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Sodium 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:

Arsenic (As) 2 atoms
Zinc (Zn) 10 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 9 in 8ack

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Sodium binding site 1 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:28.3
occ:1.00
 OE2 B:GLU448 2.0 76.1 1.0
O B:HOH884 2.3 38.3 1.0
CD B:GLU448 3.2 72.7 1.0
NE2 B:GLN452 3.5 75.0 1.0
CG B:GLU448 4.0 58.5 1.0
OE1 B:GLU448 4.1 78.8 1.0
O B:HOH1000 4.5 62.4 1.0
CD B:GLN452 4.8 66.2 1.0

Sodium binding site 2 out of 9 in 8ack

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Sodium binding site 2 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na608

b:25.1
occ:1.00
 O B:HOH716 2.1 44.4 1.0
OE1 B:GLU204 2.2 41.6 1.0
O B:HOH1023 2.2 37.8 1.0
OE2 B:GLU200 2.3 45.7 1.0
OE2 B:GLU204 2.4 28.1 1.0
CD B:GLU204 2.6 34.2 1.0
CD B:GLU200 3.3 40.0 1.0
O B:HOH709 3.5 30.6 1.0
CG B:GLU200 3.7 27.8 1.0
O B:SER236 4.0 28.6 1.0
CG B:GLU204 4.1 26.3 1.0
O B:HOH926 4.1 56.5 1.0
CG B:GLU238 4.2 40.9 1.0
OE1 B:GLU238 4.3 68.5 1.0
CD B:GLU238 4.4 60.7 1.0
OE1 B:GLU200 4.4 40.8 1.0
OG B:SER236 4.6 32.9 1.0
N B:GLU238 4.6 28.7 1.0
C B:SER236 4.7 27.1 1.0
CA B:TYR237 4.8 24.3 1.0
CB B:GLU204 4.8 24.7 1.0

Sodium binding site 3 out of 9 in 8ack

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Sodium binding site 3 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na609

b:30.4
occ:1.00
 O B:HOH878 2.1 45.2 1.0
O B:HOH1033 2.1 45.4 1.0
OE2 B:GLU235 2.2 34.0 1.0
OE1 B:GLU235 2.4 35.0 1.0
CD B:GLU235 2.6 32.5 1.0
O B:HOH872 4.0 31.9 1.0
CG B:GLU235 4.1 30.5 1.0
O B:HOH870 4.1 39.4 1.0
O B:PRO116 4.2 31.9 1.0
O B:GLU235 4.3 29.1 1.0
O B:HOH840 4.4 39.1 1.0
N B:THR118 4.5 26.7 1.0
OG1 B:THR118 4.6 32.7 1.0
C B:GLU235 4.7 31.1 1.0
CA B:PHE117 4.7 33.8 1.0
CA B:SER236 4.7 31.6 1.0
C B:PRO116 4.8 36.6 1.0
N B:SER236 4.9 29.1 1.0
N B:PHE117 4.9 33.8 1.0
CB B:GLU235 5.0 35.0 1.0
CB B:SER236 5.0 35.7 1.0

Sodium binding site 4 out of 9 in 8ack

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Sodium binding site 4 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na610

b:35.5
occ:1.00
 O B:HOH706 2.2 36.7 1.0
OE2 B:GLU177 2.3 59.7 1.0
OD2 B:ASP180 2.5 29.9 1.0
OD2 B:ASP163 2.6 43.3 1.0
OD1 B:ASP180 2.7 34.8 1.0
O B:THR173 2.7 26.1 1.0
OG1 B:THR173 2.8 32.6 1.0
CG B:ASP180 2.9 30.7 1.0
O B:HOH707 3.4 28.1 1.0
O B:HOH1038 3.5 22.4 1.0
CB B:THR173 3.5 37.6 1.0
CD B:GLU177 3.5 56.5 1.0
C B:THR173 3.5 30.0 1.0
CG B:ASP163 3.8 39.9 1.0
CA B:THR173 4.1 30.3 1.0
N B:GLU177 4.2 28.1 1.0
N B:CYS176 4.2 25.0 1.0
OE1 B:GLU177 4.2 69.0 1.0
CB B:GLU177 4.4 34.6 1.0
N B:SER174 4.4 29.1 1.0
CB B:ASP180 4.4 23.4 1.0
N B:GLY175 4.4 27.0 1.0
CB B:ASP163 4.5 34.0 1.0
CG B:GLU177 4.5 35.8 1.0
CB B:CYS176 4.6 31.0 1.0
CA B:SER174 4.6 28.6 1.0
OD1 B:ASP163 4.8 40.1 1.0
CA B:CYS176 4.8 24.1 1.0
CG2 B:THR173 4.8 34.4 1.0
C B:SER174 4.8 26.6 1.0
O B:HOH916 4.9 30.1 1.0
C B:CYS176 4.9 30.4 1.0
CA B:GLU177 4.9 29.9 1.0

Sodium binding site 5 out of 9 in 8ack

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Sodium binding site 5 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na611

b:27.6
occ:1.00
 NE2 B:HIS263 2.2 50.2 1.0
OD2 B:ASP154 2.3 53.6 1.0
OD1 B:ASP154 2.4 43.5 1.0
CG B:ASP154 2.7 45.8 1.0
CE1 B:HIS263 2.8 51.6 1.0
CD2 B:HIS263 3.4 44.1 1.0
CG2 B:VAL265 3.7 36.6 1.0
ND1 B:HIS263 4.0 47.2 1.0
O B:HOH909 4.1 43.6 1.0
CB B:ASP154 4.2 38.1 1.0
CG B:HIS263 4.4 40.6 1.0
O B:HOH908 4.7 53.6 1.0
CA B:ASP154 5.0 34.2 1.0

