Zinc in PDB 4x2t: X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum

The structure of X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum, PDB code: 4x2t 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)	48.75 / 2.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	173.715, 176.698, 223.977, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.4

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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum (pdb code 4x2t). 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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum, PDB code: 4x2t:
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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:19.7 occ:1.00 O1 A:TOD703 2.0 36.7 1.0 OD2 A:ASP379 2.1 42.1 1.0 O A:ASP459 2.1 34.8 1.0 OE2 A:GLU461 2.2 20.2 1.0 OD1 A:ASP459 2.2 19.4 1.0 O2 A:TOD703 2.5 34.6 1.0 CG A:ASP379 2.9 37.9 1.0 C7 A:TOD703 2.9 45.5 1.0 OD1 A:ASP379 3.0 47.6 1.0 C A:ASP459 3.1 26.6 1.0 CD A:GLU461 3.1 20.4 1.0 N1 A:TOD703 3.2 47.1 1.0 CG A:ASP459 3.2 39.7 1.0 OE1 A:GLU461 3.3 20.4 1.0 ZN A:ZN702 3.3 27.9 1.0 CA A:ASP459 3.5 19.6 1.0 CB A:ASP459 3.9 21.5 1.0 NZ A:LYS386 3.9 32.3 1.0 CE A:LYS386 4.1 19.1 1.0 OD2 A:ASP459 4.1 39.3 1.0 N A:ALA460 4.2 24.4 1.0 N A:GLU461 4.3 20.4 1.0 CB A:ASP379 4.3 27.5 1.0 C6 A:TOD703 4.3 43.6 1.0 CG A:GLU461 4.5 20.7 1.0 CA A:ALA460 4.6 29.9 1.0 O3 A:TOD703 4.7 42.1 1.0 OD2 A:ASP399 4.8 20.2 1.0 CA A:GLY381 4.8 25.4 1.0 C5 A:TOD703 4.8 49.3 1.0 ND2 A:ASN432 4.8 20.3 1.0 O2 A:CO3704 4.9 20.2 1.0 C4 A:TOD703 4.9 25.8 1.0 CB A:GLU461 4.9 24.1 1.0 N A:ASP459 4.9 19.7 1.0 C A:ALA460 5.0 20.3 1.0

Zinc binding site 2 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:27.9 occ:1.00 OE1 A:GLU461 2.0 20.4 1.0 O2 A:TOD703 2.0 34.6 1.0 OD2 A:ASP399 2.1 20.2 1.0 NZ A:LYS374 2.2 20.3 1.0 OD2 A:ASP379 2.3 42.1 1.0 CG A:ASP399 2.9 20.2 1.0 CE A:LYS374 3.0 20.6 1.0 OD1 A:ASP399 3.0 20.0 1.0 N1 A:TOD703 3.1 47.1 1.0 CD A:GLU461 3.1 20.4 1.0 ZN A:ZN701 3.3 19.7 1.0 CG A:ASP379 3.3 37.9 1.0 OE2 A:GLU461 3.5 20.2 1.0 C7 A:TOD703 3.9 45.5 1.0 CB A:ASP379 3.9 27.5 1.0 O1 A:TOD703 4.0 36.7 1.0 O A:THR486 4.1 20.0 1.0 OD1 A:ASP379 4.3 47.6 1.0 CB A:ASP399 4.3 33.0 1.0 O2 A:CO3704 4.4 20.2 1.0 CG A:GLU461 4.4 20.7 1.0 CD A:LYS374 4.4 23.6 1.0 CG1 A:ILE376 4.6 21.1 1.0 N A:GLY462 4.7 20.8 1.0 O A:ASP459 4.8 34.8 1.0 CB A:ILE376 4.8 20.9 1.0 CA A:GLY462 4.9 20.9 1.0 CG2 A:ILE376 5.0 20.8 1.0

