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Potassium in PDB 5wdk: A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis

Protein crystallography data

The structure of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis, PDB code: 5wdk was solved by D.W.Wolan, J.H.Xu, A.Solania, S.Chatterjee, Z.Jiang, A.J.Odonoghue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.10 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.912, 136.969, 208.235, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.1

Potassium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Potassium atom in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis (pdb code 5wdk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 11 binding sites of Potassium where determined in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis, PDB code: 5wdk:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 11 in 5wdk

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Potassium binding site 1 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K501

b:94.1
occ:1.00
 O A:GLU335 2.6 51.3 1.0
OD2 A:ASP271 2.7 72.2 1.0
OE2 A:GLU274 2.7 66.9 1.0
OG A:SER273 3.0 57.9 1.0
O A:SER273 3.4 75.8 1.0
C A:GLU335 3.5 46.8 1.0
CG A:ASP271 3.6 69.4 1.0
CD A:GLU274 3.8 75.2 1.0
OD1 A:ASP271 3.9 77.4 1.0
OG1 A:THR337 4.0 66.6 1.0
CA A:GLU335 4.1 48.8 1.0
CB A:SER273 4.2 56.7 1.0
C A:SER273 4.2 71.7 1.0
O A:TYR334 4.4 51.8 1.0
OE1 A:GLU274 4.4 78.5 1.0
N A:THR336 4.5 47.4 1.0
NZ A:LYS383 4.6 56.9 1.0
CA A:SER273 4.7 58.8 1.0
CA A:THR336 4.8 50.4 1.0
N A:THR337 4.8 55.7 1.0
CG A:GLU274 4.9 72.0 1.0
CB A:GLU335 4.9 43.1 1.0

Potassium binding site 2 out of 11 in 5wdk

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Potassium binding site 2 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:58.8
occ:1.00
 OD1 A:ASP78 2.5 70.6 1.0
OE1 A:GLU81 2.6 61.3 1.0
OE1 A:GLU126 2.6 55.3 1.0
O A:HOH602 2.7 62.6 1.0
O A:LEU79 2.8 56.2 1.0
OE2 A:GLU81 2.9 56.9 1.0
CD A:GLU81 3.1 56.5 1.0
O A:HOH610 3.4 75.4 1.0
CD A:GLU126 3.4 66.3 1.0
CG A:ASP78 3.6 67.3 1.0
OD2 A:ASP78 4.0 65.9 1.0
C A:LEU79 4.0 58.4 1.0
OE2 A:GLU126 4.0 71.6 1.0
CG A:GLU126 4.3 62.6 1.0
CE A:LYS48 4.4 63.6 1.0
CB A:GLU126 4.4 57.0 1.0
N A:GLU81 4.5 57.4 1.0
C A:ASP78 4.6 59.2 1.0
CG A:GLU81 4.6 52.2 1.0
N A:LEU79 4.6 59.8 1.0
CG A:LYS48 4.6 55.5 1.0
CD A:LYS48 4.7 58.7 1.0
CA A:SER80 4.7 56.8 1.0
O A:HOH670 4.8 55.1 1.0
N A:SER80 4.8 51.7 1.0
CE2 A:TYR59 4.8 58.5 1.0
CB A:ASP78 4.8 65.6 1.0
CA A:ASP78 4.9 66.0 1.0
O A:ASP78 4.9 53.9 1.0
OE2 A:GLU66 4.9 67.9 1.0
CA A:LEU79 5.0 62.3 1.0

