Zinc in PDB 3kr5: Structure of A Protease 4

All present enzymatic activity of Structure of A Protease 4:
3.4.11.1;

The structure of Structure of A Protease 4, PDB code: 3kr5 was solved by S.Mcgowan, J.C.Whisstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.70 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	172.080, 174.160, 227.706, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.8

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 A Protease 4 (pdb code 3kr5). 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 A Protease 4, PDB code: 3kr5:
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 A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:38.0 occ:1.00 OD2 A:ASP379 2.0 22.5 1.0 O A:ASP459 2.1 20.3 1.0 OE1 A:GLU461 2.2 22.1 1.0 O3 A:BEY1003 2.3 33.6 1.0 OD1 A:ASP459 2.3 22.0 1.0 O4 A:BEY1003 2.8 28.3 1.0 CG A:ASP379 2.8 21.9 1.0 P A:BEY1003 2.9 22.1 1.0 OD1 A:ASP379 3.0 23.4 1.0 CD A:GLU461 3.1 22.3 1.0 CG A:ASP459 3.1 22.6 1.0 C A:ASP459 3.1 19.0 1.0 ZN A:ZN1001 3.3 30.8 1.0 OE2 A:GLU461 3.3 21.9 1.0 NZ A:LYS386 3.4 17.1 1.0 CA A:ASP459 3.5 18.9 1.0 C19 A:BEY1003 3.6 22.8 1.0 N A:BEY1003 3.8 17.1 1.0 CB A:ASP459 3.9 19.7 1.0 CE A:LYS386 3.9 18.9 1.0 OD2 A:ASP459 3.9 22.9 1.0 CB A:ASP379 4.2 18.7 1.0 N A:ALA460 4.3 17.9 1.0 N A:GLU461 4.3 17.2 1.0 ND2 A:ASN432 4.4 18.6 1.0 C17 A:BEY1003 4.4 35.7 1.0 CG A:GLU461 4.5 19.1 1.0 OD2 A:ASP399 4.6 26.0 1.0 CA A:GLY381 4.7 19.2 1.0 CA A:ALA460 4.7 17.0 1.0 C8 A:BEY1003 4.7 49.1 1.0 O2 A:CO31002 4.9 40.0 1.0 N A:ASP459 4.9 18.3 1.0 CB A:GLU461 5.0 17.8 1.0 O A:THR458 5.0 19.8 1.0

Zinc binding site 2 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:30.8 occ:1.00 OD2 A:ASP399 2.0 26.0 1.0 N A:BEY1003 2.1 17.1 1.0 OE2 A:GLU461 2.1 21.9 1.0 NZ A:LYS374 2.1 14.1 1.0 O4 A:BEY1003 2.4 28.3 1.0 OD2 A:ASP379 2.7 22.5 1.0 CG A:ASP399 2.9 21.8 1.0 CE A:LYS374 3.0 16.5 1.0 OD1 A:ASP399 3.0 20.1 1.0 CD A:GLU461 3.1 22.3 1.0 C19 A:BEY1003 3.2 22.8 1.0 ZN A:ZN1004 3.3 38.0 1.0 P A:BEY1003 3.3 22.1 1.0 OE1 A:GLU461 3.5 22.1 1.0 CG A:ASP379 3.6 21.9 1.0 O2 A:CO31002 3.8 40.0 1.0 O A:THR486 4.0 22.9 1.0 O3 A:BEY1003 4.1 33.6 1.0 CB A:ASP379 4.1 18.7 1.0 CB A:ASP399 4.3 17.8 1.0 CD A:LYS374 4.4 17.9 1.0 C18 A:BEY1003 4.4 24.5 1.0 CG A:GLU461 4.5 19.1 1.0 OD1 A:ASP379 4.5 23.4 1.0 CG1 A:ILE376 4.5 18.3 1.0 N A:GLY462 4.6 18.7 1.0 O A:ASP459 4.7 20.3 1.0 CB A:ILE376 4.7 19.3 1.0 C17 A:BEY1003 4.8 35.7 1.0 CA A:GLY462 4.8 18.0 1.0 CG2 A:ILE376 4.9 18.2 1.0 C15 A:BEY1003 5.0 25.7 1.0