Sodium binding site 6 out of 9 in 8ack

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Sodium binding site 6 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:25.8
occ:1.00
 OD1 A:ASP180 2.1 40.9 1.0
OE1 A:GLU177 2.1 55.8 1.0
O A:HOH732 2.1 41.7 1.0
OD2 A:ASP163 2.2 51.7 1.0
CG A:ASP180 3.0 45.2 1.0
O A:HOH723 3.1 34.5 1.0
CD A:GLU177 3.1 63.9 1.0
OD2 A:ASP180 3.2 39.1 1.0
CG A:ASP163 3.3 47.9 1.0
CG A:GLU177 3.6 54.1 1.0
OG1 A:THR173 3.9 35.3 1.0
CB A:ASP163 4.2 35.8 1.0
O A:HOH1001 4.2 56.2 1.0
OD1 A:ASP163 4.2 54.3 1.0
OE2 A:GLU177 4.2 69.5 1.0
CB A:ASP180 4.4 35.8 1.0
CA A:ASP180 4.7 37.0 1.0
O A:THR173 4.9 36.0 1.0
N A:ASP180 4.9 42.8 1.0

Sodium binding site 7 out of 9 in 8ack

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Sodium binding site 7 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:32.6
occ:1.00
 O A:HOH716 2.0 38.7 1.0
O A:HOH975 2.1 53.5 1.0
O A:HOH1000 2.1 56.7 1.0
OE2 A:GLU200 2.3 39.8 1.0
OE1 A:GLU204 2.3 45.7 1.0
OE2 A:GLU204 2.3 41.9 1.0
CD A:GLU204 2.6 37.2 1.0
CD A:GLU200 3.2 40.9 1.0
CG A:GLU200 3.6 27.2 1.0
O A:SER236 3.8 37.1 1.0
O A:HOH976 3.9 55.6 1.0
O A:HOH724 3.9 45.5 1.0
CG A:GLU204 4.1 33.5 1.0
OG A:SER236 4.3 42.3 1.0
OE1 A:GLU200 4.3 40.0 1.0
C A:SER236 4.5 34.9 1.0
CG A:GLU238 4.5 59.7 1.0
CA A:TYR237 4.6 30.3 1.0
N A:GLU238 4.7 28.8 1.0
OE1 A:GLU238 4.8 84.1 1.0
N A:TYR237 4.8 33.0 1.0
CD A:GLU238 4.9 77.0 1.0
CB A:GLU204 4.9 25.2 1.0
CB A:SER236 5.0 42.0 1.0

Sodium binding site 8 out of 9 in 8ack

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Sodium binding site 8 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:34.1
occ:1.00
 OD2 P:ASP8 2.1 43.0 1.0
ND1 P:HIS7 2.2 59.7 1.0
O B:HOH1048 2.3 55.5 1.0
O P:HOH208 2.4 30.0 1.0
O P:HOH203 2.6 30.0 1.0
CG P:ASP8 2.8 36.9 1.0
CE1 P:HIS7 2.9 58.3 1.0
OD1 P:ASP8 3.0 50.0 1.0
CG P:HIS7 3.3 54.9 1.0
O P:HOH206 3.6 40.2 1.0
CB P:HIS7 3.8 36.0 1.0
NE2 P:HIS7 4.1 59.8 1.0
CB P:ASP8 4.2 29.3 1.0
CD2 P:HIS7 4.3 54.1 1.0
O B:HOH898 4.3 48.9 1.0
CB B:ASN230 4.4 28.6 1.0
C P:HIS7 4.5 44.3 1.0
N P:ASP8 4.5 32.2 1.0
CG B:ASN230 4.6 44.3 1.0
CA P:ASP8 4.6 25.1 1.0
O P:HIS7 4.7 38.0 1.0
CA P:HIS7 4.8 35.2 1.0
OD1 B:ASN230 4.9 41.3 1.0
ND2 B:ASN230 5.0 46.8 1.0

Sodium binding site 9 out of 9 in 8ack

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Sodium binding site 9 out of 9 in the Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Pseudomonas Aeruginosa Aminopeptidase, Paap within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:42.5
occ:1.00
 OD2 C:ASP8 2.0 51.1 1.0
O C:HOH208 2.2 30.0 1.0
ND1 C:HIS7 2.2 71.0 1.0
O C:HOH207 2.3 42.4 1.0
O C:HOH206 2.3 30.0 1.0
CG C:ASP8 2.7 40.3 1.0
CE1 C:HIS7 2.8 67.1 1.0
OD1 C:ASP8 2.8 50.1 1.0
CG C:HIS7 3.3 64.1 1.0
O C:HOH204 3.7 48.3 1.0
CB C:HIS7 3.8 43.4 1.0
NE2 C:HIS7 3.9 66.5 1.0
CB C:ASP8 4.1 34.2 1.0
CD2 C:HIS7 4.1 64.1 1.0
CB A:ASN230 4.3 43.6 1.0
N C:ASP8 4.4 38.9 1.0
C C:HIS7 4.4 43.1 1.0
CA C:ASP8 4.5 35.5 1.0
CG A:ASN230 4.6 47.0 1.0
O C:HIS7 4.7 34.6 1.0
CA C:HIS7 4.8 39.7 1.0
ND2 A:ASN230 4.9 49.1 1.0
OD1 A:ASN230 5.0 49.6 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 9 10:29:18 2024

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