C:ALA1147 3.8 31.6 1.0 CA C:CYS1097 3.9 14.3 1.0 H C:THR1098 3.9 29.0 1.0 CA C:CYS1099 4.0 33.0 1.0 HB3 C:SER1101 4.0 46.9 1.0 HB2 C:CYS1099 4.1 40.6 1.0 H C:GLY1100 4.2 38.4 1.0 H C:SER1101 4.2 54.9 1.0 HD2 C:PRO1146 4.2 39.1 1.0 HB3 C:CYS1097 4.2 25.4 1.0 N C:THR1098 4.3 24.1 1.0 H C:ALA1147 4.3 29.5 1.0 CB C:HIS1149 4.4 23.6 1.0 C C:CYS1097 4.4 23.5 1.0 HH22 C:ARG1118 4.6 48.5 1.0 N C:GLY1100 4.6 31.9 1.0 CA C:CYS1145 4.6 33.5 1.0 C C:CYS1099 4.6 28.0 1.0 HB2 C:ALA1147 4.6 31.6 1.0 CB C:ALA1147 4.7 26.3 1.0 HB3 C:HIS1149 4.7 28.4 1.0 H C:HIS1149 4.7 31.0 1.0 CG C:HIS1149 4.8 25.3 1.0 C C:THR1098 4.9 20.5 1.0 CB C:SER1101 4.9 39.0 1.0 HA C:CYS1099 4.9 39.7 1.0 HB2 C:SER1101 4.9 46.9 1.0 H C:CYS1145 4.9 33.8 1.0 HG22 C:VAL1151 4.9 34.2 1.0 N C:SER1101 5.0 45.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Mk-5172


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 Variant Y56H in Complex with Mk-5172 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1201 b:27.7 occ:1.00 SG D:CYS1145 2.3 22.2 1.0 SG D:CYS1099 2.4 30.5 1.0 ND1 D:HIS1149 2.4 19.9 1.0 SG D:CYS1097 2.5 22.5 1.0 HB2 D:HIS1149 2.5 28.5 1.0 HB2 D:CYS1099 2.9 30.7 1.0 HB3 D:CYS1145 3.1 34.8 1.0 CB D:CYS1145 3.1 29.0 1.0 CG D:HIS1149 3.1 19.3 1.0 H D:CYS1099 3.2 35.8 1.0 CB D:CYS1099 3.2 25.6 1.0 HA D:CYS1097 3.2 24.7 1.0 HB2 D:CYS1145 3.2 34.8 1.0 CB D:HIS1149 3.3 23.7 1.0 HB3 D:ALA1147 3.3 26.9 1.0 HB2 D:CYS1097 3.4 30.1 1.0 CB D:CYS1097 3.4 25.1 1.0 CE1 D:HIS1149 3.4 24.0 1.0 H D:THR1098 3.6 38.1 1.0 HE1 D:HIS1149 3.7 28.8 1.0 H D:HIS1149 3.7 25.8 1.0 HB3 D:HIS1149 3.8 28.5 1.0 CA D:CYS1097 3.8 20.6 1.0 N D:CYS1099 3.8 29.8 1.0 HB3 D:CYS1099 4.0 30.7 1.0 O D:HOH1329 4.0 21.4 1.0 N D:THR1098 4.1 31.8 1.0 CA D:CYS1099 4.2 27.0 1.0 H D:ALA1147 4.2 27.9 1.0 CB D:ALA1147 4.3 22.4 1.0 HB3 D:CYS1097 4.3 30.1 1.0 CD2 D:HIS1149 4.3 19.9 1.0 C D:CYS1097 4.4 30.3 1.0 NE2 D:HIS1149 4.4 22.2 1.0 N D:HIS1149 4.4 21.4 1.0 CA D:HIS1149 4.4 16.9 1.0 HB2 D:ALA1147 4.6 26.9 1.0 CA D:CYS1145 4.6 18.3 1.0 HA D:CYS1099 4.6 32.5 1.0 HD2 D:PRO1146 4.7 29.4 1.0 H D:CYS1145 4.7 25.7 1.0 HB1 D:ALA1147 4.8 26.9 1.0 C D:THR1098 4.9 46.1 1.0 HB3 D:SER1101 4.9 54.8 1.0 N D:ALA1147 4.9 23.2 1.0

A.N.Matthew, C.A.Schiffer. Clinical Signature Variant of Hcv NS3/4A Protease Uses A Novel Mechanism to Confer Resistance To Be Published.