Zinc binding site 3 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:36.5 occ:1.00 OD1 B:ASP459 1.9 22.3 1.0 O B:ASP459 2.1 21.2 1.0 OD2 B:ASP379 2.2 23.1 1.0 OE1 B:GLU461 2.3 22.1 1.0 O4 B:BEY1003 2.4 38.0 1.0 O3 B:BEY1003 2.5 40.3 1.0 P B:BEY1003 2.8 42.4 1.0 CG B:ASP379 2.9 22.3 1.0 CG B:ASP459 2.9 22.8 1.0 OD1 B:ASP379 3.0 23.2 1.0 C B:ASP459 3.0 19.5 1.0 CD B:GLU461 3.2 22.7 1.0 ZN B:ZN1001 3.2 35.9 1.0 CA B:ASP459 3.4 19.1 1.0 NZ B:LYS386 3.5 17.0 1.0 OE2 B:GLU461 3.6 22.5 1.0 CB B:ASP459 3.7 19.8 1.0 OD2 B:ASP459 3.8 23.0 1.0 CE B:LYS386 3.9 18.8 1.0 C19 B:BEY1003 4.0 38.5 1.0 N B:ALA460 4.2 18.8 1.0 C17 B:BEY1003 4.2 34.5 1.0 N B:GLU461 4.3 17.6 1.0 CB B:ASP379 4.3 19.4 1.0 ND2 B:ASN432 4.4 18.8 1.0 C8 B:BEY1003 4.5 35.4 1.0 CG B:GLU461 4.6 19.8 1.0 CA B:GLY381 4.6 19.1 1.0 O2 B:CO31002 4.6 11.7 1.0 CA B:ALA460 4.7 17.7 1.0 OD2 B:ASP399 4.7 26.8 1.0 N B:ASP459 4.7 18.8 1.0 O B:THR458 4.9 19.7 1.0 N B:GLY381 4.9 19.2 1.0 CB B:GLU461 5.0 18.5 1.0 C18 B:BEY1003 5.0 40.4 1.0 N B:BEY1003 5.0 41.6 1.0

Zinc binding site 4 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:35.9 occ:1.00 OD2 B:ASP399 2.0 26.8 1.0 O4 B:BEY1003 2.1 38.0 1.0 OE2 B:GLU461 2.2 22.5 1.0 NZ B:LYS374 2.3 14.7 1.0 OD2 B:ASP379 2.5 23.1 1.0 C19 B:BEY1003 2.7 38.5 1.0 P B:BEY1003 2.9 42.4 1.0 CG B:ASP399 2.9 22.8 1.0 N B:BEY1003 3.0 41.6 1.0 CD B:GLU461 3.1 22.7 1.0 CE B:LYS374 3.2 17.3 1.0 OD1 B:ASP399 3.2 20.5 1.0 ZN B:ZN1004 3.2 36.5 1.0 OE1 B:GLU461 3.4 22.1 1.0 CG B:ASP379 3.4 22.3 1.0 O3 B:BEY1003 3.9 40.3 1.0 O2 B:CO31002 3.9 11.7 1.0 CB B:ASP379 4.0 19.4 1.0 C18 B:BEY1003 4.1 40.4 1.0 O B:THR486 4.2 23.7 1.0 OD1 B:ASP379 4.3 23.2 1.0 CB B:ASP399 4.3 18.6 1.0 C17 B:BEY1003 4.4 34.5 1.0 CG B:GLU461 4.5 19.8 1.0 O B:ASP459 4.5 21.2 1.0 CD B:LYS374 4.6 19.2 1.0 N B:GLY462 4.6 19.1 1.0 CG1 B:ILE376 4.7 19.3 1.0 CB B:ILE376 4.9 20.0 1.0 CA B:GLY462 4.9 18.7 1.0 CG2 B:ILE376 4.9 18.5 1.0

