Zinc in PDB 7mg0: Crystal Structure of Ev-D68 2A Protease

All present enzymatic activity of Crystal Structure of Ev-D68 2A Protease:
3.4.22.29;

The structure of Crystal Structure of Ev-D68 2A Protease, PDB code: 7mg0 was solved by C.Liu, M.-Y.Lee, W.Liu, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.88 / 3.50
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	118.157, 118.157, 81.735, 90, 90, 90
R / Rfree (%)	23.8 / 28.5

The binding sites of Zinc atom in the Crystal Structure of Ev-D68 2A Protease (pdb code 7mg0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Ev-D68 2A Protease, PDB code: 7mg0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Ev-D68 2A Protease


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 Ev-D68 2A Protease within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:99.6 occ:1.00 ND1 E:HIS115 2.0 66.7 1.0 SG E:CYS53 2.3 112.3 1.0 SG E:CYS113 2.3 68.7 1.0 SG E:CYS55 2.3 95.8 1.0 HE1 E:HIS115 2.5 97.4 1.0 CE1 E:HIS115 2.6 81.2 1.0 HB2 E:CYS55 2.6 91.7 1.0 HB3 E:CYS53 2.9 108.2 1.0 CB E:CYS53 2.9 90.3 1.0 HB2 E:CYS53 2.9 108.2 1.0 CB E:CYS55 3.0 76.5 1.0 CG E:HIS115 3.3 66.9 1.0 H E:CYS55 3.3 129.1 1.0 CB E:CYS113 3.4 63.3 1.0 H E:HIS115 3.6 80.8 1.0 HB2 E:HIS115 3.6 89.9 1.0 HB3 E:CYS55 3.7 91.7 1.0 HB1 E:ALA51 3.7 95.5 1.0 NE2 E:HIS115 3.8 106.9 1.0 HD2 E:PRO114 4.0 103.2 1.0 N E:CYS55 4.0 107.7 1.0 CB E:HIS115 4.0 75.0 1.0 CA E:CYS55 4.0 94.7 1.0 CD2 E:HIS115 4.2 82.8 1.0 HG B:SER68 4.3 78.0 1.0 HB3 B:SER68 4.3 78.0 1.0 HA E:CYS55 4.4 113.4 1.0 N E:HIS115 4.4 67.4 1.0 CA E:CYS53 4.4 84.2 1.0 HE2 E:HIS115 4.5 128.2 1.0 H E:LYS54 4.6 124.9 1.0 CD1 E:ILE118 4.6 97.4 1.0 CB E:ALA51 4.6 79.7 1.0 CA E:CYS113 4.7 71.2 1.0 HB2 E:ALA51 4.8 95.5 1.0 CD E:PRO114 4.8 86.1 1.0 HB3 E:HIS115 4.8 89.9 1.0 N E:PRO114 4.8 82.3 1.0 N E:LYS54 4.8 104.2 1.0 OG B:SER68 4.9 65.1 1.0 H E:CYS53 4.9 106.1 1.0 CA E:HIS115 4.9 74.0 1.0 HG12 E:ILE118 4.9 104.2 1.0 C E:CYS113 4.9 83.1 1.0 HA E:CYS53 5.0 100.8 1.0 HG2 E:PRO114 5.0 97.6 1.0 C E:CYS53 5.0 95.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Ev-D68 2A Protease