Zinc binding site 3 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:19.0 occ:1.00 O1 B:TOD1004 1.9 50.8 1.0 O B:ASP459 2.0 18.9 1.0 OE1 B:GLU461 2.0 30.2 1.0 OD1 B:ASP459 2.1 39.4 1.0 OD1 B:ASP379 2.1 19.2 1.0 CG B:ASP379 2.8 19.3 1.0 OD2 B:ASP379 2.8 19.3 1.0 C B:ASP459 2.9 18.9 1.0 C7 B:TOD1004 3.0 46.3 1.0 CD B:GLU461 3.0 29.9 1.0 CG B:ASP459 3.1 39.1 1.0 ZN B:ZN1003 3.1 29.8 1.0 O2 B:TOD1004 3.2 30.7 1.0 OE2 B:GLU461 3.3 35.1 1.0 CA B:ASP459 3.3 32.1 1.0 N1 B:TOD1004 3.6 39.9 1.0 CB B:ASP459 3.7 18.8 1.0 OD2 B:ASP459 4.0 52.5 1.0 N B:ALA460 4.1 25.8 1.0 O3 B:TOD1004 4.1 37.7 1.0 N B:GLU461 4.2 19.3 1.0 NZ B:LYS386 4.2 18.6 1.0 C6 B:TOD1004 4.2 43.9 1.0 CB B:ASP379 4.2 19.4 1.0 CG B:GLU461 4.4 30.3 1.0 CE B:LYS386 4.5 18.7 1.0 CA B:ALA460 4.5 19.0 1.0 ND2 B:ASN432 4.6 19.7 1.0 O2 B:CO31001 4.7 29.7 1.0 OD2 B:ASP399 4.7 19.4 1.0 C4 B:TOD1004 4.7 36.1 1.0 CA B:GLY381 4.7 19.1 1.0 N B:ASP459 4.7 19.0 1.0 C5 B:TOD1004 4.8 45.4 1.0 CB B:GLU461 4.8 19.7 1.0 O B:THR458 4.8 19.4 1.0 C B:ALA460 4.9 22.1 1.0

Zinc binding site 4 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:29.8 occ:1.00 OE2 B:GLU461 2.1 35.1 1.0 OD2 B:ASP399 2.1 19.4 1.0 OD1 B:ASP379 2.3 19.2 1.0 NZ B:LYS374 2.3 24.0 1.0 O2 B:TOD1004 2.3 30.7 1.0 CD B:GLU461 3.0 29.9 1.0 CG B:ASP399 3.0 19.4 1.0 O1 B:TOD1004 3.1 50.8 1.0 CE B:LYS374 3.1 19.5 1.0 ZN B:ZN1002 3.1 19.0 1.0 OD1 B:ASP399 3.2 21.0 1.0 OE1 B:GLU461 3.3 30.2 1.0 CG B:ASP379 3.3 19.3 1.0 N1 B:TOD1004 3.4 39.9 1.0 C7 B:TOD1004 3.6 46.3 1.0 O2 B:CO31001 4.0 29.7 1.0 CB B:ASP379 4.0 19.4 1.0 O B:THR486 4.2 43.2 1.0 OD2 B:ASP379 4.2 19.3 1.0 CG B:GLU461 4.4 30.3 1.0 CB B:ASP399 4.4 19.5 1.0 O B:ASP459 4.4 18.9 1.0 CD B:LYS374 4.5 30.4 1.0 N B:GLY462 4.7 19.6 1.0 CG1 B:ILE376 4.8 30.5 1.0 O B:LEU487 4.9 23.6 1.0 CB B:ILE376 5.0 27.1 1.0 OD1 B:ASP459 5.0 39.4 1.0

Zinc binding site 5 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:23.8 occ:1.00 OE2 C:GLU461 2.0 26.4 1.0 NZ C:LYS374 2.1 42.5 1.0 OD1 C:ASP399 2.1 29.8 1.0 O2 C:TOD703 2.2 20.7 1.0 OD2 C:ASP379 2.4 29.5 1.0 CG C:ASP399 2.8 32.1 1.0 OD2 C:ASP399 2.8 26.4 1.0 CE C:LYS374 2.9 41.7 1.0 CD C:GLU461 3.1 19.4 1.0 N1 C:TOD703 3.2 23.9 1.0 CG C:ASP379 3.4 26.5 1.0 OE1 C:GLU461 3.4 20.4 1.0 ZN C:ZN702 3.4 27.0 1.0 CB C:ASP379 3.9 29.8 1.0 O2 C:CO3704 3.9 27.8 1.0 O C:THR486 4.1 22.9 1.0 C7 C:TOD703 4.1 37.4 1.0 O1 C:TOD703 4.2 39.8 1.0 CB C:ASP399 4.3 29.1 1.0 CD C:LYS374 4.3 44.1 1.0 OD1 C:ASP379 4.4 19.2 1.0 CG C:GLU461 4.4 19.6 1.0 CG1 C:ILE376 4.6 19.9 1.0 N C:GLY462 4.7 19.4 1.0 O C:ASP459 4.8 18.8 1.0 CB C:ILE376 4.8 22.9 1.0 CA C:GLY462 4.9 19.4 1.0

