Zinc in PDB 8ac7: Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap

The structure of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap, PDB code: 8ac7 was solved by C.J.Harding, C.M.Czekster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.63 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.952, 85.953, 98.216, 90, 93.56, 90
R / Rfree (%)	15.6 / 17.5

The structure of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap also contains other interesting chemical elements:

Sodium

(Na)

9 atoms

The binding sites of Zinc atom in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap (pdb code 8ac7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap, PDB code: 8ac7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:13.6 occ:1.00 OXT B:ACT613 1.9 14.5 1.0 OD1 B:ASP369 1.9 12.8 1.0 OD2 B:ASP308 1.9 13.4 1.0 NE2 B:HIS296 2.0 14.6 1.0 CG B:ASP369 2.6 12.3 1.0 OD2 B:ASP369 2.6 13.7 1.0 C B:ACT613 2.9 18.8 1.0 CG B:ASP308 3.0 14.5 1.0 CD2 B:HIS296 3.0 13.4 1.0 CE1 B:HIS296 3.0 14.3 1.0 CH3 B:ACT613 3.4 19.7 1.0 OD1 B:ASP308 3.4 14.5 1.0 ZN B:ZN602 3.6 15.5 1.0 OE2 B:GLU341 3.9 16.0 1.0 O B:ACT613 3.9 20.8 1.0 CB B:ASN309 4.0 12.1 1.0 OE1 B:GLU340 4.0 15.2 1.0 CB B:ASP369 4.1 13.6 1.0 ND1 B:HIS296 4.1 13.6 1.0 CG B:HIS296 4.2 11.8 1.0 CG B:MET370 4.2 12.4 1.0 CB B:ASP308 4.3 13.2 1.0 CD B:GLU340 4.3 16.1 1.0 OE2 B:GLU340 4.5 21.3 1.0 CA B:ASP308 4.5 11.8 1.0 SD B:MET370 4.6 13.9 1.0 CG B:ASN309 4.6 11.5 1.0 CD B:GLU341 4.6 15.4 1.0 C B:ASP308 4.7 13.1 1.0 CA B:ASP369 4.7 12.4 1.0 C B:ASP369 4.8 12.3 1.0 CA B:ASN309 4.8 12.3 1.0 N B:ASN309 4.8 13.5 1.0 OE1 B:GLU341 5.0 17.8 1.0

Zinc binding site 2 out of 8 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:15.5 occ:1.00 OE2 B:GLU341 2.0 16.0 1.0 OD1 B:ASP308 2.0 14.5 1.0 NE2 B:HIS467 2.0 14.1 1.0 O B:ACT613 2.2 20.8 1.0 OXT B:ACT613 2.2 14.5 1.0 C B:ACT613 2.4 18.8 1.0 OE1 B:GLU341 2.5 17.8 1.0 CD B:GLU341 2.6 15.4 1.0 CD2 B:HIS467 2.9 13.9 1.0 CG B:ASP308 3.0 14.5 1.0 CE1 B:HIS467 3.1 14.7 1.0 OD2 B:ASP308 3.4 13.4 1.0 ZN B:ZN601 3.6 13.6 1.0 O B:HOH796 3.9 20.6 1.0 CE1 B:TYR466 3.9 17.3 1.0 CH3 B:ACT613 4.0 19.7 1.0 OH B:TYR466 4.0 20.2 1.0 O B:HOH751 4.0 16.0 1.0 CG B:GLU341 4.1 17.8 1.0 CG B:HIS467 4.1 16.8 1.0 ND1 B:HIS467 4.2 21.5 1.0 OE1 B:GLU340 4.3 15.2 1.0 CZ B:TYR466 4.3 19.6 1.0 CB B:ASP308 4.3 13.2 1.0 NE2 B:HIS296 4.6 14.6 1.0 CE1 B:HIS296 4.6 14.3 1.0 CG1 B:VAL300 4.7 16.1 1.0 O B:HOH952 4.8 22.5 1.0 CD1 B:TYR466 4.8 15.5 1.0