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 Ev-D68 2A Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:148.2 occ:1.00 ND1 A:HIS115 2.1 134.5 1.0 SG A:CYS53 2.3 87.7 1.0 SG A:CYS113 2.3 104.8 1.0 SG A:CYS55 2.3 99.4 1.0 HB2 A:CYS55 2.8 121.9 1.0 HB2 A:HIS115 2.9 122.2 1.0 CE1 A:HIS115 3.0 159.8 1.0 CG A:HIS115 3.0 114.2 1.0 H A:HIS115 3.0 116.4 1.0 HE1 A:HIS115 3.1 191.6 1.0 CB A:CYS55 3.1 101.7 1.0 CB A:CYS53 3.3 97.9 1.0 HB2 A:CYS53 3.3 117.3 1.0 HB3 A:CYS53 3.3 117.3 1.0 CB A:HIS115 3.4 102.0 1.0 H A:CYS55 3.5 104.5 1.0 CB A:CYS113 3.5 117.2 1.0 HD2 A:PRO114 3.6 157.4 1.0 HB3 A:CYS55 3.8 121.9 1.0 N A:HIS115 3.8 97.1 1.0 HB1 A:ALA51 3.9 130.1 1.0 HG C:SER68 4.0 150.3 1.0 NE2 A:HIS115 4.0 160.9 1.0 CD2 A:HIS115 4.1 138.9 1.0 HB3 A:HIS115 4.2 122.2 1.0 N A:CYS55 4.2 87.2 1.0 CA A:CYS55 4.3 97.9 1.0 CA A:HIS115 4.3 112.7 1.0 CD A:PRO114 4.4 131.3 1.0 HB3 A:ALA51 4.4 130.1 1.0 N A:PRO114 4.5 123.8 1.0 CB A:ALA51 4.6 108.5 1.0 OG C:SER68 4.6 125.3 1.0 HA A:CYS55 4.6 117.4 1.0 CA A:CYS53 4.7 86.9 1.0 H A:GLY116 4.7 126.5 1.0 H A:CYS53 4.8 109.9 1.0 C A:CYS113 4.8 118.8 1.0 CA A:CYS113 4.8 119.0 1.0 CD1 A:ILE118 4.8 146.9 1.0 HE2 A:HIS115 4.8 193.0 1.0 HB2 A:PRO114 4.8 167.2 1.0 H A:LYS54 4.8 81.1 1.0 HG12 A:ILE118 4.9 162.7 1.0 HD2 A:HIS115 4.9 166.5 1.0 HA A:HIS115 4.9 135.1 1.0 C A:PRO114 5.0 102.3 1.0 HD3 A:PRO114 5.0 157.4 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Ev-D68 2A Protease


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 Ev-D68 2A Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:58.1 occ:1.00 ND1 B:HIS115 2.1 110.0 1.0 SG B:CYS53 2.3 121.8 1.0 SG B:CYS113 2.3 74.5 1.0 SG B:CYS55 2.3 92.6 1.0 HB3 B:CYS53 2.6 122.1 1.0 CB B:CYS53 2.7 101.9 1.0 HB2 B:CYS53 2.7 122.1 1.0 HB2 B:CYS55 2.8 137.1 1.0 CE1 B:HIS115 2.8 114.8 1.0 HE1 B:HIS115 2.8 137.7 1.0 CB B:CYS55 3.1 114.4 1.0 CG B:HIS115 3.2 76.1 1.0 HB2 B:HIS115 3.3 86.1 1.0 H B:CYS55 3.5 126.7 1.0 CB B:CYS113 3.5 58.4 1.0 H B:HIS115 3.6 70.4 1.0 HG E:SER68 3.7 123.5 1.0 HB1 B:ALA51 3.7 92.8 1.0 HB3 B:CYS55 3.8 137.1 1.0 CB B:HIS115 3.8 71.8 1.0 HD2 B:PRO114 3.9 105.7 1.0 NE2 B:HIS115 4.0 106.5 1.0 N B:CYS55 4.1 105.7 1.0 CA B:CYS53 4.2 99.5 1.0 CA B:CYS55 4.2 118.0 1.0 CD2 B:HIS115 4.2 88.7 1.0 OG E:SER68 4.3 103.0 1.0 N B:HIS115 4.4 58.8 1.0 HB3 B:HIS115 4.5 86.1 1.0 CB B:ALA51 4.6 77.5 1.0 HA B:CYS55 4.6 141.4 1.0 H B:LYS54 4.6 115.4 1.0 CD1 B:ILE118 4.6 79.9 1.0 H B:CYS53 4.6 114.2 1.0 HH11 B:ARG135 4.6 102.3 1.0 HG12 B:ILE118 4.7 88.9 1.0 CA B:HIS115 4.7 67.2 1.0 HB2 B:ALA51 4.7 92.8 1.0 HE2 B:HIS115 4.7 127.7 1.0 HA B:CYS53 4.7 119.3 1.0 N B:CYS53 4.8 95.3 1.0 CD B:PRO114 4.8 88.2 1.0 CA B:CYS113 4.9 70.4 1.0 N B:LYS54 4.9 96.3 1.0 C B:CYS53 4.9 105.3 1.0 N B:PRO114 5.0 81.6 1.0 H B:GLY116 5.0 88.9 1.0 HH12 B:ARG135 5.0 102.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Ev-D68 2A Protease


