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Sodium in PDB 6grj: Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.

Protein crystallography data

The structure of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila., PDB code: 6grj was solved by A.M.Churchill-Angus, J.S.Wilson, P.J.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 102.67 / 2.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 363.644, 116.526, 217.409, 90.00, 118.01, 90.00
R / Rfree (%) 22.2 / 23.9

Other elements in 6grj:

The structure of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. also contains other interesting chemical elements:

Chlorine (Cl) 27 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. (pdb code 6grj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila., PDB code: 6grj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 6grj

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Sodium binding site 1 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na404

b:62.6
occ:1.00
 O J:GLY54 2.6 47.5 1.0
ND2 J:ASN141 2.8 52.4 1.0
OD1 J:ASP138 2.9 68.9 1.0
C J:GLY54 3.4 44.7 1.0
CB J:ASN141 3.7 48.1 1.0
CG J:ASN141 3.7 50.0 1.0
CA J:GLY54 3.7 46.0 1.0
N J:ALA58 3.8 45.2 1.0
CB J:LEU57 3.8 42.8 1.0
CA J:ASP138 3.9 50.5 1.0
CG J:ASP138 3.9 58.0 1.0
CB J:ALA58 3.9 47.2 1.0
CD2 J:LEU57 4.0 42.2 1.0
CG J:LEU57 4.0 38.7 1.0
CA J:ALA58 4.2 46.4 1.0
CB J:ASP138 4.3 54.5 1.0
C J:LEU57 4.4 40.7 1.0
N J:ASP138 4.5 47.9 1.0
O J:THR137 4.5 36.3 1.0
CA J:LEU57 4.6 42.8 1.0
CE1 J:PHE142 4.6 43.1 1.0
N J:LEU55 4.7 41.8 1.0
O J:ASP138 4.7 46.4 1.0
CG2 J:THR137 4.7 38.7 1.0
C J:THR137 4.7 41.8 1.0
C J:ASP138 4.8 46.4 1.0
OD1 J:ASN141 4.8 58.1 1.0
OD2 J:ASP138 5.0 58.2 1.0
N J:LEU57 5.0 41.6 1.0
O J:GLN53 5.0 49.7 1.0
CZ J:PHE142 5.0 41.6 1.0

Sodium binding site 2 out of 10 in 6grj

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Sodium binding site 2 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:92.7
occ:1.00
 ND2 B:ASN43 2.6 89.7 1.0
OD1 B:ASP156 3.0 61.9 1.0
O B:LYS152 3.1 62.3 1.0
CB A:GLN246 3.2 73.1 1.0
CG B:ASN43 3.6 91.8 1.0
CG A:GLN246 3.6 89.1 1.0
CG B:ASP156 3.7 57.4 1.0
CA A:GLN246 3.9 68.4 1.0
OD1 B:ASN43 3.9 0.9 1.0
CA B:LYS152 3.9 63.1 1.0
C B:LYS152 3.9 58.7 1.0
N B:ASP156 3.9 57.0 1.0
OD2 B:ASP156 4.1 64.1 1.0
NE2 A:GLN242 4.2 71.0 1.0
CA B:GLY155 4.2 51.1 1.0
C B:GLY155 4.2 56.9 1.0
CB B:LYS152 4.3 63.0 1.0
CD B:LYS152 4.3 64.5 1.0
CG A:GLN242 4.3 73.7 1.0
O A:GLN242 4.4 62.2 1.0
N A:GLN246 4.4 66.0 1.0
OE2 B:GLU254 4.5 73.6 1.0
CA B:ASP156 4.6 52.0 1.0
CB B:ASP156 4.7 54.3 1.0
CD A:GLN242 4.8 71.4 1.0
N B:GLY155 4.9 53.1 1.0
CG B:LYS152 4.9 67.1 1.0
O B:SER151 5.0 72.3 1.0
CB B:ASN43 5.0 78.7 1.0