Potassium binding site 3 out of 11 in 5wdk

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Potassium binding site 3 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K501

b:56.9
occ:1.00
 OD1 B:ASP78 2.4 58.6 1.0
O B:LEU79 2.4 47.1 1.0
OE1 B:GLU81 2.5 53.6 1.0
OE1 B:GLU126 2.6 49.8 1.0
O B:HOH611 2.7 45.1 1.0
OE2 B:GLU81 2.9 48.8 1.0
CD B:GLU81 3.1 50.2 1.0
CD B:GLU126 3.3 44.8 1.0
CG B:ASP78 3.5 53.9 1.0
C B:LEU79 3.6 52.6 1.0
O B:HOH608 3.6 58.6 1.0
OE2 B:GLU126 3.9 46.3 1.0
O B:HOH605 3.9 52.0 1.0
OD2 B:ASP78 4.0 55.2 1.0
N B:LEU79 4.1 50.3 1.0
CG B:GLU126 4.2 41.2 1.0
C B:ASP78 4.3 46.8 1.0
CB B:GLU126 4.3 43.5 1.0
N B:GLU81 4.5 43.5 1.0
CD B:LYS48 4.5 43.8 1.0
CA B:LEU79 4.5 48.9 1.0
OE2 B:GLU66 4.5 56.0 1.0
CG B:GLU81 4.5 47.5 1.0
N B:SER80 4.6 53.0 1.0
CA B:SER80 4.6 48.9 1.0
NZ B:LYS48 4.7 54.9 1.0
CB B:ASP78 4.7 46.0 1.0
CA B:ASP78 4.8 43.4 1.0
O B:ASP78 4.8 44.0 1.0
CG B:LYS48 4.8 43.0 1.0
CE1 B:TYR59 5.0 49.5 1.0

Potassium binding site 4 out of 11 in 5wdk

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Potassium binding site 4 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K501

b:0.1
occ:1.00
 O C:GLU335 2.8 64.4 1.0
O C:HOH643 2.8 74.5 1.0
OD2 C:ASP271 2.9 70.4 1.0
O C:SER273 3.0 0.4 1.0
OG C:SER273 3.3 75.1 1.0
C C:GLU335 3.5 58.8 1.0
OD1 C:ASP271 3.5 84.0 1.0
NZ C:LYS383 3.6 63.6 1.0
CG C:ASP271 3.6 74.5 1.0
CA C:GLU335 4.0 59.0 1.0
C C:SER273 4.2 99.1 1.0
CB C:SER273 4.3 77.8 1.0
O C:TYR334 4.4 51.3 1.0
N C:THR336 4.4 60.8 1.0
CA C:THR336 4.7 61.3 1.0
CA C:SER273 4.8 88.4 1.0
CB C:GLU335 4.9 62.8 1.0
OD2 C:ASP339 5.0 0.9 1.0
N C:THR337 5.0 60.9 1.0
CE C:LYS383 5.0 70.5 1.0

Potassium binding site 5 out of 11 in 5wdk

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Potassium binding site 5 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:83.7
occ:1.00
 OD1 C:ASP78 2.5 77.8 1.0
OE1 C:GLU126 2.5 60.2 1.0
OE2 C:GLU81 2.7 78.9 1.0
O C:LEU79 2.9 65.8 1.0
OE1 C:GLU81 2.9 69.0 1.0
CD C:GLU81 3.2 73.8 1.0
CD C:GLU126 3.4 72.2 1.0
CG C:ASP78 3.6 80.1 1.0
OE2 C:GLU126 3.8 75.7 1.0
C C:LEU79 4.1 63.2 1.0
OD2 C:ASP78 4.1 87.6 1.0
CG C:LYS48 4.3 64.0 1.0
N C:LEU79 4.3 66.2 1.0
OE2 C:GLU66 4.4 76.4 1.0
CE1 C:TYR59 4.4 74.3 1.0
CG C:GLU126 4.5 70.1 1.0
CE C:LYS48 4.5 66.8 1.0
CD C:LYS48 4.5 67.9 1.0
CB C:GLU126 4.6 73.8 1.0
CD1 C:TYR59 4.6 71.1 1.0
C C:ASP78 4.7 69.9 1.0
CG C:GLU81 4.7 66.9 1.0
CB C:ASP78 4.8 77.7 1.0
CA C:ASP78 4.9 71.7 1.0
CA C:LEU79 4.9 65.1 1.0

