Zinc in PDB 8acg: Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant

Protein crystallography data

The structure of Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant, PDB code: 8acg 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) 49.57 / 2.84
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 186.74, 186.74, 84.73, 90, 90, 120
R / Rfree (%) 19.1 / 23.9

Other elements in 8acg:

The structure of Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant (pdb code 8acg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant, PDB code: 8acg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 8acg

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Zinc binding site 1 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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 E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn601

b:97.2
occ:1.00
 NE2 F:HIS467 2.2 90.6 1.0
OD2 F:ASP308 2.3 87.2 1.0
OE2 F:GLU341 2.3 85.1 1.0
OE1 F:GLU341 2.6 86.5 1.0
CD F:GLU341 2.8 85.9 1.0
CE1 F:HIS467 3.0 91.5 1.0
O F:HOH703 3.0 74.9 1.0
CG F:ASP308 3.1 86.2 1.0
ZN F:ZN602 3.3 86.1 1.0
OD1 F:ASP308 3.3 85.6 1.0
CD2 F:HIS467 3.3 91.3 1.0
OH F:TYR466 4.0 90.8 1.0
CE1 F:TYR466 4.0 90.7 1.0
ND1 F:HIS467 4.2 92.7 1.0
CG F:HIS467 4.4 92.8 1.0
CZ F:TYR466 4.4 91.7 1.0
CG F:GLU341 4.4 86.5 1.0
CB F:ASP308 4.5 86.3 1.0
NE2 F:HIS296 4.6 81.7 1.0
CE1 F:HIS296 4.9 82.3 1.0

Zinc binding site 2 out of 18 in 8acg

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Zinc binding site 2 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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 E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn602

b:86.1
occ:1.00
 OD1 F:ASP369 2.1 84.2 1.0
OD1 F:ASP308 2.1 85.6 1.0
NE2 F:HIS296 2.5 81.7 1.0
OD2 F:ASP369 2.6 84.0 1.0
CG F:ASP369 2.7 83.8 1.0
CG F:ASP308 3.1 86.2 1.0
O F:HOH703 3.2 74.9 1.0
ZN F:ZN601 3.3 97.2 1.0
CD2 F:HIS296 3.3 81.4 1.0
CE1 F:HIS296 3.5 82.3 1.0
OD2 F:ASP308 3.6 87.2 1.0
OE2 F:GLU341 3.8 85.1 1.0
CB F:ASP369 4.2 82.9 1.0
CG F:MET370 4.3 84.6 1.0
CB F:ASN309 4.4 83.3 1.0
CB F:ASP308 4.4 86.3 1.0
CG F:HIS296 4.5 82.7 1.0
ND1 F:HIS296 4.6 83.1 1.0
SD F:MET370 4.6 86.6 1.0
CD F:GLU341 4.7 85.9 1.0
CA F:ASP308 4.7 85.4 1.0
CA F:ASP369 4.9 82.7 1.0
C F:ASP369 4.9 83.7 1.0
OE1 F:GLU341 4.9 86.5 1.0
CG F:ASN309 4.9 82.6 1.0

Zinc binding site 3 out of 18 in 8acg

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Zinc binding site 3 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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 E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn603

b:114.9
occ:1.00
 OD1 F:ASP384 2.4 95.1 1.0
OD1 F:ASP382 2.4 92.6 1.0
OE2 F:GLU400 2.4 91.5 1.0
OG F:SER386 2.6 94.3 1.0
CB F:SER386 3.1 93.7 1.0
CD F:GLU400 3.2 88.6 1.0
CG F:ASP384 3.2 94.2 1.0
OE1 F:GLU400 3.3 87.9 1.0
OD2 F:ASP384 3.4 96.0 1.0
CG F:ASP382 3.5 92.8 1.0
N F:SER386 3.7 88.6 1.0
CA F:SER386 4.0 93.3 1.0
OE2 F:GLU404 4.1 89.3 1.0
OD2 F:ASP387 4.1 95.1 1.0
CA F:ASP382 4.3 86.7 1.0
OD2 F:ASP382 4.4 95.1 1.0
CB F:ASP382 4.4 90.4 1.0
CG F:GLU400 4.5 86.3 1.0
N F:ASP387 4.5 92.8 1.0
CB F:ASP384 4.6 91.2 1.0
C F:SER386 4.6 97.4 1.0
N F:ASP384 4.6 88.7 1.0
C F:ASP382 4.7 84.3 1.0
N F:GLY385 4.8 87.8 1.0
CG F:ASP387 4.9 98.5 1.0
C F:GLY385 4.9 94.7 1.0
CA F:ASP384 5.0 90.0 1.0

