Zinc in PDB 4zx8: X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B

All present enzymatic activity of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B:
3.4.11.1;

The structure of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B, PDB code: 4zx8 was solved by N.Drinkwater, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.95 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	174.393, 177.470, 231.292, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.5

The structure of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B also contains other interesting chemical elements:

Bromine

(Br)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B (pdb code 4zx8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B, PDB code: 4zx8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:22.9 occ:1.00 O4 A:4TY1001 2.0 11.1 0.8 OD2 A:ASP399 2.1 17.5 1.0 NZ A:LYS374 2.2 10.6 1.0 OE2 A:GLU461 2.3 15.8 1.0 OD2 A:ASP379 2.7 14.7 1.0 CG A:ASP399 2.9 10.1 1.0 N2 A:4TY1001 2.9 9.1 0.8 OD1 A:ASP399 3.0 10.9 1.0 CE A:LYS374 3.1 8.6 1.0 ZN A:ZN1003 3.3 19.0 1.0 CD A:GLU461 3.3 12.7 1.0 CG A:ASP379 3.5 10.9 1.0 OE1 A:GLU461 3.7 16.5 1.0 C11 A:4TY1001 3.8 12.9 0.8 O3 A:4TY1001 3.9 12.3 0.8 O1 A:CO31004 4.1 10.8 1.0 CB A:ASP379 4.1 8.6 1.0 O A:THR486 4.3 6.1 1.0 CB A:ASP399 4.4 8.8 1.0 OD1 A:ASP379 4.4 10.7 1.0 CD A:LYS374 4.5 7.8 1.0 CG1 A:ILE376 4.5 9.2 1.0 CG A:GLU461 4.6 11.4 1.0 N A:GLY462 4.7 9.4 1.0 O A:ASP459 4.7 15.5 1.0 CB A:ILE376 4.7 7.5 1.0 CA A:GLY462 4.9 10.0 1.0 CG2 A:ILE376 4.9 11.0 1.0

Zinc binding site 2 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:19.0 occ:1.00 O A:ASP459 2.1 15.5 1.0 OD2 A:ASP379 2.1 14.7 1.0 OD1 A:ASP459 2.1 11.0 1.0 O4 A:4TY1001 2.1 11.1 0.8 O3 A:4TY1001 2.2 12.3 0.8 OE1 A:GLU461 2.3 16.5 1.0 CG A:ASP379 2.9 10.9 1.0 N2 A:4TY1001 2.9 9.1 0.8 C11 A:4TY1001 2.9 12.9 0.8 C A:ASP459 3.0 11.1 1.0 OD1 A:ASP379 3.0 10.7 1.0 CG A:ASP459 3.1 15.6 1.0 CD A:GLU461 3.2 12.7 1.0 ZN A:ZN1002 3.3 22.9 1.0 OE2 A:GLU461 3.3 15.8 1.0 CA A:ASP459 3.4 14.4 1.0 CB A:ASP459 3.8 13.8 1.0 NZ A:LYS386 3.9 11.9 1.0 OD2 A:ASP459 4.0 22.8 1.0 N A:ALA460 4.1 7.4 1.0 CE A:LYS386 4.2 9.7 1.0 N A:GLU461 4.3 5.6 1.0 CB A:ASP379 4.3 8.6 1.0 C5 A:4TY1001 4.4 11.9 0.8 CA A:ALA460 4.6 13.7 1.0 CG A:GLU461 4.6 11.4 1.0 ND2 A:ASN432 4.6 10.7 1.0 CA A:GLY381 4.7 7.8 1.0 O1 A:CO31004 4.7 10.8 1.0 N A:ASP459 4.8 16.5 1.0 N1 A:4TY1001 4.8 15.3 0.8 OD2 A:ASP399 4.8 17.5 1.0 O A:THR458 4.8 7.9 1.0