Zinc binding site 6 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:27.0 occ:1.00 OD1 C:ASP459 1.9 35.2 1.0 O C:ASP459 2.0 18.8 1.0 O1 C:TOD703 2.1 39.8 1.0 O2 C:TOD703 2.1 20.7 1.0 OD2 C:ASP379 2.2 29.5 1.0 OE1 C:GLU461 2.2 20.4 1.0 C7 C:TOD703 2.8 37.4 1.0 CG C:ASP459 2.9 33.6 1.0 C C:ASP459 2.9 18.8 1.0 N1 C:TOD703 2.9 23.9 1.0 CG C:ASP379 3.0 26.5 1.0 OD1 C:ASP379 3.1 19.2 1.0 CD C:GLU461 3.2 19.4 1.0 CA C:ASP459 3.3 31.1 1.0 ZN C:ZN701 3.4 23.8 1.0 OE2 C:GLU461 3.5 26.4 1.0 CB C:ASP459 3.6 32.1 1.0 OD2 C:ASP459 3.7 28.8 1.0 NZ C:LYS386 3.9 32.7 1.0 N C:ALA460 4.1 18.8 1.0 CE C:LYS386 4.1 32.5 1.0 N C:GLU461 4.3 19.2 1.0 C6 C:TOD703 4.3 37.7 1.0 O2 C:CO3704 4.3 27.8 1.0 CB C:ASP379 4.4 29.8 1.0 CG C:GLU461 4.5 19.6 1.0 CA C:ALA460 4.6 25.2 1.0 N C:ASP459 4.7 27.0 1.0 CA C:GLY381 4.7 21.1 1.0 ND2 C:ASN432 4.8 27.7 1.0 OD1 C:ASP399 4.8 29.8 1.0 O C:THR458 4.9 19.3 1.0 CB C:GLU461 4.9 25.5 1.0 C5 C:TOD703 5.0 32.7 1.0 O3 C:TOD703 5.0 46.3 1.0 C C:ALA460 5.0 23.2 1.0

Zinc binding site 7 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:26.9 occ:1.00 O D:ASP459 2.0 14.9 1.0 OD2 D:ASP379 2.1 32.8 1.0 OD1 D:ASP459 2.1 27.1 1.0 OE1 D:GLU461 2.1 22.7 1.0 CG D:ASP379 3.0 31.4 1.0 ZN D:ZN702 3.0 23.9 1.0 C D:ASP459 3.0 14.8 1.0 CG D:ASP459 3.1 28.0 1.0 CD D:GLU461 3.1 16.0 1.0 OD1 D:ASP379 3.2 36.5 1.0 OE2 D:GLU461 3.3 14.5 1.0 CA D:ASP459 3.6 14.8 1.0 NZ D:LYS386 3.8 24.8 1.0 CB D:ASP459 3.8 26.5 1.0 OD2 D:ASP459 3.9 31.1 1.0 CE D:LYS386 4.1 20.1 1.0 N D:ALA460 4.2 14.9 1.0 N D:GLU461 4.2 14.7 1.0 O2 D:CO3703 4.2 24.0 1.0 CB D:ASP379 4.4 31.1 1.0 CG D:GLU461 4.5 15.2 1.0 CA D:ALA460 4.6 15.0 1.0 OD2 D:ASP399 4.6 23.8 1.0 ND2 D:ASN432 4.7 14.3 1.0 NZ D:LYS374 4.8 14.8 1.0 O3 D:CO3703 4.8 20.9 1.0 C D:CO3703 4.9 19.8 1.0 CB D:GLU461 4.9 15.5 1.0 C D:ALA460 4.9 17.6 1.0 N D:ASP459 5.0 14.7 1.0

Zinc binding site 8 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:23.9 occ:1.00 OD2 D:ASP399 1.9 23.8 1.0 NZ D:LYS374 2.0 14.8 1.0 OE2 D:GLU461 2.1 14.5 1.0 OD2 D:ASP379 2.3 32.8 1.0 CG D:ASP399 2.9 26.2 1.0 ZN D:ZN701 3.0 26.9 1.0 CD D:GLU461 3.1 16.0 1.0 CE D:LYS374 3.1 14.7 1.0 OD1 D:ASP399 3.2 36.9 1.0 CG D:ASP379 3.3 31.4 1.0 OE1 D:GLU461 3.3 22.7 1.0 O2 D:CO3703 3.8 24.0 1.0 CB D:ASP379 3.9 31.1 1.0 O D:THR486 4.2 18.5 1.0 OD1 D:ASP379 4.2 36.5 1.0 CB D:ASP399 4.3 22.2 1.0 CG D:GLU461 4.4 15.2 1.0 CD D:LYS374 4.4 32.0 1.0 O D:ASP459 4.6 14.9 1.0 CG1 D:ILE376 4.7 14.3 1.0 N D:GLY462 4.7 14.7 1.0 CB D:ILE376 4.9 14.2 1.0 C D:CO3703 4.9 19.8 1.0 OD1 D:ASP459 4.9 27.1 1.0