Zinc binding site 5 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:26.4 occ:1.00 OD2 C:ASP399 1.9 26.2 1.0 O4 C:BEY1003 2.2 32.6 1.0 NZ C:LYS374 2.3 14.1 1.0 OE2 C:GLU461 2.3 22.1 1.0 N C:BEY1003 2.3 19.9 1.0 OD2 C:ASP379 2.4 23.4 1.0 CG C:ASP399 2.8 22.1 1.0 OD1 C:ASP399 3.0 19.9 1.0 P C:BEY1003 3.1 20.3 1.0 C19 C:BEY1003 3.1 20.3 1.0 CE C:LYS374 3.1 17.0 1.0 ZN C:ZN1004 3.2 42.8 1.0 CD C:GLU461 3.3 22.4 1.0 CG C:ASP379 3.4 22.3 1.0 OE1 C:GLU461 3.6 22.2 1.0 O3 C:BEY1003 3.8 16.4 1.0 CB C:ASP379 4.0 19.3 1.0 CB C:ASP399 4.1 18.2 1.0 O C:THR486 4.2 23.6 1.0 O1 C:CO31002 4.3 13.0 1.0 OD1 C:ASP379 4.4 23.5 1.0 C18 C:BEY1003 4.4 21.9 1.0 CD C:LYS374 4.6 18.4 1.0 C17 C:BEY1003 4.6 36.4 1.0 CG1 C:ILE376 4.6 18.4 1.0 CG C:GLU461 4.6 19.6 1.0 CB C:ILE376 4.7 19.5 1.0 O C:ASP459 4.8 21.5 1.0 CG2 C:ILE376 4.8 18.2 1.0 N C:GLY462 4.8 19.4 1.0

Zinc binding site 6 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1004 b:42.8 occ:1.00 O C:ASP459 2.0 21.5 1.0 OE1 C:GLU461 2.0 22.2 1.0 OD1 C:ASP459 2.2 22.7 1.0 O3 C:BEY1003 2.3 16.4 1.0 OD2 C:ASP379 2.4 23.4 1.0 O4 C:BEY1003 2.4 32.6 1.0 P C:BEY1003 2.8 20.3 1.0 C C:ASP459 2.9 19.1 1.0 CD C:GLU461 3.0 22.4 1.0 CG C:ASP379 3.1 22.3 1.0 CG C:ASP459 3.2 23.4 1.0 OD1 C:ASP379 3.2 23.5 1.0 ZN C:ZN1001 3.2 26.4 1.0 OE2 C:GLU461 3.3 22.1 1.0 CA C:ASP459 3.4 19.1 1.0 NZ C:LYS386 3.8 17.1 1.0 CB C:ASP459 3.8 20.3 1.0 C19 C:BEY1003 4.1 20.3 1.0 N C:ALA460 4.1 18.6 1.0 OD2 C:ASP459 4.1 23.2 1.0 N C:GLU461 4.1 17.8 1.0 C17 C:BEY1003 4.2 36.4 1.0 CE C:LYS386 4.2 19.2 1.0 CG C:GLU461 4.3 19.6 1.0 ND2 C:ASN432 4.4 18.8 1.0 N C:BEY1003 4.4 19.9 1.0 CB C:ASP379 4.5 19.3 1.0 CA C:ALA460 4.5 17.5 1.0 O1 C:CO31002 4.6 13.0 1.0 N C:ASP459 4.7 19.1 1.0 CB C:GLU461 4.7 18.1 1.0 OD2 C:ASP399 4.8 26.2 1.0 O C:THR458 4.8 20.1 1.0 C8 C:BEY1003 4.8 42.8 1.0 C C:ALA460 4.9 18.1 1.0 NZ C:LYS374 4.9 14.1 1.0 CA C:GLY381 4.9 19.5 1.0