Potassium binding site 6 out of 11 in 5wdk

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Potassium binding site 6 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K501

b:0.1
occ:1.00
 OD1 D:ASP78 2.5 0.1 1.0
OE2 D:GLU126 2.5 63.4 1.0
OE2 D:GLU81 2.6 69.1 1.0
OE1 D:GLU81 3.2 68.2 1.0
O D:LEU79 3.2 63.5 1.0
CD D:GLU81 3.3 67.0 1.0
CG D:ASP78 3.6 91.5 1.0
OE2 D:GLU66 3.7 82.7 1.0
CD D:GLU126 3.7 71.0 1.0
CD D:LYS48 3.9 74.7 1.0
CG D:LYS48 4.0 69.8 1.0
CE D:LYS48 4.1 82.7 1.0
OD2 D:ASP78 4.2 89.8 1.0
CG D:GLU126 4.2 72.5 1.0
NZ D:LYS48 4.2 88.5 1.0
C D:LEU79 4.4 66.4 1.0
N D:LEU79 4.4 76.0 1.0
OE1 D:GLU126 4.7 62.2 1.0
C D:ASP78 4.7 72.2 1.0
CB D:LYS48 4.7 72.1 1.0
CD2 D:TYR59 4.7 62.6 1.0
CD D:GLU66 4.7 84.1 1.0
CG D:GLU81 4.8 55.5 1.0
CA D:ASP78 4.8 73.8 1.0
CB D:ASP78 4.8 78.7 1.0
CE2 D:TYR59 4.8 61.9 1.0
CA D:LEU79 5.0 72.8 1.0

Potassium binding site 7 out of 11 in 5wdk

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Potassium binding site 7 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:0.2
occ:1.00
 O D:GLU335 2.6 67.1 1.0
O D:SER273 2.9 0.7 1.0
OD2 D:ASP271 3.0 91.4 1.0
OG D:SER273 3.3 75.0 1.0
OE1 D:GLU274 3.3 0.3 1.0
C D:GLU335 3.4 58.4 1.0
CG D:ASP271 3.9 82.7 1.0
CA D:GLU335 3.9 59.5 1.0
C D:SER273 4.1 96.2 1.0
OD1 D:ASP271 4.1 86.6 1.0
O D:HOH607 4.2 73.4 1.0
O D:TYR334 4.3 53.0 1.0
CD D:GLU274 4.3 0.8 1.0
CG2 D:THR337 4.5 78.3 1.0
N D:THR336 4.5 44.5 1.0
CB D:SER273 4.5 75.4 1.0
CB D:GLU335 4.7 62.0 1.0
OE2 D:GLU274 4.8 0.8 1.0
CA D:THR336 4.8 53.6 1.0
N D:THR337 4.9 63.1 1.0
CA D:SER273 4.9 85.3 1.0
N D:GLU274 5.0 92.1 1.0

Potassium binding site 8 out of 11 in 5wdk

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Potassium binding site 8 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K501

b:41.4
occ:1.00
 OD1 E:ASP78 2.4 42.8 1.0
O E:HOH733 2.5 35.9 1.0
O E:HOH613 2.5 31.4 1.0
O E:LEU79 2.5 41.8 1.0
OE1 E:GLU81 2.6 45.6 1.0
OE1 E:GLU126 2.6 40.3 1.0
OE2 E:GLU81 2.8 39.5 1.0
CD E:GLU81 3.0 42.1 1.0
CD E:GLU126 3.4 40.8 1.0
C E:LEU79 3.6 40.4 1.0
CG E:ASP78 3.6 44.3 1.0
O E:HOH612 3.9 38.9 1.0
N E:LEU79 4.0 32.9 1.0
OE2 E:GLU126 4.1 41.6 1.0
O E:HOH652 4.1 40.2 1.0
CB E:GLU126 4.1 37.9 1.0
OD2 E:ASP78 4.2 42.4 1.0
CG E:GLU126 4.3 41.5 1.0
C E:ASP78 4.3 39.6 1.0
N E:GLU81 4.4 35.8 1.0
CA E:LEU79 4.4 40.7 1.0
CD E:LYS48 4.4 36.7 1.0
OE2 E:GLU66 4.5 37.0 1.0
N E:SER80 4.5 44.8 1.0
CG E:GLU81 4.5 41.0 1.0
CA E:SER80 4.6 39.7 1.0
CA E:ASP78 4.7 33.8 1.0
CB E:ASP78 4.8 45.2 1.0
O E:HOH662 4.8 48.1 1.0
O E:HOH714 4.8 50.4 1.0
O E:ASP78 4.8 33.4 1.0
NZ E:LYS48 4.9 41.8 1.0
CE1 E:TYR59 4.9 34.2 1.0
CG E:LYS48 4.9 38.1 1.0
CE E:LYS48 4.9 36.4 1.0
C E:SER80 5.0 40.5 1.0