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 Ev-D68 2A Protease within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:138.9 occ:1.00 HB2 C:CYS55 2.0 129.7 1.0 SG C:CYS113 2.0 113.1 1.0 SG C:CYS53 2.3 101.5 1.0 SG C:CYS55 2.3 116.3 1.0 CB C:CYS55 2.5 108.2 1.0 ND1 C:HIS115 3.0 118.6 1.0 CB C:CYS113 3.0 126.9 1.0 HB3 C:CYS55 3.1 129.7 1.0 H C:CYS55 3.2 101.8 1.0 CB C:CYS53 3.5 107.0 1.0 HB2 C:CYS53 3.6 128.3 1.0 HB3 C:CYS53 3.6 128.3 1.0 HB2 C:HIS115 3.6 124.3 1.0 CD1 C:ILE118 3.7 140.1 1.0 HB1 C:ALA51 3.7 151.9 1.0 CA C:CYS55 3.8 111.0 1.0 H C:HIS115 3.8 152.1 1.0 HE1 C:HIS115 3.8 163.3 1.0 CE1 C:HIS115 3.8 136.2 1.0 HD2 C:PRO114 3.8 155.0 1.0 N C:CYS55 3.8 84.9 1.0 HG12 C:ILE118 4.0 149.6 1.0 HG A:SER68 4.0 185.9 1.0 CG C:HIS115 4.0 112.7 1.0 CG1 C:ILE118 4.2 124.8 1.0 HG13 C:ILE118 4.2 149.6 1.0 HA C:CYS55 4.3 133.0 1.0 CB C:HIS115 4.3 103.7 1.0 CA C:CYS113 4.4 122.8 1.0 CB C:ALA51 4.5 126.7 1.0 HB2 C:ALA51 4.5 151.9 1.0 HH11 C:ARG135 4.6 104.9 1.0 N C:HIS115 4.6 126.9 1.0 CD C:PRO114 4.6 129.2 1.0 HB3 A:SER68 4.7 181.8 1.0 OG A:SER68 4.7 155.0 1.0 HB3 C:ALA51 4.8 151.9 1.0 C C:CYS113 4.8 127.6 1.0 C C:CYS55 4.8 118.6 1.0 N C:PRO114 4.8 125.7 1.0 CA C:CYS53 4.9 85.7 1.0 HH12 C:ARG135 4.9 104.9 1.0 H C:LYS54 4.9 78.0 1.0 NH1 C:ARG135 5.0 87.6 1.0 H C:GLY116 5.0 156.4 1.0 HD3 C:PRO114 5.0 155.0 1.0 HA C:CYS113 5.0 147.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Ev-D68 2A Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Ev-D68 2A Protease within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:99.5 occ:1.00 ND1 D:HIS115 2.0 102.7 1.0 SG D:CYS53 2.3 148.8 1.0 SG D:CYS113 2.3 74.0 1.0 SG D:CYS55 2.3 94.2 1.0 HB2 D:CYS55 2.6 145.2 1.0 CE1 D:HIS115 2.8 95.1 1.0 HE1 D:HIS115 2.9 114.0 1.0 HB3 D:CYS53 3.0 170.8 1.0 CB D:CYS53 3.0 142.4 1.0 HB2 D:CYS53 3.0 170.8 1.0 CB D:CYS55 3.0 121.1 1.0 HB2 D:HIS115 3.1 101.1 1.0 CG D:HIS115 3.2 91.2 1.0 H D:CYS55 3.3 154.7 1.0 H D:HIS115 3.4 133.8 1.0 CB D:CYS113 3.5 97.9 1.0 HD2 D:PRO114 3.6 167.3 1.0 CB D:HIS115 3.7 84.4 1.0 HB3 D:CYS55 3.7 145.2 1.0 HB1 D:ALA51 3.7 142.5 1.0 