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

Protein crystallography data

The structure of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap, PDB code: 8ack 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) 42.83 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.292, 85.661, 98.097, 90, 93.85, 90
R / Rfree (%) 17.1 / 21

Other elements in 8ack:

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

Sodium (Na) 9 atoms
Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap (pdb code 8ack). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap, PDB code: 8ack:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8ack

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Zinc binding site 1 out of 10 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:Zn602

b:31.9
occ:1.00
 OD2 B:ASP308 2.0 34.0 1.0
OE2 B:GLU341 2.1 32.3 1.0
NE2 B:HIS467 2.2 30.3 1.0
O2 B:CAC601 2.3 39.1 1.0
H13 B:CAC601 2.5 85.7 1.0
OE1 B:GLU341 2.6 31.5 1.0
CD B:GLU341 2.7 36.7 1.0
CG B:ASP308 3.0 28.8 1.0
AS B:CAC601 3.0 55.8 1.0
CD2 B:HIS467 3.1 33.2 1.0
C1 B:CAC601 3.2 71.4 1.0
CE1 B:HIS467 3.3 34.6 1.0
OD1 B:ASP308 3.4 23.8 1.0
ZN B:ZN603 3.5 29.7 1.0
O1 B:CAC601 3.5 35.2 1.0
H12 B:CAC601 3.7 85.7 1.0
H11 B:CAC601 3.9 85.7 1.0
OH B:TYR466 3.9 35.2 1.0
CE1 B:TYR466 3.9 37.1 1.0
O B:HOH790 4.1 24.6 1.0
CG B:GLU341 4.2 31.9 1.0
CZ B:TYR466 4.3 42.7 1.0
CG B:HIS467 4.3 33.8 1.0
OE1 B:GLU340 4.3 30.9 1.0
ND1 B:HIS467 4.3 37.8 1.0
CB B:ASP308 4.4 31.2 1.0
CG1 B:VAL300 4.5 47.1 1.0
NE2 B:HIS296 4.6 26.6 1.0
CE1 B:HIS296 4.8 31.7 1.0
O B:HOH898 4.9 48.9 1.0
C2 B:CAC601 4.9 67.5 1.0
CD1 B:TYR466 4.9 40.4 1.0

Zinc binding site 2 out of 10 in 8ack

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Zinc binding site 2 out of 10 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:Zn603

b:29.7
occ:1.00
 OD1 B:ASP308 1.9 23.8 1.0
NE2 B:HIS296 2.2 26.6 1.0
OD1 B:ASP369 2.2 29.1 1.0
O2 B:CAC601 2.2 39.1 1.0
OD2 B:ASP369 2.6 25.8 1.0
CG B:ASP369 2.7 22.1 1.0
CG B:ASP308 2.9 28.8 1.0
CD2 B:HIS296 3.1 26.0 1.0
CE1 B:HIS296 3.2 31.7 1.0
AS B:CAC601 3.3 55.8 1.0
O1 B:CAC601 3.3 35.2 1.0
OD2 B:ASP308 3.4 34.0 1.0
ZN B:ZN602 3.5 31.9 1.0
H21 B:CAC601 3.8 81.0 1.0
OE1 B:GLU340 3.8 30.9 1.0
OE2 B:GLU341 3.9 32.3 1.0
OE2 B:GLU340 4.0 40.9 1.0
CD B:GLU340 4.1 37.8 1.0
CB B:ASN309 4.1 25.6 1.0
C2 B:CAC601 4.1 67.5 1.0
CB B:ASP369 4.2 23.6 1.0
CB B:ASP308 4.3 31.2 1.0
ND1 B:HIS296 4.3 25.2 1.0
CG B:HIS296 4.3 27.6 1.0
CG B:MET370 4.3 27.3 1.0
H22 B:CAC601 4.5 81.0 1.0
CA B:ASP308 4.6 27.4 1.0
CD B:GLU341 4.6 36.7 1.0
SD B:MET370 4.7 32.9 1.0
CG B:ASN309 4.7 22.3 1.0
CA B:ASP369 4.8 25.6 1.0
C B:ASP308 4.8 26.9 1.0
C B:ASP369 4.9 27.6 1.0
N B:ASN309 4.9 22.8 1.0
H23 B:CAC601 4.9 81.0 1.0
C1 B:CAC601 5.0 71.4 1.0
CA B:ASN309 5.0 24.6 1.0
H13 B:CAC601 5.0 85.7 1.0