Zinc binding site 3 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:23.1 occ:1.00 O4 B:4TY1001 2.1 12.3 0.8 OD2 B:ASP399 2.2 12.1 1.0 OE2 B:GLU461 2.2 13.3 1.0 NZ B:LYS374 2.4 10.0 1.0 O B:HOH1162 2.5 11.0 1.0 OD2 B:ASP379 2.6 14.4 1.0 CG B:ASP399 3.0 11.2 1.0 CE B:LYS374 3.1 11.6 1.0 OD1 B:ASP399 3.1 12.7 1.0 ZN B:ZN1003 3.1 17.9 1.0 CD B:GLU461 3.2 9.7 1.0 N2 B:4TY1001 3.2 12.2 0.8 CG B:ASP379 3.4 9.6 1.0 OE1 B:GLU461 3.6 11.9 1.0 CB B:ASP379 4.0 10.7 1.0 C11 B:4TY1001 4.1 13.2 0.8 O3 B:4TY1001 4.1 13.2 0.8 O2 B:CO31004 4.2 10.7 1.0 OD1 B:ASP379 4.2 9.5 1.0 O B:THR486 4.3 11.9 1.0 CB B:ASP399 4.4 8.6 1.0 CG1 B:ILE376 4.5 10.0 1.0 CD B:LYS374 4.5 10.1 1.0 CG B:GLU461 4.5 8.3 1.0 N B:GLY462 4.6 9.9 1.0 CB B:ILE376 4.7 15.5 1.0 O B:ASP459 4.8 14.0 1.0 CA B:GLY462 4.8 10.0 1.0 CG2 B:ILE376 4.8 14.3 1.0

Zinc binding site 4 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:17.9 occ:1.00 O4 B:4TY1001 2.1 12.3 0.8 O B:ASP459 2.1 14.0 1.0 OD2 B:ASP379 2.1 14.4 1.0 OE1 B:GLU461 2.2 11.9 1.0 O3 B:4TY1001 2.3 13.2 0.8 OD1 B:ASP459 2.3 10.8 1.0 N2 B:4TY1001 2.9 12.2 0.8 C11 B:4TY1001 2.9 13.2 0.8 CG B:ASP379 3.0 9.6 1.0 C B:ASP459 3.0 9.8 1.0 CD B:GLU461 3.1 9.7 1.0 OD1 B:ASP379 3.1 9.5 1.0 ZN B:ZN1002 3.1 23.1 1.0 OE2 B:GLU461 3.2 13.3 1.0 CG B:ASP459 3.3 12.3 1.0 CA B:ASP459 3.6 10.0 1.0 O B:HOH1162 3.8 11.0 1.0 NZ B:LYS386 4.0 7.0 1.0 CB B:ASP459 4.0 9.5 1.0 OD2 B:ASP459 4.1 16.9 1.0 N B:ALA460 4.1 8.4 1.0 CE B:LYS386 4.2 11.9 1.0 N B:GLU461 4.3 8.8 1.0 CB B:ASP379 4.4 10.7 1.0 C5 B:4TY1001 4.4 15.3 0.8 CG B:GLU461 4.5 8.3 1.0 CA B:ALA460 4.6 15.1 1.0 O2 B:CO31004 4.6 10.7 1.0 OD2 B:ASP399 4.8 12.1 1.0 ND2 B:ASN432 4.8 7.3 1.0 N1 B:4TY1001 4.8 15.5 0.8 CA B:GLY381 4.9 9.1 1.0 O B:THR458 4.9 10.9 1.0 N B:ASP459 4.9 8.8 1.0 C B:ALA460 4.9 16.0 1.0

Zinc binding site 5 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:24.4 occ:1.00 OD2 C:ASP379 2.0 18.4 1.0 O4 C:4TY1001 2.1 12.8 0.8 O C:ASP459 2.2 10.8 1.0 OE1 C:GLU461 2.2 16.3 1.0 O3 C:4TY1001 2.3 19.5 0.8 OD1 C:ASP459 2.5 9.9 1.0 CG C:ASP379 2.9 11.2 1.0 N2 C:4TY1001 2.9 15.9 0.8 C11 C:4TY1001 2.9 14.0 0.8 ZN C:ZN1003 3.0 25.2 1.0 CD C:GLU461 3.0 12.2 1.0 OE2 C:GLU461 3.0 12.6 1.0 OD1 C:ASP379 3.1 9.9 1.0 C C:ASP459 3.1 9.2 1.0 CG C:ASP459 3.4 15.1 1.0 CA C:ASP459 3.7 7.2 1.0 NZ C:LYS386 4.0 13.1 1.0 CB C:ASP459 4.1 15.3 1.0 CE C:LYS386 4.2 12.8 1.0 N C:ALA460 4.2 10.3 1.0 OD2 C:ASP459 4.2 11.9 1.0 N C:GLU461 4.3 8.8 1.0 CB C:ASP379 4.3 9.9 1.0 C5 C:4TY1001 4.4 14.9 0.8 CG C:GLU461 4.5 11.3 1.0 CA C:ALA460 4.6 9.3 1.0 OD2 C:ASP399 4.6 16.2 1.0 O1 C:CO31004 4.7 11.0 1.0 ND2 C:ASN432 4.8 7.8 1.0 N1 C:4TY1001 4.9 21.4 0.8 NZ C:LYS374 5.0 7.3 1.0 C C:ALA460 5.0 10.4 1.0