Zinc binding site 7 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:41.0 occ:1.00 O4 D:BEY1003 2.0 39.0 1.0 OD2 D:ASP399 2.0 26.5 1.0 OE2 D:GLU461 2.1 21.9 1.0 NZ D:LYS374 2.2 14.3 1.0 OD2 D:ASP379 2.6 22.8 1.0 N D:BEY1003 2.8 38.0 1.0 CG D:ASP399 3.0 22.2 1.0 ZN D:ZN1004 3.0 39.3 1.0 CD D:GLU461 3.1 22.3 1.0 CE D:LYS374 3.1 16.7 1.0 P D:BEY1003 3.1 41.9 1.0 OD1 D:ASP399 3.2 19.6 1.0 OE1 D:GLU461 3.4 21.5 1.0 CG D:ASP379 3.5 21.8 1.0 C19 D:BEY1003 3.6 35.1 1.0 O1 D:CO31002 3.6 24.1 1.0 O3 D:BEY1003 3.9 47.2 1.0 CB D:ASP379 4.1 18.9 1.0 O D:THR486 4.2 23.0 1.0 OD1 D:ASP379 4.3 23.2 1.0 CB D:ASP399 4.3 18.2 1.0 CG D:GLU461 4.5 19.4 1.0 CD D:LYS374 4.5 18.5 1.0 C17 D:BEY1003 4.5 40.2 1.0 O D:ASP459 4.5 20.8 1.0 N D:GLY462 4.6 19.1 1.0 CG1 D:ILE376 4.6 18.7 1.0 C18 D:BEY1003 4.7 31.6 1.0 CB D:ILE376 4.8 19.4 1.0 CG2 D:ILE376 4.8 18.4 1.0 CA D:GLY462 4.9 18.0 1.0 C D:CO31002 4.9 25.4 1.0

Zinc binding site 8 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1004 b:39.3 occ:1.00 OD2 D:ASP379 2.0 22.8 1.0 OD1 D:ASP459 2.1 21.9 1.0 OE1 D:GLU461 2.2 21.5 1.0 O D:ASP459 2.2 20.8 1.0 O3 D:BEY1003 2.3 47.2 1.0 O4 D:BEY1003 2.5 39.0 1.0 P D:BEY1003 2.8 41.9 1.0 CG D:ASP379 2.9 21.8 1.0 ZN D:ZN1001 3.0 41.0 1.0 OD1 D:ASP379 3.1 23.2 1.0 CD D:GLU461 3.1 22.3 1.0 C D:ASP459 3.2 18.9 1.0 CG D:ASP459 3.2 22.4 1.0 OE2 D:GLU461 3.3 21.9 1.0 NZ D:LYS386 3.4 17.0 1.0 CA D:ASP459 3.6 18.8 1.0 CE D:LYS386 3.9 18.6 1.0 C19 D:BEY1003 4.0 35.1 1.0 CB D:ASP459 4.0 19.6 1.0 OD2 D:ASP459 4.1 22.5 1.0 N D:BEY1003 4.1 38.0 1.0 O1 D:CO31002 4.2 24.1 1.0 C17 D:BEY1003 4.2 40.2 1.0 CB D:ASP379 4.3 18.9 1.0 N D:GLU461 4.3 17.3 1.0 N D:ALA460 4.4 18.3 1.0 OD2 D:ASP399 4.5 26.5 1.0 CG D:GLU461 4.5 19.4 1.0 ND2 D:ASN432 4.6 18.7 1.0 C8 D:BEY1003 4.6 45.0 1.0 CA D:ALA460 4.8 16.9 1.0 CA D:GLY381 4.8 18.8 1.0 NZ D:LYS374 4.9 14.3 1.0 CB D:GLU461 5.0 18.0 1.0 N D:ASP459 5.0 18.4 1.0

