Zinc in PDB 3t8w: A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases

The structure of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases, PDB code: 3t8w was solved by S.Mcgowan, M.Klemba, D.C.Greebaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.32 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	173.748, 177.057, 231.221, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20

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 A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases (pdb code 3t8w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases, PDB code: 3t8w:
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 A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn613 b:26.2 occ:1.00 O9 A:DGZ615 2.1 6.0 1.0 OD2 A:ASP379 2.1 10.0 1.0 OE1 A:GLU461 2.1 3.7 1.0 OD1 A:ASP459 2.2 9.8 1.0 O A:ASP459 2.3 8.5 1.0 CG A:ASP379 3.0 8.9 1.0 O8 A:DGZ615 3.0 16.7 1.0 CD A:GLU461 3.0 3.7 1.0 C48 A:DGZ615 3.1 35.0 1.0 C A:ASP459 3.1 9.6 1.0 OD1 A:ASP379 3.2 9.1 1.0 C47 A:DGZ615 3.2 27.3 1.0 ZN A:ZN614 3.2 17.2 1.0 OE2 A:GLU461 3.2 3.7 1.0 CG A:ASP459 3.3 9.3 1.0 CA A:ASP459 3.5 6.1 1.0 C49 A:DGZ615 3.9 18.3 1.0 CB A:ASP459 3.9 6.6 1.0 NZ A:LYS386 4.0 12.8 1.0 N5 A:DGZ615 4.1 21.2 1.0 CE A:LYS386 4.2 16.1 1.0 O2 A:CO3612 4.2 14.5 1.0 N6 A:DGZ615 4.2 22.8 1.0 OD2 A:ASP459 4.2 10.5 1.0 N A:ALA460 4.3 6.6 1.0 N A:GLU461 4.3 5.8 1.0 CB A:ASP379 4.4 7.8 1.0 CG A:GLU461 4.4 3.8 1.0 ND2 A:ASN432 4.5 6.0 1.0 OD2 A:ASP399 4.7 10.2 1.0 CA A:ALA460 4.7 6.4 1.0 CA A:GLY381 4.8 5.9 1.0 NZ A:LYS374 4.9 4.0 1.0 CB A:GLU461 4.9 5.2 1.0 N A:ASP459 4.9 5.2 1.0 C35 A:DGZ615 5.0 44.6 1.0

Zinc binding site 2 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn614 b:17.2 occ:1.00 OD2 A:ASP399 1.9 10.2 1.0 OE2 A:GLU461 2.1 3.7 1.0 O9 A:DGZ615 2.2 6.0 1.0 NZ A:LYS374 2.2 4.0 1.0 N6 A:DGZ615 2.5 22.8 1.0 OD2 A:ASP379 2.6 10.0 1.0 CG A:ASP399 2.8 9.2 1.0 OD1 A:ASP399 3.0 7.5 1.0 CE A:LYS374 3.0 10.9 1.0 C48 A:DGZ615 3.1 35.0 1.0 CD A:GLU461 3.2 3.7 1.0 ZN A:ZN613 3.2 26.2 1.0 C49 A:DGZ615 3.3 18.3 1.0 CG A:ASP379 3.4 8.9 1.0 OE1 A:GLU461 3.5 3.7 1.0 CB A:ASP379 3.8 7.8 1.0 O2 A:CO3612 3.9 14.5 1.0 CB A:ASP399 4.2 5.0 1.0 O A:THR486 4.2 9.3 1.0 C47 A:DGZ615 4.3 27.3 1.0 OD1 A:ASP379 4.4 9.1 1.0 CD A:LYS374 4.4 8.0 1.0 C50 A:DGZ615 4.5 16.8 1.0 CG A:GLU461 4.5 3.8 1.0 CG1 A:ILE376 4.5 14.8 1.0 CB A:ILE376 4.7 13.7 1.0 O8 A:DGZ615 4.8 16.7 1.0 CG2 A:ILE376 4.8 13.6 1.0 N A:GLY462 4.8 5.1 1.0