Zinc binding site 6 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:25.2 occ:1.00 O4 C:4TY1001 2.0 12.8 0.8 OE2 C:GLU461 2.2 12.6 1.0 OD2 C:ASP399 2.2 16.2 1.0 NZ C:LYS374 2.3 7.3 1.0 OD2 C:ASP379 2.7 18.4 1.0 CG C:ASP399 2.9 12.4 1.0 ZN C:ZN1002 3.0 24.4 1.0 OD1 C:ASP399 3.0 10.1 1.0 N2 C:4TY1001 3.1 15.9 0.8 CE C:LYS374 3.1 7.5 1.0 CD C:GLU461 3.2 12.2 1.0 CG C:ASP379 3.5 11.2 1.0 OE1 C:GLU461 3.6 16.3 1.0 C11 C:4TY1001 3.9 14.0 0.8 O3 C:4TY1001 3.9 19.5 0.8 CB C:ASP379 4.0 9.9 1.0 O1 C:CO31004 4.1 11.0 1.0 OD1 C:ASP379 4.3 9.9 1.0 O C:THR486 4.3 8.8 1.0 CB C:ASP399 4.4 8.8 1.0 CG C:GLU461 4.5 11.3 1.0 CD C:LYS374 4.5 14.6 1.0 N C:GLY462 4.5 8.3 1.0 CG1 C:ILE376 4.5 7.0 1.0 O C:ASP459 4.7 10.8 1.0 CA C:GLY462 4.8 7.5 1.0 CB C:ILE376 4.8 11.0 1.0 CG2 C:ILE376 4.9 9.0 1.0

Zinc binding site 7 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:29.4 occ:1.00 OD2 D:ASP379 2.1 17.7 1.0 O D:ASP459 2.1 18.2 1.0 O3 D:4TY1001 2.2 15.3 0.8 O4 D:4TY1001 2.2 16.4 0.8 OE1 D:GLU461 2.3 15.3 1.0 OD1 D:ASP459 2.3 19.0 1.0 CG D:ASP379 2.9 14.0 1.0 C11 D:4TY1001 3.0 15.8 0.8 N2 D:4TY1001 3.0 13.6 0.8 OD1 D:ASP379 3.0 17.6 1.0 C D:ASP459 3.1 10.6 1.0 CD D:GLU461 3.1 12.2 1.0 ZN D:ZN1003 3.2 26.7 1.0 OE2 D:GLU461 3.2 12.4 1.0 CG D:ASP459 3.3 15.4 1.0 CA D:ASP459 3.6 9.9 1.0 NZ D:LYS386 3.9 13.5 1.0 CB D:ASP459 4.0 10.7 1.0 OD2 D:ASP459 4.1 18.3 1.0 CE D:LYS386 4.2 8.2 1.0 N D:ALA460 4.2 7.5 1.0 CB D:ASP379 4.3 10.0 1.0 N D:GLU461 4.3 9.1 1.0 C5 D:4TY1001 4.4 14.8 0.8 CG D:GLU461 4.6 9.6 1.0 ND2 D:ASN432 4.6 9.7 1.0 CA D:ALA460 4.6 9.6 1.0 O3 D:CO31004 4.6 12.4 1.0 OD2 D:ASP399 4.7 19.4 1.0 N1 D:4TY1001 4.8 15.5 0.8 CA D:GLY381 4.8 11.7 1.0 N D:ASP459 4.9 12.3 1.0

Zinc binding site 8 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1003 b:26.7 occ:1.00 OD2 D:ASP399 2.0 19.4 1.0 O4 D:4TY1001 2.0 16.4 0.8 OE2 D:GLU461 2.3 12.4 1.0 NZ D:LYS374 2.4 7.3 1.0 OD2 D:ASP379 2.7 17.7 1.0 CG D:ASP399 2.8 17.3 1.0 OD1 D:ASP399 2.9 15.2 1.0 N2 D:4TY1001 3.0 13.6 0.8 CE D:LYS374 3.0 7.0 1.0 ZN D:ZN1002 3.2 29.4 1.0 CD D:GLU461 3.3 12.2 1.0 CG D:ASP379 3.4 14.0 1.0 OE1 D:GLU461 3.7 15.3 1.0 C11 D:4TY1001 3.8 15.8 0.8 O3 D:4TY1001 3.9 15.3 0.8 CB D:ASP379 4.0 10.0 1.0 CB D:ASP399 4.2 5.7 1.0 O3 D:CO31004 4.2 12.4 1.0 OD1 D:ASP379 4.3 17.6 1.0 O D:THR486 4.3 11.1 1.0 CG1 D:ILE376 4.4 9.5 1.0 CD D:LYS374 4.4 8.1 1.0 CG D:GLU461 4.6 9.6 1.0 CB D:ILE376 4.7 9.1 1.0 N D:GLY462 4.8 8.6 1.0 O D:ASP459 4.8 18.2 1.0 CG2 D:ILE376 4.9 9.7 1.0 CA D:GLY462 5.0 7.5 1.0