Zinc binding site 3 out of 10 in 8ack

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Zinc binding site 3 out of 10 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:Zn604

b:37.3
occ:1.00
 OD1 B:ASP384 2.0 39.6 1.0
O B:HOH786 2.0 33.5 1.0
OD1 B:ASP382 2.1 35.6 1.0
OE2 B:GLU400 2.3 38.4 1.0
OG B:SER386 2.3 41.0 1.0
O B:HOH731 2.4 31.7 1.0
CG B:ASP384 2.9 43.4 1.0
CD B:GLU400 3.0 34.6 1.0
OE1 B:GLU400 3.0 39.0 1.0
OD2 B:ASP384 3.2 43.9 1.0
CG B:ASP382 3.3 44.0 1.0
CB B:SER386 3.5 40.8 1.0
O B:HOH713 3.8 31.2 1.0
N B:SER386 3.8 41.1 1.0
CA B:ASP382 3.9 33.9 1.0
CB B:ASP382 4.0 39.3 1.0
OE1 B:GLU404 4.1 46.9 1.0
OD2 B:ASP382 4.2 48.0 1.0
CA B:SER386 4.2 41.7 1.0
OD2 B:ASP387 4.3 48.0 1.0
O B:HOH752 4.3 53.3 1.0
CB B:ASP384 4.3 43.6 1.0
N B:ASP384 4.3 31.1 1.0
C B:ASP382 4.3 31.5 1.0
CG B:GLU400 4.4 33.3 1.0
N B:ASP387 4.4 49.9 1.0
N B:GLY385 4.5 39.8 1.0
CG B:ASP387 4.5 49.2 1.0
CA B:ASP384 4.7 32.6 1.0
C B:SER386 4.7 45.6 1.0
N B:GLY383 4.7 34.6 1.0
O B:ASP382 4.7 36.0 1.0
C B:ASP384 4.8 38.7 1.0
OD1 B:ASP387 4.8 58.4 1.0
C B:GLY385 4.9 44.5 1.0
O B:HOH902 5.0 43.2 1.0

Zinc binding site 4 out of 10 in 8ack

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Zinc binding site 4 out of 10 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:Zn605

b:31.2
occ:1.00
 OE1 B:GLU179 2.0 37.3 1.0
O B:HOH993 2.3 22.9 1.0
CD B:GLU179 2.8 29.8 1.0
OE2 B:GLU179 3.0 31.7 1.0
CB B:GLU177 4.1 34.6 1.0
N B:ALA178 4.2 24.7 1.0
CG B:GLU179 4.2 30.4 1.0
CG B:GLU177 4.2 35.8 1.0
N B:GLU179 4.5 28.1 1.0
CA B:GLU177 4.6 29.9 1.0
CB B:ALA178 4.7 31.9 1.0
C B:GLU177 4.8 26.2 1.0
CB B:GLU179 4.8 28.4 1.0
CA B:ALA178 4.9 31.6 1.0

Zinc binding site 5 out of 10 in 8ack

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Zinc binding site 5 out of 10 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
B:Zn606

b:44.5
occ:1.00
 OD2 B:ASP82 2.4 51.6 1.0
OD1 B:ASP82 2.5 41.1 1.0
CG B:ASP82 2.7 43.5 1.0
O B:HOH738 3.4 50.6 1.0
CB B:ASP82 4.2 35.9 1.0
O B:HOH733 4.4 48.3 1.0
O B:HOH1001 4.8 56.6 1.0