Zinc binding site 3 out of 8 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:18.3 occ:1.00 OE2 B:GLU400 2.0 16.7 1.0 OD1 B:ASP382 2.1 18.6 1.0 O B:HOH736 2.1 19.8 1.0 OD1 B:ASP384 2.1 20.3 1.0 OG B:SER386 2.1 19.1 1.0 O B:HOH749 2.2 20.1 1.0 CD B:GLU400 3.0 19.8 1.0 CG B:ASP384 3.0 26.4 1.0 OE1 B:GLU400 3.2 22.5 1.0 CB B:SER386 3.3 21.4 1.0 CG B:ASP382 3.3 20.0 1.0 OD2 B:ASP384 3.3 28.3 1.0 N B:SER386 3.7 20.5 1.0 O B:HOH872 3.9 22.5 1.0 CA B:ASP382 3.9 14.3 1.0 CA B:SER386 4.0 20.9 1.0 CB B:ASP382 4.0 15.8 1.0 OD2 B:ASP387 4.1 27.7 1.0 OE1 B:GLU404 4.1 21.2 1.0 OD2 B:ASP382 4.2 19.2 1.0 CG B:GLU400 4.3 15.2 1.0 C B:ASP382 4.3 15.9 1.0 O B:HOH806 4.4 33.8 1.0 CB B:ASP384 4.4 21.7 1.0 N B:ASP384 4.4 17.9 1.0 N B:ASP387 4.5 20.5 1.0 N B:GLY385 4.5 18.8 1.0 C B:SER386 4.7 22.6 1.0 CA B:ASP384 4.7 20.0 1.0 CG B:ASP387 4.7 25.7 1.0 O B:ASP382 4.7 17.2 1.0 C B:ASP384 4.7 19.0 1.0 N B:GLY383 4.8 15.8 1.0 C B:GLY385 4.8 20.2 1.0 O B:HOH1222 5.0 38.0 1.0

Zinc binding site 4 out of 8 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:18.4 occ:1.00 OXT B:ACT608 1.8 29.7 1.0 OD2 B:ASP486 1.9 16.7 1.0 OE2 B:GLU482 2.0 16.4 1.0 O B:HOH1116 2.0 20.1 1.0 C B:ACT608 2.6 32.2 1.0 CG B:ASP486 2.8 15.0 1.0 CD B:GLU482 2.9 15.4 1.0 O B:ACT608 2.9 33.2 1.0 OD1 B:ASP486 3.0 16.1 1.0 O B:HOH713 3.1 10.7 1.0 CG B:GLU482 3.2 14.2 1.0 NH2 B:ARG410 3.9 28.1 1.0 NH1 B:ARG410 4.0 30.0 1.0 CH3 B:ACT608 4.0 35.1 1.0 OE1 B:GLU482 4.0 16.7 1.0 H3 B:ACT608 4.1 42.1 1.0 O B:HOH975 4.2 22.1 1.0 CB B:ASP486 4.2 15.4 1.0 O B:GLU482 4.3 15.3 1.0 CZ B:ARG410 4.4 32.9 1.0 H2 B:ACT608 4.5 42.1 1.0 H1 B:ACT608 4.6 42.1 1.0 CB B:GLU482 4.6 14.9 1.0 O B:HOH881 4.7 21.8 1.0 O B:HOH1077 4.7 27.0 1.0 C B:GLU482 4.7 14.2 1.0 O B:PRO59 4.8 17.3 1.0 CD1 B:ILE483 4.9 32.1 1.0

Zinc binding site 5 out of 8 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:13.8 occ:1.00 O A:ACT610 1.9 14.1 1.0 OD2 A:ASP308 1.9 14.8 1.0 OD1 A:ASP369 2.0 12.9 1.0 NE2 A:HIS296 2.0 13.2 1.0 CG A:ASP369 2.6 14.0 1.0 OD2 A:ASP369 2.7 14.2 1.0 C A:ACT610 2.9 18.7 1.0 CG A:ASP308 3.0 16.2 1.0 CE1 A:HIS296 3.0 11.7 1.0 CD2 A:HIS296 3.0 14.0 1.0 CH3 A:ACT610 3.4 19.8 1.0 OD1 A:ASP308 3.4 14.9 1.0 ZN A:ZN602 3.6 15.5 1.0 OE2 A:GLU341 3.8 16.0 1.0 OXT A:ACT610 3.9 18.8 1.0 CB A:ASN309 4.0 11.4 1.0 OE1 A:GLU340 4.0 15.6 1.0 ND1 A:HIS296 4.1 12.5 1.0 CB A:ASP369 4.1 13.2 1.0 CG A:HIS296 4.2 11.2 1.0 CG A:MET370 4.2 13.2 1.0 CB A:ASP308 4.3 16.0 1.0 CD A:GLU340 4.4 17.0 1.0 OE2 A:GLU340 4.5 18.3 1.0 CA A:ASP308 4.5 12.7 1.0 SD A:MET370 4.6 14.5 1.0 CG A:ASN309 4.6 11.1 1.0 CD A:GLU341 4.6 13.8 1.0 C A:ASP308 4.7 15.9 1.0 CA A:ASP369 4.7 12.3 1.0 N A:ASN309 4.8 12.5 1.0 C A:ASP369 4.8 12.8 1.0 CA A:ASN309 4.8 11.8 1.0 OE1 A:GLU341 5.0 17.5 1.0

