Zinc in PDB 8ac9: Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T

Protein crystallography data

The structure of Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T, PDB code: 8ac9 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) 48.05 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.997, 52.502, 114.383, 90, 95.76, 90
R / Rfree (%) 18.2 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T (pdb code 8ac9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T, PDB code: 8ac9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8ac9

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Zinc binding site 1 out of 7 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T


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_T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:48.4
occ:1.00
 NE2 A:HIS296 2.0 36.5 1.0
OD1 A:ASP308 2.0 44.8 1.0
OD1 A:ASP369 2.1 35.2 1.0
O A:HOH712 2.3 43.0 1.0
OD2 A:ASP369 2.6 35.6 1.0
CG A:ASP369 2.7 37.0 1.0
CE1 A:HIS296 2.9 30.1 1.0
CD2 A:HIS296 3.0 29.3 1.0
CG A:ASP308 3.1 35.3 1.0
ZN A:ZN602 3.4 47.7 1.0
OD2 A:ASP308 3.5 44.3 1.0
OE1 A:GLU340 3.8 36.5 1.0
O A:HOH730 3.9 44.5 1.0
CB A:ASN309 4.0 30.4 1.0
OE2 A:GLU340 4.0 42.1 1.0
OE2 A:GLU341 4.0 38.9 1.0
ND1 A:HIS296 4.1 32.9 1.0
CD A:GLU340 4.1 36.1 1.0
CG A:MET370 4.1 30.8 1.0
CG A:HIS296 4.2 34.5 1.0
CB A:ASP369 4.2 25.9 1.0
CB A:ASP308 4.3 36.4 1.0
SD A:MET370 4.6 37.8 1.0
CD A:GLU341 4.6 36.6 1.0
CA A:ASP308 4.6 34.1 1.0
CG A:ASN309 4.7 34.6 1.0
C A:ASP308 4.8 34.3 1.0
OE1 A:GLU341 4.8 36.6 1.0
CA A:ASP369 4.9 30.1 1.0
CA A:ASN309 4.9 40.4 1.0
N A:ASN309 4.9 33.7 1.0
C A:ASP369 5.0 31.2 1.0
OG A:SER423 5.0 38.7 1.0

Zinc binding site 2 out of 7 in 8ac9

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Zinc binding site 2 out of 7 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T


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_T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:47.7
occ:1.00
 O A:HOH712 2.1 43.0 1.0
OD2 A:ASP308 2.1 44.3 1.0
NE2 A:HIS467 2.2 37.8 1.0
OE2 A:GLU341 2.2 38.9 1.0
O A:HOH730 2.3 44.5 1.0
OE1 A:GLU341 2.4 36.6 1.0
CD A:GLU341 2.6 36.6 1.0
CG A:ASP308 3.1 35.3 1.0
CD2 A:HIS467 3.2 38.7 1.0
CE1 A:HIS467 3.2 39.8 1.0
OD1 A:ASP308 3.3 44.8 1.0
ZN A:ZN601 3.4 48.4 1.0
OH A:TYR466 3.9 44.9 1.0
CE1 A:TYR466 4.1 40.0 1.0
OE1 A:GLU340 4.1 36.5 1.0
O A:HOH728 4.1 30.8 1.0
CG A:GLU341 4.2 35.0 1.0
ND1 A:HIS467 4.3 44.1 1.0
CG A:HIS467 4.3 48.2 1.0
CZ A:TYR466 4.4 40.4 1.0
CB A:ASP308 4.4 36.4 1.0
NE2 A:HIS296 4.5 36.5 1.0
CE1 A:HIS296 4.6 30.1 1.0
CG1 A:VAL300 4.8 27.7 1.0
OE2 A:GLU340 4.8 42.1 1.0
CD A:GLU340 4.9 36.1 1.0

Zinc binding site 3 out of 7 in 8ac9

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Zinc binding site 3 out of 7 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T