Zinc binding site 6 out of 10 in 8ack

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Zinc binding site 6 out of 10 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:33.2
occ:1.00
 OD2 A:ASP308 2.0 34.3 1.0
OE2 A:GLU341 2.1 38.8 1.0
NE2 A:HIS467 2.1 32.4 1.0
H22 A:CAC601 2.4 77.1 1.0
O2 A:CAC601 2.4 32.4 1.0
OE1 A:GLU341 2.5 34.4 1.0
CD A:GLU341 2.6 40.2 1.0
C2 A:CAC601 2.9 64.3 1.0
CG A:ASP308 3.0 33.7 1.0
CD2 A:HIS467 3.0 34.2 1.0
AS A:CAC601 3.0 52.8 1.0
CE1 A:HIS467 3.1 29.8 1.0
H21 A:CAC601 3.2 77.1 1.0
OD1 A:ASP308 3.4 26.3 1.0
ZN A:ZN603 3.6 30.3 1.0
O1 A:CAC601 3.6 38.2 1.0
H23 A:CAC601 3.8 77.1 1.0
CE1 A:TYR466 3.9 31.6 1.0
O A:HOH741 3.9 27.0 1.0
OH A:TYR466 4.0 36.8 1.0
CG A:GLU341 4.1 35.3 1.0
CG A:HIS467 4.2 37.6 1.0
ND1 A:HIS467 4.2 33.6 1.0
OE1 A:GLU340 4.2 35.2 1.0
CZ A:TYR466 4.3 36.1 1.0
CB A:ASP308 4.3 33.8 1.0
NE2 A:HIS296 4.6 26.7 1.0
CG1 A:VAL300 4.6 31.7 1.0
CE1 A:HIS296 4.7 28.3 1.0
CD1 A:TYR466 4.8 33.7 1.0
C1 A:CAC601 4.9 66.4 1.0

Zinc binding site 7 out of 10 in 8ack

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Zinc binding site 7 out of 10 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:30.3
occ:1.00
 OD1 A:ASP308 1.9 26.3 1.0
NE2 A:HIS296 2.1 26.7 1.0
O2 A:CAC601 2.1 32.4 1.0
OD1 A:ASP369 2.1 27.4 1.0
OD2 A:ASP369 2.5 30.2 1.0
CG A:ASP369 2.6 23.5 1.0
CG A:ASP308 2.9 33.7 1.0
CD2 A:HIS296 3.0 24.4 1.0
CE1 A:HIS296 3.1 28.3 1.0
AS A:CAC601 3.3 52.8 1.0
OD2 A:ASP308 3.4 34.3 1.0
O1 A:CAC601 3.4 38.2 1.0
ZN A:ZN602 3.6 33.2 1.0
OE1 A:GLU340 3.8 35.2 1.0
H11 A:CAC601 3.9 79.7 1.0
OE2 A:GLU341 4.0 38.8 1.0
CB A:ASN309 4.0 26.0 1.0
CB A:ASP369 4.1 24.0 1.0
OE2 A:GLU340 4.1 53.4 1.0
CD A:GLU340 4.1 40.2 1.0
ND1 A:HIS296 4.2 28.4 1.0
CG A:HIS296 4.2 27.6 1.0
CB A:ASP308 4.2 33.8 1.0
C1 A:CAC601 4.2 66.4 1.0
CG A:MET370 4.3 22.1 1.0
CA A:ASP308 4.6 28.8 1.0
CD A:GLU341 4.6 40.2 1.0
CG A:ASN309 4.7 25.9 1.0
SD A:MET370 4.7 31.3 1.0
CA A:ASP369 4.7 23.0 1.0
C A:ASP308 4.8 25.6 1.0
H12 A:CAC601 4.8 79.7 1.0
C A:ASP369 4.8 27.2 1.0
C2 A:CAC601 4.9 64.3 1.0
OE1 A:GLU341 4.9 34.4 1.0
H13 A:CAC601 4.9 79.7 1.0
N A:ASN309 4.9 30.0 1.0
CA A:ASN309 4.9 26.9 1.0
H22 A:CAC601 4.9 77.1 1.0