Zinc binding site 9 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:30.9 occ:1.00 NZ E:LYS374 1.8 30.9 1.0 OE2 E:GLU461 1.9 21.6 1.0 O2 E:TOD703 1.9 49.4 1.0 OD2 E:ASP399 2.0 15.4 1.0 OD1 E:ASP399 2.5 14.7 1.0 CG E:ASP399 2.6 18.0 1.0 OD2 E:ASP379 2.6 27.3 1.0 CE E:LYS374 2.7 24.0 1.0 N1 E:TOD703 2.9 51.4 1.0 CD E:GLU461 3.1 23.2 1.0 ZN E:ZN702 3.4 30.1 1.0 CG E:ASP379 3.6 17.2 1.0 OE1 E:GLU461 3.7 30.9 1.0 O E:THR486 3.9 19.8 1.0 C7 E:TOD703 3.9 47.3 1.0 O2 E:CO3704 3.9 38.9 1.0 CD E:LYS374 4.0 20.4 1.0 CB E:ASP399 4.1 21.0 1.0 O1 E:TOD703 4.2 51.6 1.0 CB E:ASP379 4.2 14.4 1.0 CG E:GLU461 4.3 16.2 1.0 CG1 E:ILE376 4.5 35.3 1.0 OD1 E:ASP379 4.5 20.9 1.0 OG1 E:THR486 4.6 28.3 1.0 N E:GLY462 4.7 22.5 1.0 CB E:ILE376 4.8 37.2 1.0 O E:ASP459 4.9 15.3 1.0 CA E:GLY462 4.9 26.4 1.0

Zinc binding site 10 out of 24 in the X-Ray Crystal Structure of the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum


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 the Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to the M17 Leucyl Aminopeptidase From P. Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn702 b:30.1 occ:1.00 O2 E:TOD703 1.7 49.4 1.0 OE1 E:GLU461 2.1 30.9 1.0 OD1 E:ASP459 2.1 35.2 1.0 OD2 E:ASP379 2.1 27.3 1.0 O E:ASP459 2.1 15.3 1.0 N1 E:TOD703 2.6 51.4 1.0 O1 E:TOD703 2.6 51.6 1.0 CD E:GLU461 2.8 23.2 1.0 CG E:ASP379 2.9 17.2 1.0 C7 E:TOD703 2.9 47.3 1.0 OE2 E:GLU461 2.9 21.6 1.0 OD1 E:ASP379 2.9 20.9 1.0 CG E:ASP459 3.1 33.6 1.0 C E:ASP459 3.1 21.4 1.0 ZN E:ZN701 3.4 30.9 1.0 CA E:ASP459 3.5 21.3 1.0 CB E:ASP459 3.9 19.5 1.0 OD2 E:ASP459 3.9 23.0 1.0 NZ E:LYS386 4.1 21.5 1.0 CE E:LYS386 4.1 14.8 1.0 N E:GLU461 4.2 14.2 1.0 N E:ALA460 4.3 20.4 1.0 CG E:GLU461 4.3 16.2 1.0 C6 E:TOD703 4.3 42.4 1.0 CB E:ASP379 4.3 14.4 1.0 OD2 E:ASP399 4.5 15.4 1.0 O2 E:CO3704 4.6 38.9 1.0 CA E:ALA460 4.6 18.6 1.0 ND2 E:ASN432 4.6 14.0 1.0 O3 E:TOD703 4.7 45.0 1.0 CB E:GLU461 4.8 14.0 1.0 CA E:GLY381 4.8 19.0 1.0 NZ E:LYS374 4.8 30.9 1.0 C5 E:TOD703 4.9 39.8 1.0 N E:ASP459 4.9 27.4 1.0 C E:ALA460 5.0 14.3 1.0

N.Drinkwater, R.S.Bamert, K.Kannan Sivaraman, A.Paiardini, S.Mcgowan. X-Ray Crystal Structures of An Orally Available Aminopeptidase Inhibitor, Tosedostat, Bound to Anti-Malarial Drug Targets Pfa-M1 and Pfa-M17. Proteins 2015.
ISSN: ESSN 1097-0134
PubMed: 25645579
DOI: 10.1002/PROT.24771