Zinc in PDB 4r7m: Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor

The structure of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor, PDB code: 4r7m 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)	36.01 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	172.560, 175.590, 225.480, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 29.1

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 Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor (pdb code 4r7m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor, PDB code: 4r7m:
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 Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:27.1 occ:1.00 OD2 A:ASP399 1.9 41.8 1.0 OE2 A:GLU461 2.1 9.7 1.0 O17 A:3MW1006 2.2 14.7 1.0 NZ A:LYS374 2.4 7.7 1.0 OD2 A:ASP379 2.5 18.9 1.0 O15 A:3MW1006 2.5 36.8 1.0 CG A:ASP399 2.8 29.7 1.0 OD1 A:ASP399 3.1 25.6 1.0 N16 A:3MW1006 3.1 20.1 1.0 C14 A:3MW1006 3.2 29.9 1.0 CD A:GLU461 3.2 9.8 1.0 CE A:LYS374 3.2 7.6 1.0 CG A:ASP379 3.2 17.2 1.0 ZN A:ZN1003 3.3 31.2 1.0 OE1 A:GLU461 3.6 9.9 1.0 CB A:ASP379 3.7 17.7 1.0 OD1 A:ASP379 4.1 21.0 1.0 CB A:ASP399 4.2 21.3 1.0 O2 A:CO31002 4.3 7.8 1.0 CG A:GLU461 4.5 17.7 1.0 O A:THR486 4.6 11.9 1.0 O A:ASP459 4.6 25.3 1.0 N A:GLY462 4.6 7.6 1.0 CD A:LYS374 4.6 7.4 1.0 C12 A:3MW1006 4.7 25.2 1.0 CB A:ILE376 4.9 21.1 1.0 CG1 A:ILE376 4.9 25.1 1.0 CA A:GLY462 4.9 7.4 1.0 CG2 A:ILE376 5.0 18.6 1.0

Zinc binding site 2 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:31.2 occ:1.00 O A:ASP459 2.0 25.3 1.0 OD2 A:ASP379 2.0 18.9 1.0 O17 A:3MW1006 2.1 14.7 1.0 OD1 A:ASP459 2.1 12.3 1.0 N16 A:3MW1006 2.4 20.1 1.0 OE1 A:GLU461 2.7 9.9 1.0 CG A:ASP379 2.9 17.2 1.0 C A:ASP459 3.0 14.4 1.0 C14 A:3MW1006 3.0 29.9 1.0 CG A:ASP459 3.1 14.5 1.0 OD1 A:ASP379 3.2 21.0 1.0 ZN A:ZN1001 3.3 27.1 1.0 O15 A:3MW1006 3.3 36.8 1.0 CA A:ASP459 3.4 12.2 1.0 CD A:GLU461 3.5 9.8 1.0 OE2 A:GLU461 3.6 9.7 1.0 NZ A:LYS386 3.6 10.0 1.0 CB A:ASP459 3.8 16.3 1.0 CE A:LYS386 3.8 10.0 1.0 OD2 A:ASP459 3.9 14.7 1.0 N13 A:3MW1006 4.1 22.7 1.0 C12 A:3MW1006 4.2 25.2 1.0 N A:ALA460 4.2 19.6 1.0 CB A:ASP379 4.3 17.7 1.0 N A:GLU461 4.5 9.8 1.0 CA A:GLY381 4.6 18.7 1.0 CA A:ALA460 4.6 18.3 1.0 N A:ASP459 4.8 12.2 1.0 OD2 A:ASP399 4.9 41.8 1.0 C03 A:3MW1006 4.9 22.5 1.0 CG A:GLU461 4.9 17.7 1.0 O A:THR458 5.0 26.3 1.0

Zinc binding site 3 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:15.9 occ:1.00 O17 B:3MW1005 2.0 32.2 1.0 OE2 B:GLU461 2.0 13.7 1.0 OD2 B:ASP399 2.1 15.7 1.0 NZ B:LYS374 2.4 17.8 1.0 OD2 B:ASP379 2.9 20.1 1.0 CG B:ASP399 3.0 11.6 1.0 ZN B:ZN1003 3.0 34.5 1.0 CE B:LYS374 3.0 17.3 1.0 N16 B:3MW1005 3.0 33.0 1.0 CD B:GLU461 3.0 17.4 1.0 OD1 B:ASP399 3.2 10.3 1.0 O15 B:3MW1005 3.2 33.4 1.0 O B:HOH1111 3.3 10.4 1.0 OE1 B:GLU461 3.4 14.3 1.0 C14 B:3MW1005 3.5 31.9 1.0 CG B:ASP379 3.5 19.1 1.0 O2 B:CO31002 3.9 11.4 1.0 CB B:ASP379 4.1 22.0 1.0 OD1 B:ASP379 4.2 19.1 1.0 CG B:GLU461 4.4 17.8 1.0 CB B:ASP399 4.4 9.9 1.0 O B:THR486 4.4 10.9 1.0 CD B:LYS374 4.5 17.3 1.0 O B:ASP459 4.5 12.7 1.0 N B:GLY462 4.5 20.3 1.0 CG1 B:ILE376 4.5 10.2 1.0 CB B:ILE376 4.8 10.0 1.0 CA B:GLY462 4.8 19.2 1.0 C12 B:3MW1005 4.9 30.7 1.0 CG2 B:ILE376 5.0 9.9 1.0