Zinc binding site 3 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn613 b:26.7 occ:1.00 OD2 B:ASP379 2.0 7.5 1.0 OD1 B:ASP459 2.1 6.0 1.0 OE1 B:GLU461 2.2 13.2 1.0 O9 B:DGZ615 2.2 11.6 1.0 O B:ASP459 2.3 8.7 1.0 O8 B:DGZ615 2.8 19.8 1.0 CG B:ASP379 2.9 5.2 1.0 CD B:GLU461 3.1 12.9 1.0 OD1 B:ASP379 3.1 3.0 1.0 ZN B:ZN614 3.1 16.3 1.0 CG B:ASP459 3.2 6.7 1.0 C47 B:DGZ615 3.2 19.1 1.0 C B:ASP459 3.2 9.2 1.0 C48 B:DGZ615 3.2 35.6 1.0 OE2 B:GLU461 3.3 15.6 1.0 CA B:ASP459 3.5 5.1 1.0 CB B:ASP459 3.9 6.1 1.0 NZ B:LYS386 3.9 8.6 1.0 C49 B:DGZ615 4.0 9.4 1.0 OD2 B:ASP459 4.1 9.7 1.0 CE B:LYS386 4.1 7.4 1.0 N5 B:DGZ615 4.1 26.0 1.0 N6 B:DGZ615 4.2 33.5 1.0 O2 B:CO3612 4.2 15.2 1.0 CB B:ASP379 4.3 6.1 1.0 N B:ALA460 4.3 7.4 1.0 N B:GLU461 4.4 7.1 1.0 CG B:GLU461 4.5 9.6 1.0 ND2 B:ASN432 4.6 5.4 1.0 OD2 B:ASP399 4.7 12.4 1.0 CA B:GLY381 4.8 4.6 1.0 CA B:ALA460 4.8 7.5 1.0 C35 B:DGZ615 4.9 29.7 1.0 N B:ASP459 4.9 5.7 1.0 NZ B:LYS374 4.9 3.7 1.0 CB B:GLU461 5.0 7.1 1.0

Zinc binding site 4 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn614 b:16.3 occ:1.00 OD2 B:ASP399 2.0 12.4 1.0 O9 B:DGZ615 2.0 11.6 1.0 OE2 B:GLU461 2.1 15.6 1.0 NZ B:LYS374 2.2 3.7 1.0 N6 B:DGZ615 2.6 33.5 1.0 OD2 B:ASP379 2.6 7.5 1.0 CG B:ASP399 2.9 11.9 1.0 C48 B:DGZ615 3.0 35.6 1.0 CE B:LYS374 3.1 4.4 1.0 OD1 B:ASP399 3.1 11.4 1.0 CD B:GLU461 3.1 12.9 1.0 ZN B:ZN613 3.1 26.7 1.0 C49 B:DGZ615 3.3 9.4 1.0 CG B:ASP379 3.4 5.2 1.0 OE1 B:GLU461 3.4 13.2 1.0 O2 B:CO3612 3.8 15.2 1.0 CB B:ASP379 3.9 6.1 1.0 C47 B:DGZ615 4.2 19.1 1.0 CB B:ASP399 4.2 8.2 1.0 O B:THR486 4.3 12.1 1.0 OD1 B:ASP379 4.3 3.0 1.0 CD B:LYS374 4.5 7.0 1.0 CG B:GLU461 4.5 9.6 1.0 O8 B:DGZ615 4.6 19.8 1.0 CG1 B:ILE376 4.6 11.3 1.0 C50 B:DGZ615 4.6 23.8 1.0 CB B:ILE376 4.7 11.0 1.0 CG2 B:ILE376 4.8 11.7 1.0 N B:GLY462 4.8 6.7 1.0 O B:ASP459 4.8 8.7 1.0