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_T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:80.6
occ:1.00
 OG1 A:THR173 2.3 48.1 1.0
O A:THR173 2.5 49.6 1.0
OD2 A:ASP163 2.5 62.1 1.0
OE1 A:GLU177 2.5 68.9 1.0
OD2 A:ASP180 2.6 54.1 1.0
OD1 A:ASP180 2.6 55.4 1.0
CG A:ASP180 2.9 47.6 1.0
C A:THR173 3.3 45.7 1.0
CG A:ASP163 3.3 57.9 1.0
CB A:THR173 3.4 50.2 1.0
CD A:GLU177 3.7 75.3 1.0
OD1 A:ASP163 3.9 62.0 1.0
CA A:THR173 3.9 44.0 1.0
N A:SER174 4.1 41.9 1.0
CB A:ASP163 4.2 56.2 1.0
N A:CYS176 4.3 51.4 1.0
N A:GLY175 4.3 52.2 1.0
N A:GLU177 4.3 62.1 1.0
CA A:SER174 4.4 50.8 1.0
OE2 A:GLU177 4.4 77.3 1.0
CB A:ASP180 4.4 61.2 1.0
C A:SER174 4.6 58.9 1.0
CG2 A:THR173 4.7 49.4 1.0
CB A:GLU177 4.7 62.8 1.0
N A:THR173 4.7 44.4 1.0
CB A:CYS176 4.8 62.4 1.0
CG A:GLU177 4.8 70.9 1.0
CA A:CYS176 4.9 58.7 1.0

Zinc binding site 4 out of 7 in 8ac9

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Zinc binding site 4 out of 7 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T


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_T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:78.7
occ:1.00
 OD1 A:ASP384 2.1 94.9 1.0
OD1 A:ASP382 2.3 59.7 1.0
O A:HOH708 2.6 54.7 1.0
OE2 A:GLU400 2.7 61.3 1.0
O A:HOH705 2.8 69.5 1.0
OG A:SER386 2.8 59.4 1.0
OE1 A:GLU400 2.9 57.2 1.0
CD A:GLU400 3.0 56.0 1.0
CG A:ASP384 3.1 74.7 1.0
CB A:SER386 3.3 59.3 1.0
OD2 A:ASP384 3.4 80.7 1.0
CG A:ASP382 3.5 53.8 1.0
N A:SER386 3.8 62.7 1.0
CA A:SER386 4.1 58.2 1.0
CA A:ASP382 4.2 58.9 1.0
OE2 A:GLU404 4.2 86.5 1.0
OD2 A:ASP387 4.3 78.3 1.0
CB A:ASP382 4.3 58.5 1.0
CG A:GLU400 4.4 52.7 1.0
N A:ASP387 4.4 73.8 1.0
OD2 A:ASP382 4.4 60.6 1.0
CB A:ASP384 4.4 64.1 1.0
C A:ASP382 4.6 59.6 1.0
N A:ASP384 4.6 60.1 1.0
CG A:ASP387 4.6 82.5 1.0
C A:SER386 4.7 69.9 1.0
N A:GLY385 4.7 59.0 1.0
C A:ASP384 4.8 63.2 1.0
CA A:ASP384 4.8 63.0 1.0
N A:GLY383 4.9 63.0 1.0
C A:GLY385 5.0 66.2 1.0
O A:ASP382 5.0 57.8 1.0

Zinc binding site 5 out of 7 in 8ac9

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Zinc binding site 5 out of 7 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T


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_T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:43.9
occ:1.00
 O B:HOH737 2.2 50.4 1.0
OD2 B:ASP308 2.2 41.3 1.0
O B:HOH707 2.2 34.2 1.0
NE2 B:HIS467 2.2 38.0 1.0
OE2 B:GLU341 2.2 41.2 1.0
OE1 B:GLU341 2.4 37.0 1.0
CD B:GLU341 2.6 40.5 1.0
CE1 B:HIS467 3.1 37.0 1.0
CG B:ASP308 3.1 35.5 1.0
CD2 B:HIS467 3.3 37.8 1.0
ZN B:ZN602 3.3 46.5 1.0
OD1 B:ASP308 3.3 35.1 1.0
OH B:TYR466 3.8 47.2 1.0
CE1 B:TYR466 4.0 40.2 1.0
OE1 B:GLU340 4.1 33.2 1.0
CG B:GLU341 4.2 38.2 1.0
ND1 B:HIS467 4.3 35.9 1.0
CZ B:TYR466 4.3 42.8 1.0
O B:HOH738 4.3 40.9 1.0
CG B:HIS467 4.4 43.6 1.0
CB B:ASP308 4.5 40.3 1.0
NE2 B:HIS296 4.5 34.8 1.0
CE1 B:HIS296 4.6 26.7 1.0
CG1 B:VAL300 4.8 31.9 1.0
OE2 B:GLU340 4.9 35.8 1.0
CD B:GLU340 4.9 33.8 1.0