Zinc binding site 4 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:34.5 occ:1.00 O B:ASP459 2.0 12.7 1.0 O17 B:3MW1005 2.1 32.2 1.0 OE1 B:GLU461 2.2 14.3 1.0 OD1 B:ASP459 2.3 10.5 1.0 OD2 B:ASP379 2.3 20.1 1.0 O15 B:3MW1005 2.5 33.4 1.0 N16 B:3MW1005 2.8 33.0 1.0 C14 B:3MW1005 2.9 31.9 1.0 C B:ASP459 2.9 11.2 1.0 ZN B:ZN1001 3.0 15.9 1.0 CG B:ASP379 3.0 19.1 1.0 CD B:GLU461 3.1 17.4 1.0 OD1 B:ASP379 3.1 19.1 1.0 OE2 B:GLU461 3.3 13.7 1.0 CG B:ASP459 3.3 10.7 1.0 CA B:ASP459 3.5 10.7 1.0 CB B:ASP459 3.9 10.8 1.0 N B:ALA460 4.1 15.1 1.0 N B:GLU461 4.2 17.9 1.0 OD2 B:ASP459 4.2 10.7 1.0 NZ B:LYS386 4.2 10.5 1.0 O B:HOH1111 4.2 10.4 1.0 C12 B:3MW1005 4.3 30.7 1.0 CE B:LYS386 4.4 10.3 1.0 CB B:ASP379 4.4 22.0 1.0 CA B:ALA460 4.5 12.2 1.0 N13 B:3MW1005 4.5 22.9 1.0 CG B:GLU461 4.5 17.8 1.0 O2 B:CO31002 4.6 11.4 1.0 OD2 B:ASP399 4.6 15.7 1.0 ND2 B:ASN432 4.7 27.9 1.0 N B:ASP459 4.8 10.7 1.0 CA B:GLY381 4.8 10.1 1.0 NZ B:LYS374 4.9 17.8 1.0 C B:ALA460 4.9 16.9 1.0 O B:THR458 4.9 12.9 1.0 CB B:GLU461 4.9 15.7 1.0

Zinc binding site 5 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:18.4 occ:1.00 O17 C:3MW1007 2.0 13.5 1.0 OD2 C:ASP399 2.0 14.5 1.0 OE2 C:GLU461 2.1 17.8 1.0 NZ C:LYS374 2.1 21.7 1.0 OD2 C:ASP379 2.7 19.5 1.0 CG C:ASP399 2.9 12.7 1.0 N16 C:3MW1007 3.0 13.9 1.0 CE C:LYS374 3.0 22.2 1.0 OD1 C:ASP399 3.2 12.9 1.0 CD C:GLU461 3.3 24.9 1.0 ZN C:ZN1003 3.3 33.6 1.0 CG C:ASP379 3.4 16.6 1.0 O15 C:3MW1007 3.6 24.0 1.0 C14 C:3MW1007 3.6 11.1 1.0 CB C:ASP379 3.8 15.4 1.0 OE1 C:GLU461 3.9 30.0 1.0 O1 C:CO31002 4.1 11.0 1.0 OD1 C:ASP379 4.2 19.0 1.0 O C:THR486 4.3 12.4 1.0 CB C:ASP399 4.3 12.8 1.0 CD C:LYS374 4.4 30.1 1.0 CG C:GLU461 4.4 26.3 1.0 N C:GLY462 4.5 17.4 1.0 CG1 C:ILE376 4.5 14.3 1.0 CA C:GLY462 4.7 13.3 1.0 CB C:ILE376 4.7 18.9 1.0 O C:ASP459 4.8 26.3 1.0 CG2 C:ILE376 4.8 25.4 1.0 C12 C:3MW1007 4.9 11.3 1.0