Zinc binding site 5 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn613 b:17.1 occ:1.00 OD2 C:ASP399 2.0 19.7 1.0 O9 C:DGZ615 2.1 21.6 1.0 OE2 C:GLU461 2.2 9.3 1.0 NZ C:LYS374 2.2 3.6 1.0 N6 C:DGZ615 2.5 25.6 1.0 OD2 C:ASP379 2.6 14.1 1.0 CG C:ASP399 2.8 16.5 1.0 OD1 C:ASP399 3.0 17.4 1.0 C48 C:DGZ615 3.0 13.9 1.0 CE C:LYS374 3.1 6.1 1.0 CD C:GLU461 3.2 10.2 1.0 ZN C:ZN614 3.2 25.4 1.0 C49 C:DGZ615 3.3 11.8 1.0 CG C:ASP379 3.4 9.1 1.0 OE1 C:GLU461 3.5 5.0 1.0 CB C:ASP379 3.9 6.5 1.0 O1 C:CO3612 3.9 15.4 1.0 CB C:ASP399 4.2 11.6 1.0 O C:THR486 4.2 6.6 1.0 C47 C:DGZ615 4.3 17.0 1.0 OD1 C:ASP379 4.3 7.8 1.0 C50 C:DGZ615 4.5 11.1 1.0 CD C:LYS374 4.5 5.8 1.0 CG C:GLU461 4.6 3.9 1.0 CG1 C:ILE376 4.6 8.2 1.0 CB C:ILE376 4.7 8.5 1.0 O8 C:DGZ615 4.8 16.0 1.0 CG2 C:ILE376 4.8 7.1 1.0 N C:GLY462 4.9 11.2 1.0 O C:ASP459 4.9 10.3 1.0

Zinc binding site 6 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn614 b:25.4 occ:1.00 OD1 C:ASP459 2.0 7.0 1.0 O9 C:DGZ615 2.1 21.6 1.0 OD2 C:ASP379 2.1 14.1 1.0 O C:ASP459 2.2 10.3 1.0 OE1 C:GLU461 2.2 5.0 1.0 O8 C:DGZ615 2.9 16.0 1.0 C48 C:DGZ615 3.0 13.9 1.0 CG C:ASP379 3.0 9.1 1.0 CG C:ASP459 3.0 9.8 1.0 C47 C:DGZ615 3.1 17.0 1.0 C C:ASP459 3.1 9.1 1.0 CD C:GLU461 3.1 10.2 1.0 OD1 C:ASP379 3.2 7.8 1.0 ZN C:ZN613 3.2 17.1 1.0 OE2 C:GLU461 3.4 9.3 1.0 CA C:ASP459 3.5 5.0 1.0 C49 C:DGZ615 3.8 11.8 1.0 CB C:ASP459 3.8 6.3 1.0 NZ C:LYS386 3.8 13.2 1.0 OD2 C:ASP459 3.9 10.5 1.0 N5 C:DGZ615 4.1 12.7 1.0 CE C:LYS386 4.1 13.3 1.0 O1 C:CO3612 4.1 15.4 1.0 N6 C:DGZ615 4.2 25.6 1.0 N C:ALA460 4.3 4.7 1.0 N C:GLU461 4.4 6.7 1.0 CB C:ASP379 4.4 6.5 1.0 CG C:GLU461 4.5 3.9 1.0 ND2 C:ASN432 4.6 5.2 1.0 CA C:ALA460 4.7 4.7 1.0 OD2 C:ASP399 4.7 19.7 1.0 CA C:GLY381 4.8 7.9 1.0 C35 C:DGZ615 4.8 17.8 1.0 N C:ASP459 4.9 4.7 1.0 NZ C:LYS374 4.9 3.6 1.0 CB C:GLU461 5.0 6.2 1.0