Zinc binding site 4 out of 18 in 8acg

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Zinc binding site 4 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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 E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:88.4
occ:1.00
 OD1 D:ASP369 2.1 81.6 1.0
OD1 D:ASP308 2.1 82.3 1.0
NE2 D:HIS296 2.3 79.5 1.0
OD2 D:ASP369 2.7 81.8 1.0
CG D:ASP369 2.7 81.2 1.0
CG D:ASP308 3.1 83.3 1.0
O D:HOH701 3.1 78.3 1.0
CD2 D:HIS296 3.2 78.9 1.0
CE1 D:HIS296 3.3 80.0 1.0
ZN D:ZN602 3.4 98.1 1.0
OD2 D:ASP308 3.5 84.5 1.0
OE2 D:GLU341 4.0 94.1 1.0
CB D:ASP369 4.2 80.2 1.0
CB D:ASN309 4.2 79.2 1.0
CG D:HIS296 4.4 79.5 1.0
ND1 D:HIS296 4.4 80.1 1.0
CB D:ASP308 4.4 83.4 1.0
CG D:MET370 4.6 82.3 1.0
CD D:GLU341 4.6 95.0 1.0
CG D:ASN309 4.8 78.2 1.0
OE1 D:GLU341 4.8 96.0 1.0
CA D:ASP308 4.8 82.5 1.0
CA D:ASP369 4.8 79.6 1.0
SD D:MET370 4.8 83.8 1.0

Zinc binding site 5 out of 18 in 8acg

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Zinc binding site 5 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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 E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:98.1
occ:1.00
 OD2 D:ASP308 2.3 84.5 1.0
NE2 D:HIS467 2.3 95.8 1.0
OE2 D:GLU341 2.5 94.1 1.0
OE1 D:GLU341 2.5 96.0 1.0
CD D:GLU341 2.9 95.0 1.0
CE1 D:HIS467 3.1 97.4 1.0
O D:HOH701 3.3 78.3 1.0
CG D:ASP308 3.3 83.3 1.0
ZN D:ZN601 3.4 88.4 1.0
CD2 D:HIS467 3.5 96.0 1.0
OD1 D:ASP308 3.6 82.3 1.0
OH D:TYR466 3.7 96.1 1.0
CE1 D:TYR466 4.0 94.9 1.0
CZ D:TYR466 4.2 96.2 1.0
ND1 D:HIS467 4.3 98.5 1.0
CG D:GLU341 4.4 94.9 1.0
CG D:HIS467 4.5 97.7 1.0
CB D:ASP308 4.7 83.4 1.0
NE2 D:HIS296 4.8 79.5 1.0

Zinc binding site 6 out of 18 in 8acg

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Zinc binding site 6 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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 E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:116.3
occ:1.00
 OE2 D:GLU400 2.3 83.1 1.0
OD1 D:ASP384 2.4 92.2 1.0
OD1 D:ASP382 2.6 94.2 1.0
OG D:SER386 2.9 97.0 1.0
CD D:GLU400 3.0 83.8 1.0
OE1 D:GLU400 3.1 85.2 1.0
CG D:ASP384 3.2 92.8 1.0
OD2 D:ASP384 3.4 92.7 1.0
CB D:SER386 3.5 97.1 1.0
CG D:ASP382 3.7 93.3 1.0
OD2 D:ASP387 3.8 95.2 1.0
OE2 D:GLU404 4.0 86.7 1.0
CA D:ASP382 4.1 91.0 1.0
N D:SER386 4.1 97.3 1.0
CG D:GLU400 4.3 82.9 1.0
CB D:ASP382 4.4 91.3 1.0
CA D:SER386 4.4 97.8 1.0
C D:ASP382 4.5 92.1 1.0
CB D:ASP384 4.6 93.5 1.0
N D:ASP384 4.6 91.6 1.0
OD2 D:ASP382 4.7 94.1 1.0
CG D:ASP387 4.7 96.1 1.0
N D:ASP387 4.7 98.3 1.0
N D:GLY383 4.8 87.8 1.0
C D:SER386 4.9 97.5 1.0
CA D:ASP384 5.0 93.3 1.0
N D:GLY385 5.0 93.7 1.0

Zinc binding site 7 out of 18 in 8acg

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Zinc binding site 7 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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 E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:107.2
occ:1.00
 OD2 A:ASP308 2.4 88.7 1.0
OE2 A:GLU341 2.5 101.0 1.0
OE1 A:GLU341 2.6 98.3 1.0
CE1 A:HIS467 2.6 95.3 1.0
CD A:GLU341 2.9 99.6 1.0
ZN A:ZN602 3.1 96.1 1.0
NE2 A:HIS467 3.2 95.6 1.0
CG A:ASP308 3.3 90.2 1.0
OD1 A:ASP308 3.5 90.0 1.0
O A:HOH701 3.6 82.8 1.0
ND1 A:HIS467 3.8 96.9 1.0
OH A:TYR466 4.0 96.2 1.0
CE1 A:TYR466 4.3 97.8 1.0
CG A:GLU341 4.5 100.3 1.0
NE2 A:HIS296 4.5 90.2 1.0
CD2 A:HIS467 4.5 97.3 1.0
CZ A:TYR466 4.6 97.7 1.0
CE1 A:HIS296 4.7 91.3 1.0
CB A:ASP308 4.7 93.4 1.0
CG A:HIS467 4.8 98.3 1.0