N D:CYS55 4.0 129.0 1.0 NE2 D:HIS115 4.0 87.7 1.0 CA D:CYS55 4.1 124.4 1.0 N D:HIS115 4.2 111.6 1.0 CD2 D:HIS115 4.2 91.1 1.0 HB3 D:HIS115 4.4 101.1 1.0 CA D:CYS53 4.5 136.7 1.0 HA D:CYS55 4.5 149.2 1.0 CD D:PRO114 4.5 139.5 1.0 CA D:HIS115 4.6 103.2 1.0 CB D:ALA51 4.6 118.9 1.0 H D:LYS54 4.6 160.4 1.0 HB2 D:ALA51 4.7 142.5 1.0 HE2 D:HIS115 4.8 105.1 1.0 CD1 D:ILE118 4.8 132.6 1.0 N D:PRO114 4.8 144.8 1.0 HH11 D:ARG135 4.8 140.6 1.0 HG12 D:ILE118 4.8 150.7 1.0 CA D:CYS113 4.8 114.8 1.0 H D:GLY116 4.9 143.6 1.0 N D:LYS54 4.9 133.8 1.0 H D:CYS53 4.9 146.1 1.0 C D:CYS113 5.0 127.3 1.0 HD3 D:PRO114 5.0 167.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Ev-D68 2A Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Ev-D68 2A Protease within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:123.0 occ:1.00 ND1 F:HIS115 2.0 111.8 1.0 SG F:CYS53 2.3 139.9 1.0 SG F:CYS113 2.3 81.3 1.0 SG F:CYS55 2.3 139.0 1.0 HB2 F:CYS55 2.6 157.8 1.0 CE1 F:HIS115 2.8 108.9 1.0 HE1 F:HIS115 2.8 130.6 1.0 CB F:CYS55 3.0 131.6 1.0 HB2 F:CYS53 3.0 154.3 1.0 CB F:CYS53 3.0 128.7 1.0 HB3 F:CYS53 3.1 154.3 1.0 CG F:HIS115 3.2 114.3 1.0 HB2 F:HIS115 3.2 129.5 1.0 H F:CYS55 3.3 125.7 1.0 H F:HIS115 3.4 147.2 1.0 CB F:CYS113 3.5 82.1 1.0 HD2 F:PRO114 3.6 135.7 1.0 HB3 F:CYS55 3.7 157.8 1.0 HB1 F:ALA51 3.7 126.9 1.0 CB F:HIS115 3.8 108.0 1.0 N F:CYS55 4.0 104.8 1.0 NE2 F:HIS115 4.0 114.7 1.0 CA F:CYS55 4.1 112.8 1.0 CD2 F:HIS115 4.2 116.7 1.0 N F:HIS115 4.2 122.8 1.0 HA F:CYS55 4.4 135.2 1.0 HB3 F:HIS115 4.5 129.5 1.0 CA F:CYS53 4.5 123.0 1.0 CB F:ALA51 4.5 105.9 1.0 CD F:PRO114 4.5 113.2 1.0 CD1 F:ILE118 4.6 97.6 1.0 H F:LYS54 4.6 135.1 1.0 HB2 F:ALA51 4.6 126.9 1.0 CA F:HIS115 4.6 114.8 1.0 HG12 F:ILE118 4.7 120.4 1.0 HE2 F:HIS115 4.7 137.5 1.0 CA F:CYS113 4.8 90.9 1.0 N F:PRO114 4.8 119.7 1.0 HB3 F:ALA51 4.8 126.9 1.0 N F:LYS54 4.9 112.7 1.0 HH11 F:ARG135 4.9 135.1 1.0 H F:GLY116 4.9 113.5 1.0 C F:CYS113 4.9 108.6 1.0 H F:CYS53 4.9 134.3 1.0 HD3 F:PRO114 5.0 135.7 1.0

C.Liu, M.-Y.Lee, C.Ma, W.Liu, J.Wang. Crystal Structure of Ev-D68 2A Protease To Be Published.