Sodium binding site 3 out of 10 in 6grj

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Sodium binding site 3 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na408

b:39.0
occ:1.00
 OD1 C:ASP287 3.2 55.6 1.0
OG1 C:THR290 3.6 61.3 1.0
OG C:SER291 3.7 76.3 1.0
CB C:THR290 4.2 56.8 1.0
CG C:ASP287 4.4 56.1 1.0
N C:SER291 4.4 55.9 1.0
OE1 C:GLN118 4.6 54.0 1.0
O C:ASP287 4.7 52.0 1.0
CA C:SER291 4.8 60.1 1.0
CB C:SER291 4.8 58.7 1.0
C C:THR290 4.9 54.9 1.0
OD2 C:ASP287 5.0 67.6 1.0

Sodium binding site 4 out of 10 in 6grj

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Sodium binding site 4 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na409

b:83.7
occ:1.00
 OG1 D:THR321 3.2 45.0 1.0
N C:ASN82 3.4 52.5 1.0
CA C:ASN82 3.5 47.4 1.0
OD1 C:ASN82 3.6 48.8 1.0
CG2 D:THR321 3.7 54.0 1.0
O C:SER78 3.7 46.8 1.0
C C:SER81 3.8 55.4 1.0
CB C:ASN82 3.8 51.4 1.0
CB D:SER295 3.8 55.9 1.0
OD1 D:ASP292 3.9 58.8 1.0
CB D:THR321 3.9 49.4 1.0
OG D:SER295 3.9 64.5 1.0
CB C:SER81 3.9 63.5 1.0
OG C:SER81 3.9 72.4 1.0
CG C:ASN82 4.1 49.3 1.0
O C:SER81 4.1 52.2 1.0
CA D:THR321 4.3 46.8 1.0
CA C:SER81 4.4 54.9 1.0
CG2 D:THR324 4.7 50.9 1.0
C C:SER78 4.7 58.4 1.0
OG1 D:THR324 4.8 53.5 1.0
CG D:ASP292 4.8 56.3 1.0
CB D:THR324 4.9 51.4 1.0
C C:ASN82 5.0 44.7 1.0

Sodium binding site 5 out of 10 in 6grj

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Sodium binding site 5 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na410

b:60.4
occ:1.00
 OE1 C:GLN16 2.7 37.5 1.0
OD1 C:ASN76 3.1 54.0 1.0
O C:ILE73 3.5 41.5 1.0
CG C:ASN76 3.6 44.5 1.0
CB C:ASN76 3.6 51.2 1.0
CD C:GLN16 3.6 49.0 1.0
CG2 C:ILE73 3.7 41.2 1.0
CB C:GLN16 3.9 53.1 1.0
CG C:GLN16 3.9 54.1 1.0
CG1 C:ILE77 3.9 48.5 1.0
CG C:MSE282 4.0 45.0 1.0
CE C:MSE282 4.2 45.5 1.0
C C:ILE73 4.3 43.5 1.0
O C:MSE13 4.4 52.5 1.0
N C:ILE77 4.5 55.6 1.0
C C:ASN76 4.6 53.6 1.0
CD1 C:ILE77 4.6 47.5 1.0
CA C:MSE13 4.6 42.6 1.0
CA C:ILE73 4.6 41.1 1.0
ND2 C:ASN76 4.7 36.8 1.0
CG C:MSE13 4.7 40.1 1.0
SE C:MSE282 4.7 47.1 1.0
CA C:ASN76 4.7 50.1 1.0
CB C:ILE73 4.8 41.3 1.0
NE2 C:GLN16 4.8 46.0 1.0
CD1 C:ILE80 5.0 66.5 1.0