Zinc binding site 7 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn613 b:16.3 occ:1.00 OD2 D:ASP399 2.0 11.1 1.0 O9 D:DGZ615 2.1 11.0 1.0 NZ D:LYS374 2.1 5.0 1.0 OE2 D:GLU461 2.2 8.0 1.0 N6 D:DGZ615 2.5 9.2 1.0 OD2 D:ASP379 2.6 9.1 1.0 CG D:ASP399 2.9 13.0 1.0 CE D:LYS374 3.0 3.1 1.0 C48 D:DGZ615 3.0 28.9 1.0 OD1 D:ASP399 3.0 15.2 1.0 ZN D:ZN614 3.1 29.8 1.0 CD D:GLU461 3.2 10.2 1.0 C49 D:DGZ615 3.2 15.3 1.0 CG D:ASP379 3.5 9.5 1.0 OE1 D:GLU461 3.5 11.3 1.0 O1 D:CO3612 3.9 15.2 1.0 CB D:ASP379 4.0 7.9 1.0 O D:THR486 4.2 11.3 1.0 CB D:ASP399 4.3 7.0 1.0 C47 D:DGZ615 4.3 12.5 1.0 OD1 D:ASP379 4.4 9.8 1.0 CD D:LYS374 4.4 4.7 1.0 C50 D:DGZ615 4.4 25.1 1.0 CG D:GLU461 4.5 6.9 1.0 CG1 D:ILE376 4.6 8.3 1.0 O D:ASP459 4.8 9.2 1.0 CB D:ILE376 4.8 7.5 1.0 N D:GLY462 4.8 9.1 1.0 O8 D:DGZ615 4.8 25.8 1.0 CG2 D:ILE376 4.9 5.5 1.0

Zinc binding site 8 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn614 b:29.8 occ:1.00 OD2 D:ASP379 2.0 9.1 1.0 O9 D:DGZ615 2.1 11.0 1.0 OD1 D:ASP459 2.2 11.3 1.0 OE1 D:GLU461 2.2 11.3 1.0 O D:ASP459 2.3 9.2 1.0 CG D:ASP379 2.9 9.5 1.0 C48 D:DGZ615 3.0 28.9 1.0 CD D:GLU461 3.1 10.2 1.0 ZN D:ZN613 3.1 16.3 1.0 O8 D:DGZ615 3.1 25.8 1.0 OD1 D:ASP379 3.1 9.8 1.0 C D:ASP459 3.2 10.1 1.0 CG D:ASP459 3.2 12.8 1.0 C47 D:DGZ615 3.3 12.5 1.0 OE2 D:GLU461 3.3 8.0 1.0 CA D:ASP459 3.5 5.5 1.0 C49 D:DGZ615 3.7 15.3 1.0 NZ D:LYS386 3.9 14.3 1.0 CB D:ASP459 3.9 6.2 1.0 CE D:LYS386 4.1 9.2 1.0 OD2 D:ASP459 4.1 17.2 1.0 N6 D:DGZ615 4.1 9.2 1.0 N5 D:DGZ615 4.2 15.2 1.0 CB D:ASP379 4.3 7.9 1.0 O1 D:CO3612 4.3 15.2 1.0 N D:ALA460 4.3 5.8 1.0 N D:GLU461 4.4 5.9 1.0 CG D:GLU461 4.5 6.9 1.0 ND2 D:ASN432 4.6 10.1 1.0 OD2 D:ASP399 4.6 11.1 1.0 CA D:GLY381 4.8 6.9 1.0 CA D:ALA460 4.8 5.2 1.0 NZ D:LYS374 4.8 5.0 1.0 N D:ASP459 4.9 6.2 1.0 CB D:GLU461 4.9 6.1 1.0