Zinc binding site 8 out of 18 in 8acg

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Zinc binding site 8 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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_T E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:96.1
occ:1.00
 OD1 A:ASP308 2.0 90.0 1.0
OD1 A:ASP369 2.2 89.0 1.0
NE2 A:HIS296 2.4 90.2 1.0
OD2 A:ASP369 2.6 86.7 1.0
CG A:ASP369 2.7 87.8 1.0
CG A:ASP308 3.0 90.2 1.0
ZN A:ZN601 3.1 107.2 1.0
OD2 A:ASP308 3.3 88.7 1.0
CE1 A:HIS296 3.4 91.3 1.0
CD2 A:HIS296 3.4 89.3 1.0
O A:HOH701 3.4 82.8 1.0
OE2 A:GLU341 4.1 101.0 1.0
CB A:ASP369 4.2 88.0 1.0
CB A:ASP308 4.3 93.4 1.0
CG A:MET370 4.3 89.5 1.0
CB A:ASN309 4.5 90.5 1.0
ND1 A:HIS296 4.5 91.2 1.0
SD A:MET370 4.5 86.9 1.0
CG A:HIS296 4.5 89.9 1.0
CA A:ASP308 4.8 97.3 1.0
CD A:GLU341 4.8 99.6 1.0
OE1 A:GLU341 4.9 98.3 1.0
CA A:ASP369 4.9 90.2 1.0
C A:ASP369 4.9 90.8 1.0
CG A:ASN309 5.0 90.2 1.0

Zinc binding site 9 out of 18 in 8acg

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Zinc binding site 9 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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_T E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:113.6
occ:1.00
 OD1 A:ASP384 2.3 93.6 1.0
OD1 A:ASP382 2.5 92.2 1.0
OE2 A:GLU400 2.7 88.8 1.0
CB A:SER386 2.8 95.3 1.0
OG A:SER386 2.9 95.2 1.0
OD2 A:ASP384 3.0 92.9 1.0
CG A:ASP384 3.0 93.8 1.0
CD A:GLU400 3.4 89.0 1.0
OE1 A:GLU400 3.4 89.7 1.0
OD2 A:ASP387 3.5 91.2 1.0
N A:SER386 3.7 95.7 1.0
CG A:ASP382 3.7 92.2 1.0
CA A:SER386 3.7 97.2 1.0
OE2 A:GLU404 4.3 86.6 1.0
N A:ASP387 4.4 96.6 1.0
CG A:ASP387 4.4 93.5 1.0
C A:SER386 4.4 98.2 1.0
CB A:ASP384 4.4 95.2 1.0
CA A:ASP382 4.4 90.1 1.0
CB A:ASP382 4.5 90.4 1.0
OD2 A:ASP382 4.6 94.0 1.0
CG A:GLU400 4.8 88.5 1.0
N A:ASP384 4.8 94.9 1.0
C A:ASP382 4.8 92.4 1.0
N A:GLY385 4.9 93.5 1.0
C A:GLY385 4.9 97.1 1.0
CA A:ASP384 5.0 96.1 1.0

Zinc binding site 10 out of 18 in 8acg

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Zinc binding site 10 out of 18 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, PAAP_T E340A Mutant


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_T E340A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:104.2
occ:1.00
 OD2 E:ASP308 2.3 97.0 1.0
NE2 E:HIS467 2.4 101.2 1.0
OE1 E:GLU341 2.5 103.0 1.0
OE2 E:GLU341 2.6 102.3 1.0
CD E:GLU341 2.9 102.4 1.0
CE1 E:HIS467 3.2 102.0 1.0
CG E:ASP308 3.3 96.5 1.0
O E:HOH701 3.3 86.4 1.0
ZN E:ZN602 3.4 99.5 1.0
CD2 E:HIS467 3.6 102.4 1.0
OD1 E:ASP308 3.6 95.3 1.0
OH E:TYR466 4.0 99.9 1.0
CE1 E:TYR466 4.2 100.6 1.0
CG E:GLU341 4.4 102.5 1.0
ND1 E:HIS467 4.4 103.5 1.0
CZ E:TYR466 4.5 101.0 1.0
CB E:ASP308 4.6 98.0 1.0
CG E:HIS467 4.6 103.8 1.0
NE2 E:HIS296 4.8 96.2 1.0
CG1 E:VAL300 4.9 105.0 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: Fri Jul 28 06:20:16 2023

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