Zinc binding site 8 out of 10 in 8ack

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Zinc binding site 8 out of 10 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:31.4
occ:1.00
 OD2 A:ASP486 2.0 29.9 1.0
OE1 A:GLU482 2.0 35.7 1.0
O A:HOH985 2.1 34.0 1.0
CG A:ASP486 2.8 29.6 1.0
O A:HOH993 2.8 29.9 1.0
CD A:GLU482 2.9 30.1 1.0
OD1 A:ASP486 2.9 25.6 1.0
CG A:GLU482 3.1 28.1 1.0
O A:HOH706 3.3 17.3 1.0
NH1 A:ARG410 3.7 48.6 1.0
NH2 A:ARG410 4.0 44.7 1.0
OE2 A:GLU482 4.0 28.8 1.0
CB A:ASP486 4.2 24.5 1.0
O A:HOH982 4.3 44.8 1.0
O A:GLU482 4.3 25.4 1.0
CZ A:ARG410 4.3 47.8 1.0
O A:HOH939 4.4 43.4 1.0
CB A:GLU482 4.6 24.3 1.0
O A:HOH802 4.6 49.0 1.0
C A:GLU482 4.7 26.9 1.0
O A:PRO59 4.9 35.0 1.0

Zinc binding site 9 out of 10 in 8ack

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Zinc binding site 9 out of 10 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 9 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:39.1
occ:1.00
 O A:HOH786 1.9 41.7 1.0
OD1 A:ASP382 2.0 39.6 1.0
OE2 A:GLU400 2.0 39.0 1.0
OD1 A:ASP384 2.0 48.8 1.0
O A:HOH784 2.3 34.7 1.0
OG A:SER386 2.5 38.4 1.0
CG A:ASP384 2.9 49.5 1.0
CD A:GLU400 3.0 39.5 1.0
OD2 A:ASP384 3.2 48.3 1.0
CG A:ASP382 3.2 33.3 1.0
OE1 A:GLU400 3.2 37.7 1.0
CB A:SER386 3.5 39.4 1.0
O A:HOH739 3.7 36.0 1.0
N A:SER386 3.8 46.5 1.0
CA A:ASP382 4.0 30.9 1.0
CB A:ASP382 4.0 33.2 1.0
OE1 A:GLU404 4.1 42.6 1.0
OD2 A:ASP382 4.1 44.0 1.0
CA A:SER386 4.2 41.3 1.0
CB A:ASP384 4.3 42.4 1.0
OD2 A:ASP387 4.3 45.4 1.0
CG A:GLU400 4.3 32.8 1.0
C A:ASP382 4.3 31.6 1.0
O A:HOH750 4.4 49.4 1.0
N A:ASP384 4.4 44.4 1.0
N A:GLY385 4.5 35.8 1.0
N A:ASP387 4.5 36.9 1.0
CA A:ASP384 4.7 42.1 1.0
C A:ASP384 4.7 36.7 1.0
N A:GLY383 4.7 33.6 1.0
O A:ASP382 4.7 35.2 1.0
C A:SER386 4.8 38.9 1.0
CG A:ASP387 4.8 48.1 1.0
O A:HOH806 4.8 45.4 1.0
C A:GLY385 4.9 54.7 1.0

Zinc binding site 10 out of 10 in 8ack

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Zinc binding site 10 out of 10 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 10 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:94.6
occ:1.00
 O A:HOH875 2.2 70.5 1.0
O A:HOH1050 2.5 67.2 1.0
OE1 A:GLU235 2.6 40.4 1.0
OE2 A:GLU235 2.7 39.8 1.0
CD A:GLU235 3.1 42.8 1.0
O A:HOH1021 3.3 55.2 1.0
O A:HOH872 4.3 39.9 1.0
O A:HOH933 4.3 40.1 1.0
CA A:SER236 4.5 36.8 1.0
O A:GLU235 4.5 33.6 1.0
O A:PRO116 4.5 42.2 1.0
CB A:SER236 4.5 42.0 1.0
CG A:GLU235 4.6 38.5 1.0
N A:SER236 4.8 30.7 1.0
C A:GLU235 4.8 33.1 1.0

Reference:

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
Page generated: Fri Aug 22 08:13:12 2025

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