Zinc binding site 6 out of 8 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:15.5 occ:1.00 OE2 A:GLU341 2.0 16.0 1.0 OD1 A:ASP308 2.0 14.9 1.0 NE2 A:HIS467 2.1 13.7 1.0 OXT A:ACT610 2.1 18.8 1.0 O A:ACT610 2.3 14.1 1.0 C A:ACT610 2.5 18.7 1.0 OE1 A:GLU341 2.6 17.5 1.0 CD A:GLU341 2.6 13.8 1.0 CD2 A:HIS467 3.0 16.4 1.0 CG A:ASP308 3.0 16.2 1.0 CE1 A:HIS467 3.1 14.1 1.0 OD2 A:ASP308 3.4 14.8 1.0 ZN A:ZN601 3.6 13.8 1.0 O A:HOH857 3.8 19.5 1.0 CE1 A:TYR466 3.9 17.9 1.0 O A:HOH756 4.0 15.0 1.0 OH A:TYR466 4.0 19.5 1.0 CH3 A:ACT610 4.0 19.8 1.0 CG A:GLU341 4.1 16.6 1.0 CG A:HIS467 4.2 19.6 1.0 ND1 A:HIS467 4.2 20.7 1.0 CZ A:TYR466 4.3 19.9 1.0 CB A:ASP308 4.3 16.0 1.0 OE1 A:GLU340 4.4 15.6 1.0 CG1 A:VAL300 4.6 16.6 1.0 NE2 A:HIS296 4.6 13.2 1.0 CE1 A:HIS296 4.7 11.7 1.0 O A:HOH902 4.8 22.1 1.0 CD1 A:TYR466 4.9 17.4 1.0

Zinc binding site 7 out of 8 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:17.1 occ:1.00 OD1 A:ASP384 2.0 17.5 1.0 OE2 A:GLU400 2.0 15.3 1.0 O A:HOH773 2.0 19.0 1.0 OD1 A:ASP382 2.0 17.1 1.0 OG A:SER386 2.2 19.8 1.0 O A:HOH724 2.2 18.2 1.0 CG A:ASP384 2.9 25.8 1.0 CD A:GLU400 3.0 19.4 1.0 OD2 A:ASP384 3.2 27.2 1.0 CG A:ASP382 3.2 15.4 1.0 OE1 A:GLU400 3.3 22.5 1.0 CB A:SER386 3.3 19.4 1.0 N A:SER386 3.8 19.2 1.0 CA A:ASP382 3.9 14.5 1.0 O A:HOH950 4.0 21.3 1.0 CB A:ASP382 4.0 16.5 1.0 OE1 A:GLU404 4.0 21.2 1.0 CA A:SER386 4.1 22.1 1.0 OD2 A:ASP387 4.2 26.5 1.0 OD2 A:ASP382 4.2 18.0 1.0 O A:HOH716 4.3 31.2 1.0 CG A:GLU400 4.3 14.0 1.0 CB A:ASP384 4.3 17.0 1.0 C A:ASP382 4.3 15.3 1.0 N A:ASP384 4.4 18.2 1.0 O A:HOH1196 4.4 38.5 1.0 N A:ASP387 4.5 20.8 1.0 N A:GLY385 4.6 18.1 1.0 CA A:ASP384 4.7 16.4 1.0 C A:SER386 4.7 21.0 1.0 CG A:ASP387 4.7 21.3 1.0 O A:ASP382 4.7 17.1 1.0 N A:GLY383 4.8 16.1 1.0 C A:ASP384 4.8 18.6 1.0 C A:GLY385 4.9 21.0 1.0

Zinc binding site 8 out of 8 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:17.5 occ:1.00 O A:HOH701 1.7 17.9 1.0 OE2 A:GLU482 1.9 19.9 1.0 OD2 A:ASP486 2.0 14.6 1.0 CG A:ASP486 2.9 17.2 1.0 CD A:GLU482 2.9 23.1 1.0 OD1 A:ASP486 3.1 14.8 1.0 CG A:GLU482 3.3 19.7 1.0 O A:HOH1037 3.9 19.2 1.0 NH1 A:ARG410 4.0 19.1 1.0 OE1 A:GLU482 4.1 20.6 1.0 NH2 A:ARG410 4.1 18.9 1.0 O A:GLU482 4.2 16.3 1.0 CB A:ASP486 4.3 16.3 1.0 O A:HOH709 4.4 9.9 1.0 CZ A:ARG410 4.6 19.5 1.0 C A:GLU482 4.6 15.2 1.0 O A:HOH894 4.6 26.1 1.0 CB A:GLU482 4.7 16.8 1.0

C.J.Harding, M.Bischoff, M.Bergkessel, C.M.Czekster. An Anti-Biofilm Cyclic Peptide Targets A Secreted Aminopeptidase From P. Aeruginosa. Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
PubMed: 37386135
DOI: 10.1038/S41589-023-01373-8