Zinc binding site 9 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn613 b:18.0 occ:1.00 OD2 E:ASP399 1.9 15.4 1.0 O9 E:DGZ615 2.1 10.7 1.0 OE2 E:GLU461 2.1 9.8 1.0 NZ E:LYS374 2.2 5.7 1.0 N6 E:DGZ615 2.5 21.3 1.0 OD2 E:ASP379 2.7 11.0 1.0 CG E:ASP399 2.8 12.3 1.0 OD1 E:ASP399 3.0 12.4 1.0 CE E:LYS374 3.0 6.5 1.0 C48 E:DGZ615 3.1 18.6 1.0 ZN E:ZN614 3.2 28.0 1.0 CD E:GLU461 3.2 12.2 1.0 C49 E:DGZ615 3.3 19.7 1.0 CG E:ASP379 3.5 10.7 1.0 OE1 E:GLU461 3.6 6.5 1.0 O3 E:CO3612 3.9 14.1 1.0 CB E:ASP379 3.9 8.5 1.0 O E:THR486 4.1 10.4 1.0 CB E:ASP399 4.2 7.5 1.0 C47 E:DGZ615 4.3 12.0 1.0 OD1 E:ASP379 4.4 12.7 1.0 CD E:LYS374 4.4 3.4 1.0 CG E:GLU461 4.5 13.7 1.0 C50 E:DGZ615 4.5 31.4 1.0 CG1 E:ILE376 4.6 9.6 1.0 O8 E:DGZ615 4.7 10.6 1.0 CB E:ILE376 4.7 8.4 1.0 CG2 E:ILE376 4.8 5.0 1.0 N E:GLY462 4.8 11.4 1.0 O E:ASP459 5.0 7.7 1.0

Zinc binding site 10 out of 24 in the A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of A Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn614 b:28.0 occ:1.00 OD2 E:ASP379 2.0 11.0 1.0 OE1 E:GLU461 2.1 6.5 1.0 O9 E:DGZ615 2.1 10.7 1.0 OD1 E:ASP459 2.2 15.7 1.0 O E:ASP459 2.4 7.7 1.0 O8 E:DGZ615 2.8 10.6 1.0 CG E:ASP379 2.9 10.7 1.0 CD E:GLU461 3.0 12.2 1.0 C48 E:DGZ615 3.1 18.6 1.0 OD1 E:ASP379 3.1 12.7 1.0 ZN E:ZN613 3.2 18.0 1.0 OE2 E:GLU461 3.2 9.8 1.0 C47 E:DGZ615 3.2 12.0 1.0 C E:ASP459 3.2 9.4 1.0 CG E:ASP459 3.2 16.0 1.0 CA E:ASP459 3.6 7.9 1.0 C49 E:DGZ615 3.8 19.7 1.0 NZ E:LYS386 3.9 7.2 1.0 CB E:ASP459 4.0 9.8 1.0 CE E:LYS386 4.1 4.7 1.0 N6 E:DGZ615 4.1 21.3 1.0 OD2 E:ASP459 4.2 11.9 1.0 N5 E:DGZ615 4.2 20.6 1.0 CB E:ASP379 4.3 8.5 1.0 O3 E:CO3612 4.3 14.1 1.0 N E:GLU461 4.4 9.7 1.0 N E:ALA460 4.4 7.4 1.0 CG E:GLU461 4.4 13.7 1.0 ND2 E:ASN432 4.6 5.6 1.0 OD2 E:ASP399 4.6 15.4 1.0 CA E:GLY381 4.8 5.3 1.0 NZ E:LYS374 4.8 5.7 1.0 CA E:ALA460 4.8 6.8 1.0 CB E:GLU461 4.9 11.9 1.0 N E:ASP459 5.0 8.3 1.0

M.B.Harbut, G.Velmourougane, S.Dalal, G.Reiss, J.C.Whisstock, O.Onder, D.Brisson, S.Mcgowan, M.Klemba, D.C.Greenbaum. Bestatin-Based Chemical Biology Strategy Reveals Distinct Roles For Malaria M1- and M17-Family Aminopeptidases Proc.Natl.Acad.Sci.Usa V. 108 E526 2011.
ISSN: ISSN 0027-8424
PubMed: 21844374
DOI: 10.1073/PNAS.1105601108