Zinc binding site 9 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:30.8 occ:1.00 OD2 E:ASP399 2.0 26.8 1.0 O4 E:BEY1003 2.0 36.9 1.0 NZ E:LYS374 2.2 14.3 1.0 OE2 E:GLU461 2.3 22.9 1.0 OD2 E:ASP379 2.5 23.6 1.0 N E:BEY1003 2.6 22.8 1.0 CG E:ASP399 2.8 22.7 1.0 OD1 E:ASP399 3.0 20.3 1.0 CE E:LYS374 3.0 17.3 1.0 P E:BEY1003 3.1 32.2 1.0 CD E:GLU461 3.3 23.1 1.0 C19 E:BEY1003 3.3 25.1 1.0 ZN E:ZN1004 3.4 45.9 1.0 CG E:ASP379 3.5 22.8 1.0 OE1 E:GLU461 3.6 22.8 1.0 O3 E:CO31002 3.7 31.5 1.0 CB E:ASP379 4.0 19.6 1.0 O E:THR486 4.1 23.5 1.0 CB E:ASP399 4.2 18.6 1.0 O3 E:BEY1003 4.2 36.9 1.0 OD1 E:ASP379 4.4 24.0 1.0 C17 E:BEY1003 4.5 40.9 1.0 CD E:LYS374 4.5 19.0 1.0 C18 E:BEY1003 4.6 22.5 1.0 CG E:GLU461 4.7 20.2 1.0 CG1 E:ILE376 4.7 19.2 1.0 O E:ASP459 4.7 21.5 1.0 N E:GLY462 4.8 19.8 1.0 CB E:ILE376 4.8 20.0 1.0 CG2 E:ILE376 4.9 18.9 1.0 C E:CO31002 5.0 33.8 1.0

Zinc binding site 10 out of 24 in the Structure of A Protease 4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of A Protease 4 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1004 b:45.9 occ:1.00 O E:ASP459 1.9 21.5 1.0 OE1 E:GLU461 2.1 22.8 1.0 OD1 E:ASP459 2.1 22.6 1.0 OD2 E:ASP379 2.2 23.6 1.0 O4 E:BEY1003 2.3 36.9 1.0 O3 E:BEY1003 2.7 36.9 1.0 C E:ASP459 2.9 19.7 1.0 P E:BEY1003 2.9 32.2 1.0 CG E:ASP379 3.1 22.8 1.0 CD E:GLU461 3.1 23.1 1.0 CG E:ASP459 3.1 23.5 1.0 OD1 E:ASP379 3.2 24.0 1.0 CA E:ASP459 3.3 19.5 1.0 ZN E:ZN1001 3.4 30.8 1.0 OE2 E:GLU461 3.4 22.9 1.0 NZ E:LYS386 3.6 17.4 1.0 CB E:ASP459 3.7 20.4 1.0 OD2 E:ASP459 4.0 23.5 1.0 N E:ALA460 4.0 18.9 1.0 C17 E:BEY1003 4.1 40.9 1.0 CE E:LYS386 4.1 19.4 1.0 N E:GLU461 4.2 18.2 1.0 C7 E:BEY1003 4.2 48.8 1.0 C19 E:BEY1003 4.3 25.1 1.0 ND2 E:ASN432 4.4 19.4 1.0 CG E:GLU461 4.4 20.2 1.0 CB E:ASP379 4.5 19.6 1.0 O3 E:CO31002 4.5 31.5 1.0 CA E:ALA460 4.5 17.7 1.0 C8 E:BEY1003 4.5 48.6 1.0 N E:ASP459 4.7 19.6 1.0 CA E:GLY381 4.7 19.8 1.0 N E:BEY1003 4.7 22.8 1.0 O E:THR458 4.8 20.7 1.0 OD2 E:ASP399 4.8 26.8 1.0 CB E:GLU461 4.9 18.7 1.0 C E:ALA460 4.9 18.5 1.0

S.Mcgowan, C.A.Oellig, W.A.Birru, T.T.Caradoc-Davies, C.M.Stack, J.Lowther, T.Skinner-Adams, A.Mucha, P.Kafarski, J.Grembecka, K.R.Trenholme, A.M.Buckle, D.L.Gardiner, J.P.Dalton, J.C.Whisstock. Structure of the Plasmodium Falciparum M17 Aminopeptidase and Significance For the Design of Drugs Targeting the Neutral Exopeptidases Proc.Natl.Acad.Sci.Usa V. 107 2449 2010.
ISSN: ISSN 0027-8424
PubMed: 20133789
DOI: 10.1073/PNAS.0911813107