Potassium binding site 9 out of 11 in 5wdk

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Potassium binding site 9 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K502

b:0.4
occ:1.00
 NZ E:LYS383 2.9 64.8 1.0
OD2 E:ASP271 2.9 57.4 1.0
O E:GLU335 3.0 45.0 1.0
OG E:SER273 3.0 62.2 1.0
CG E:ASP271 3.6 50.8 1.0
CB E:GLU274 3.6 0.9 1.0
OD1 E:ASP271 3.7 51.4 1.0
N E:GLU274 3.9 92.1 1.0
C E:GLU335 4.2 50.2 1.0
CE E:LYS383 4.3 52.1 1.0
CA E:GLU274 4.4 97.2 1.0
CB E:SER273 4.4 57.6 1.0
N E:SER273 4.8 45.5 1.0
CB E:ASP271 4.8 41.2 1.0
C E:SER273 4.8 79.8 1.0
CD E:LYS383 4.8 51.9 1.0
CA E:GLU335 4.9 53.2 1.0
CA E:SER273 4.9 61.9 1.0

Potassium binding site 10 out of 11 in 5wdk

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Potassium binding site 10 out of 11 in the A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of A Processive Dipeptidyl Aminopeptidase Secreted From An Established Commensal Bacterium P. Distasonis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K501

b:67.6
occ:1.00
 OE2 F:GLU274 2.5 66.0 1.0
O F:GLU335 2.5 49.7 1.0
OD2 F:ASP271 2.5 70.4 1.0
O F:SER273 2.7 50.7 1.0
OG F:SER273 2.8 45.0 1.0
CG F:ASP271 3.3 59.7 1.0
OD1 F:ASP271 3.4 75.8 1.0
CD F:GLU274 3.5 63.2 1.0
C F:GLU335 3.6 43.0 1.0
C F:SER273 3.7 54.4 1.0
CB F:SER273 3.9 50.0 1.0
O F:HOH709 4.0 56.3 1.0
OE1 F:GLU274 4.2 58.9 1.0
CA F:SER273 4.3 52.6 1.0
CA F:GLU335 4.3 41.1 1.0
CG F:GLU274 4.3 56.5 1.0
OG1 F:THR337 4.5 50.9 1.0
N F:THR336 4.5 35.7 1.0
NZ F:LYS383 4.5 45.1 1.0
N F:SER273 4.6 52.4 1.0
CA F:THR336 4.6 41.8 1.0
N F:GLU274 4.8 54.0 1.0
CB F:ASP271 4.8 44.2 1.0
N F:THR337 4.8 48.4 1.0
O F:TYR334 4.8 42.7 1.0
OD2 F:ASP339 4.9 75.3 1.0

Reference:

J.H.Xu, Z.Jiang, A.Solania, S.Chatterjee, B.Suzuki, C.B.Lietz, V.Y.H.Hook, A.J.O'donoghue, D.W.Wolan. A Commensal Dipeptidyl Aminopeptidase with Specificity For N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro. Acs Chem.Biol. V. 13 2513 2018.
ISSN: ESSN 1554-8937
PubMed: 30085657
DOI: 10.1021/ACSCHEMBIO.8B00420
Page generated: Sat Aug 9 10:03:19 2025

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