Zinc binding site 6 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:33.6 occ:1.00 OD2 C:ASP379 2.0 19.5 1.0 O C:ASP459 2.0 26.3 1.0 OD1 C:ASP459 2.2 40.0 1.0 O15 C:3MW1007 2.2 24.0 1.0 O17 C:3MW1007 2.3 13.5 1.0 OE1 C:GLU461 2.5 30.0 1.0 C14 C:3MW1007 2.8 11.1 1.0 CG C:ASP379 2.8 16.6 1.0 N16 C:3MW1007 2.9 13.9 1.0 OD1 C:ASP379 3.0 19.0 1.0 C C:ASP459 3.0 26.0 1.0 OE2 C:GLU461 3.0 17.8 1.0 CD C:GLU461 3.1 24.9 1.0 CG C:ASP459 3.2 40.4 1.0 ZN C:ZN1001 3.3 18.4 1.0 CA C:ASP459 3.5 28.7 1.0 NZ C:LYS386 3.9 19.4 1.0 CB C:ASP459 3.9 36.5 1.0 OD2 C:ASP459 4.0 41.2 1.0 CE C:LYS386 4.1 22.9 1.0 N C:ALA460 4.2 25.2 1.0 C12 C:3MW1007 4.2 11.3 1.0 CB C:ASP379 4.3 15.4 1.0 N C:GLU461 4.4 25.2 1.0 N13 C:3MW1007 4.5 12.3 1.0 ND2 C:ASN432 4.5 18.3 1.0 CA C:ALA460 4.6 24.8 1.0 CG C:GLU461 4.6 26.3 1.0 CA C:GLY381 4.6 10.2 1.0 O1 C:CO31002 4.7 11.0 1.0 C03 C:3MW1007 4.9 13.2 1.0 N C:ASP459 4.9 24.1 1.0 OD2 C:ASP399 4.9 14.5 1.0

Zinc binding site 7 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:31.1 occ:1.00 O17 D:3MW1004 1.9 15.7 1.0 OD2 D:ASP399 2.0 32.8 1.0 OE2 D:GLU461 2.1 23.9 1.0 NZ D:LYS374 2.2 18.4 1.0 CE D:LYS374 2.8 19.9 1.0 CG D:ASP399 2.8 29.9 1.0 N16 D:3MW1004 3.0 17.4 1.0 OD2 D:ASP379 3.0 24.0 1.0 OD1 D:ASP399 3.0 31.9 1.0 CD D:GLU461 3.2 29.2 1.0 ZN D:ZN1003 3.3 41.9 1.0 CG D:ASP379 3.6 22.2 1.0 OE1 D:GLU461 3.8 42.9 1.0 CB D:ASP379 4.0 20.1 1.0 C14 D:3MW1004 4.0 14.6 1.0 CG1 D:ILE376 4.1 15.4 1.0 CB D:ASP399 4.2 26.0 1.0 O1 D:CO31002 4.2 15.0 1.0 CD D:LYS374 4.2 18.1 1.0 O15 D:3MW1004 4.3 14.3 1.0 CB D:ILE376 4.4 15.2 1.0 OD1 D:ASP379 4.4 22.9 1.0 O D:THR486 4.4 14.5 1.0 CG D:GLU461 4.4 21.6 1.0 N D:GLY462 4.5 30.4 1.0 CG2 D:ILE376 4.6 15.1 1.0 CA D:GLY462 4.7 29.5 1.0 O D:ASP459 4.9 14.7 1.0

Zinc binding site 8 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1003 b:41.9 occ:1.00 O17 D:3MW1004 1.9 15.7 1.0 O D:ASP459 2.0 14.7 1.0 O15 D:3MW1004 2.1 14.3 1.0 OD2 D:ASP379 2.2 24.0 1.0 OE1 D:GLU461 2.4 42.9 1.0 OD1 D:ASP459 2.5 14.3 1.0 C14 D:3MW1004 2.6 14.6 1.0 N16 D:3MW1004 2.6 17.4 1.0 C D:ASP459 3.0 14.8 1.0 CG D:ASP379 3.1 22.2 1.0 OE2 D:GLU461 3.1 23.9 1.0 CD D:GLU461 3.1 29.2 1.0 ZN D:ZN1001 3.3 31.1 1.0 OD1 D:ASP379 3.3 22.9 1.0 CG D:ASP459 3.4 14.2 1.0 CA D:ASP459 3.7 16.4 1.0 NZ D:LYS386 3.8 13.9 1.0 CB D:ASP459 4.1 15.1 1.0 C12 D:3MW1004 4.1 17.8 1.0 N D:ALA460 4.1 15.0 1.0 CE D:LYS386 4.2 13.9 1.0 N D:GLU461 4.2 25.4 1.0 OD2 D:ASP459 4.2 14.0 1.0 CB D:ASP379 4.5 20.1 1.0 N13 D:3MW1004 4.5 23.2 1.0 CA D:ALA460 4.5 15.1 1.0 CG D:GLU461 4.6 21.6 1.0 O1 D:CO31002 4.6 15.0 1.0 OD2 D:ASP399 4.7 32.8 1.0 ND2 D:ASN432 4.8 24.7 1.0 NZ D:LYS374 4.8 18.4 1.0 C03 D:3MW1004 4.8 16.3 1.0 C D:ALA460 4.9 15.3 1.0 CA D:GLY381 5.0 29.6 1.0