Zinc binding site 6 out of 7 in 8ac9

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Zinc binding site 6 out of 7 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T


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_T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:46.5
occ:1.00
 OD1 B:ASP308 2.1 35.1 1.0
NE2 B:HIS296 2.1 34.8 1.0
OD1 B:ASP369 2.2 42.0 1.0
O B:HOH707 2.4 34.2 1.0
OD2 B:ASP369 2.7 36.7 1.0
CG B:ASP369 2.7 32.2 1.0
CG B:ASP308 3.1 35.5 1.0
CD2 B:HIS296 3.1 28.8 1.0
CE1 B:HIS296 3.1 26.7 1.0
ZN B:ZN601 3.3 43.9 1.0
OD2 B:ASP308 3.4 41.3 1.0
O B:HOH737 3.6 50.4 1.0
OE1 B:GLU340 3.8 33.2 1.0
OE2 B:GLU340 4.0 35.8 1.0
OE2 B:GLU341 4.0 41.2 1.0
CD B:GLU340 4.1 33.8 1.0
CB B:ASN309 4.1 33.8 1.0
CG B:MET370 4.2 35.4 1.0
ND1 B:HIS296 4.2 31.7 1.0
CG B:HIS296 4.2 31.8 1.0
CB B:ASP369 4.3 24.4 1.0
CB B:ASP308 4.4 40.3 1.0
SD B:MET370 4.5 37.2 1.0
CD B:GLU341 4.6 40.5 1.0
OE1 B:GLU341 4.7 37.0 1.0
CA B:ASP308 4.7 41.4 1.0
CG B:ASN309 4.8 39.8 1.0
C B:ASP308 4.9 36.1 1.0
CA B:ASP369 4.9 30.6 1.0
C B:ASP369 5.0 34.8 1.0
CA B:ASN309 5.0 37.9 1.0

Zinc binding site 7 out of 7 in 8ac9

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


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_T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:68.8
occ:1.00
 O B:HOH710 2.2 43.3 1.0
O B:HOH724 2.4 40.1 1.0
OD1 B:ASP384 2.4 55.9 1.0
OD1 B:ASP382 2.5 49.7 1.0
OE2 B:GLU400 2.5 42.1 1.0
OG B:SER386 2.8 47.4 1.0
OE1 B:GLU400 2.9 50.9 1.0
CD B:GLU400 2.9 41.4 1.0
CG B:ASP384 3.2 54.5 1.0
OD2 B:ASP384 3.4 52.1 1.0
CB B:SER386 3.5 48.9 1.0
CG B:ASP382 3.7 50.7 1.0
N B:SER386 4.0 45.8 1.0
CA B:ASP382 4.1 39.7 1.0
OE2 B:GLU404 4.2 78.9 1.0
CA B:SER386 4.2 51.4 1.0
O B:HOH703 4.2 50.6 1.0
CG B:GLU400 4.3 44.1 1.0
N B:ASP387 4.4 51.2 1.0
CB B:ASP382 4.4 46.5 1.0
C B:ASP382 4.5 39.6 1.0
N B:ASP384 4.5 43.6 1.0
CB B:ASP384 4.6 47.7 1.0
CG B:ASP387 4.6 54.6 1.0
OD2 B:ASP382 4.6 48.9 1.0
OD2 B:ASP387 4.6 61.3 1.0
OD1 B:ASP387 4.7 62.1 1.0
N B:GLY383 4.7 46.5 1.0
C B:SER386 4.7 50.4 1.0
N B:GLY385 4.8 50.3 1.0
CA B:ASP384 4.9 48.0 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: Wed Oct 30 17:39:24 2024

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