Zinc binding site 9 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1002 b:23.3 occ:1.00 OD2 E:ASP399 2.2 20.1 1.0 O4 E:4TY1001 2.2 11.2 0.8 NZ E:LYS374 2.3 12.3 1.0 OE2 E:GLU461 2.3 15.8 1.0 OD2 E:ASP379 2.7 16.7 1.0 CG E:ASP399 2.9 22.8 1.0 OD1 E:ASP399 2.9 19.6 1.0 N2 E:4TY1001 3.1 14.8 0.8 CE E:LYS374 3.1 9.4 1.0 ZN E:ZN1003 3.2 25.3 1.0 CD E:GLU461 3.4 16.8 1.0 CG E:ASP379 3.5 13.2 1.0 C11 E:4TY1001 3.7 15.3 0.8 O3 E:4TY1001 3.7 14.4 0.8 OE1 E:GLU461 3.8 22.6 1.0 CB E:ASP379 4.0 13.3 1.0 O E:THR486 4.2 10.3 1.0 O1 E:CO31004 4.3 11.2 1.0 CB E:ASP399 4.3 15.1 1.0 OD1 E:ASP379 4.4 10.4 1.0 CD E:LYS374 4.5 13.0 1.0 CG1 E:ILE376 4.6 8.6 1.0 N E:GLY462 4.6 12.7 1.0 CG E:GLU461 4.7 12.6 1.0 O E:ASP459 4.7 16.7 1.0 C3 E:4TY1001 4.8 12.8 0.8 CA E:GLY462 4.8 16.9 1.0 CB E:ILE376 4.9 12.3 1.0 C5 E:4TY1001 5.0 11.9 0.8

Zinc binding site 10 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1003 b:25.3 occ:1.00 O E:ASP459 2.0 16.7 1.0 O4 E:4TY1001 2.1 11.2 0.8 OD2 E:ASP379 2.1 16.7 1.0 O3 E:4TY1001 2.2 14.4 0.8 OE1 E:GLU461 2.3 22.6 1.0 OD1 E:ASP459 2.3 10.5 1.0 N2 E:4TY1001 2.8 14.8 0.8 C11 E:4TY1001 2.8 15.3 0.8 CG E:ASP379 3.0 13.2 1.0 C E:ASP459 3.0 11.8 1.0 CD E:GLU461 3.1 16.8 1.0 ZN E:ZN1002 3.2 23.3 1.0 OE2 E:GLU461 3.2 15.8 1.0 OD1 E:ASP379 3.2 10.4 1.0 CG E:ASP459 3.2 13.3 1.0 CA E:ASP459 3.5 10.9 1.0 NZ E:LYS386 3.9 14.2 1.0 CB E:ASP459 3.9 7.8 1.0 OD2 E:ASP459 4.1 9.6 1.0 N E:ALA460 4.1 10.4 1.0 N E:GLU461 4.2 10.8 1.0 CE E:LYS386 4.3 10.3 1.0 C5 E:4TY1001 4.3 11.9 0.8 CB E:ASP379 4.4 13.3 1.0 CA E:ALA460 4.5 14.1 1.0 ND2 E:ASN432 4.5 8.6 1.0 CG E:GLU461 4.5 12.6 1.0 N1 E:4TY1001 4.7 18.2 0.8 OD2 E:ASP399 4.8 20.1 1.0 CA E:GLY381 4.9 8.9 1.0 N E:ASP459 4.9 11.6 1.0 C E:ALA460 4.9 13.9 1.0 O1 E:CO31004 4.9 11.2 1.0 O E:THR458 4.9 10.9 1.0

N.Drinkwater, N.B.Vinh, S.N.Mistry, R.S.Bamert, C.Ruggeri, J.P.Holleran, S.Loganathan, A.Paiardini, S.A.Charman, A.K.Powell, V.M.Avery, S.Mcgowan, P.J.Scammells. Potent Dual Inhibitors of Plasmodium Falciparum M1 and M17 Aminopeptidases Through Optimization of S1 Pocket Interactions. Eur.J.Med.Chem. V. 110 43 2016.
ISSN: ISSN 0223-5234
PubMed: 26807544
DOI: 10.1016/J.EJMECH.2016.01.015