Zinc binding site 9 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:15.3 occ:1.00 O17 E:3MW1007 2.0 53.4 1.0 OD2 E:ASP399 2.0 25.1 1.0 OE2 E:GLU461 2.1 29.6 1.0 NZ E:LYS374 2.2 38.9 1.0 CG E:ASP399 2.8 21.5 1.0 N16 E:3MW1007 2.8 44.5 1.0 OD1 E:ASP399 2.9 21.4 1.0 O15 E:3MW1007 3.0 14.8 1.0 OD2 E:ASP379 3.0 26.4 1.0 CE E:LYS374 3.0 30.6 1.0 C14 E:3MW1007 3.2 28.0 1.0 CD E:GLU461 3.3 27.8 1.0 ZN E:ZN1003 3.4 37.0 1.0 CG E:ASP379 3.7 23.3 1.0 OE1 E:GLU461 3.8 29.8 1.0 O E:THR486 4.0 15.4 1.0 CB E:ASP379 4.0 24.0 1.0 CB E:ASP399 4.2 21.7 1.0 CD E:LYS374 4.4 23.2 1.0 CG E:GLU461 4.5 22.5 1.0 CG1 E:ILE376 4.6 25.9 1.0 C12 E:3MW1007 4.6 19.0 1.0 OD1 E:ASP379 4.7 24.4 1.0 N E:GLY462 4.7 23.7 1.0 O3 E:CO31002 4.7 25.9 1.0 CB E:ILE376 4.8 28.1 1.0 OG1 E:THR486 4.8 15.8 1.0 O E:ASP459 4.9 31.3 1.0 CA E:GLY462 4.9 24.5 1.0 CG2 E:ILE376 4.9 26.8 1.0

Zinc binding site 10 out of 24 in the Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the M17 Leucyl Aminopeptidase From Malaria Complexed with A Hydroxamic Acid-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1003 b:37.0 occ:1.00 O E:ASP459 2.0 31.3 1.0 OD2 E:ASP379 2.0 26.4 1.0 OE1 E:GLU461 2.2 29.8 1.0 OD1 E:ASP459 2.3 24.5 1.0 O15 E:3MW1007 2.3 14.8 1.0 O17 E:3MW1007 2.6 53.4 1.0 C14 E:3MW1007 2.9 28.0 1.0 C E:ASP459 3.0 29.6 1.0 CG E:ASP379 3.0 23.3 1.0 CD E:GLU461 3.0 27.8 1.0 N16 E:3MW1007 3.1 44.5 1.0 OE2 E:GLU461 3.2 29.6 1.0 CG E:ASP459 3.3 24.1 1.0 ZN E:ZN1001 3.4 15.3 1.0 OD1 E:ASP379 3.4 24.4 1.0 CA E:ASP459 3.5 21.7 1.0 CB E:ASP459 3.9 23.0 1.0 NZ E:LYS386 4.0 14.4 1.0 CE E:LYS386 4.1 15.2 1.0 N E:ALA460 4.1 14.4 1.0 OD2 E:ASP459 4.1 21.0 1.0 C12 E:3MW1007 4.2 19.0 1.0 N E:GLU461 4.2 23.9 1.0 N13 E:3MW1007 4.3 14.3 1.0 CB E:ASP379 4.4 24.0 1.0 CG E:GLU461 4.5 22.5 1.0 CA E:ALA460 4.6 14.5 1.0 ND2 E:ASN432 4.8 15.1 1.0 CA E:GLY381 4.8 14.6 1.0 OD2 E:ASP399 4.8 25.1 1.0 N E:ASP459 4.9 22.1 1.0 C E:ALA460 4.9 14.7 1.0 CB E:GLU461 5.0 22.8 1.0 O E:THR458 5.0 29.4 1.0 NZ E:LYS374 5.0 38.9 1.0

S.N.Mistry, N.Drinkwater, C.Ruggeri, K.Kannan Sivaraman, S.Loganathan, S.Fletcher, M.Drag, A.Paiardini, V.M.Avery, P.J.Scammells, S.Mcgowan. A Two-Pronged Attack: Dual Inhibition of Plasmodium Falciparum M1 and M17 Metalloaminopeptidases By A Novel Series of Hydroxamic Acid-Based Inhibitors. J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
PubMed: 25299353
DOI: 10.1021/JM501323A