Sodium binding site 6 out of 10 in 6grj

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Sodium binding site 6 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:60.2
occ:1.00
 ND2 D:ASN134 2.7 55.6 1.0
O D:HIS61 2.9 49.1 1.0
CB D:ASN134 3.4 50.4 1.0
CG D:ASN134 3.5 51.2 1.0
C D:HIS61 3.5 51.1 1.0
CB D:HIS61 3.6 59.4 1.0
CA D:HIS61 3.6 55.0 1.0
CD1 D:LEU131 3.8 40.1 1.0
CD2 D:LEU64 4.2 51.5 1.0
CG D:HIS61 4.2 59.8 1.0
N D:TYR65 4.3 42.4 1.0
CB D:LEU64 4.3 45.0 1.0
CD1 D:ILE69 4.4 51.7 1.0
CB D:TYR65 4.4 42.6 1.0
CG D:LEU64 4.4 44.8 1.0
CA D:LEU131 4.5 38.6 1.0
OD1 D:ASN134 4.6 54.2 1.0
CD2 D:HIS61 4.7 66.9 1.0
CA D:TYR65 4.7 40.2 1.0
N D:ALA62 4.7 45.7 1.0
O D:LEU131 4.7 35.3 1.0
CA D:ASN134 4.9 50.6 1.0
C D:LEU64 5.0 46.0 1.0

Sodium binding site 7 out of 10 in 6grj

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Sodium binding site 7 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na406

b:65.3
occ:1.00
 O E:GLY12 2.6 43.0 1.0
O E:ALA278 2.7 35.7 1.0
NE2 E:GLN281 3.1 94.5 1.0
CB E:GLN281 3.3 67.3 1.0
CB E:ASN15 3.4 63.0 1.0
N E:GLN16 3.5 46.8 1.0
C E:ALA278 3.5 41.2 1.0
C E:GLY12 3.6 51.1 1.0
CA E:ALA278 3.7 44.3 1.0
CA E:GLY12 3.8 56.5 1.0
CB E:GLN16 3.9 52.8 1.0
CA E:GLN16 3.9 51.6 1.0
C E:ASN15 3.9 47.5 1.0
N E:MSE282 3.9 54.3 1.0
CD E:GLN281 4.0 93.9 1.0
CB E:ALA278 4.1 58.1 1.0
CA E:ASN15 4.2 51.7 1.0
ND2 E:ASN15 4.2 71.4 1.0
C E:GLN281 4.3 52.3 1.0
CG E:GLN281 4.3 79.6 1.0
CA E:GLN281 4.3 57.4 1.0
CG E:ASN15 4.4 72.1 1.0
CA E:MSE282 4.6 53.5 1.0
O E:GLN11 4.6 48.5 1.0
N E:ASN15 4.6 45.9 1.0
O E:ASN15 4.7 47.0 1.0
CB E:MSE282 4.7 53.0 1.0
N E:GLN281 4.7 56.6 1.0
N E:ALA279 4.8 45.5 1.0
N E:MSE13 4.8 48.1 1.0
CG E:GLN16 4.9 55.7 1.0
O E:THR277 5.0 43.2 1.0
N E:ALA278 5.0 40.7 1.0

Sodium binding site 8 out of 10 in 6grj

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Sodium binding site 8 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na407

b:45.3
occ:1.00
 OG E:SER139 2.9 65.0 1.0
CB E:SER139 3.6 57.6 1.0
CG E:GLN269 4.5 49.6 1.0
OG E:SER140 4.7 73.1 1.0
CG E:LYS266 4.7 45.5 1.0
O E:ILE136 4.7 51.6 1.0
NE2 E:GLN269 4.7 41.7 1.0
C E:SER139 4.8 55.7 1.0
N E:SER140 4.8 59.0 1.0
CA E:SER139 4.8 54.7 1.0
CB E:GLN269 4.8 50.5 1.0
CA E:LYS266 4.9 49.1 1.0

Sodium binding site 9 out of 10 in 6grj

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Sodium binding site 9 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na406

b:60.1
occ:1.00
 OD1 F:ASP138 2.6 62.9 1.0
ND2 F:ASN141 2.6 54.4 1.0
O F:GLY54 3.0 43.4 1.0
CA F:ASP138 3.6 51.4 1.0
CG F:ASN141 3.6 52.3 1.0
CG F:ASP138 3.6 65.4 1.0
CB F:ASN141 3.7 52.1 1.0
CD2 F:LEU57 3.8 52.1 1.0
CG F:LEU57 3.9 46.5 1.0
CB F:LEU57 3.9 47.4 1.0
C F:GLY54 3.9 45.9 1.0
N F:ALA58 4.0 46.5 1.0
CB F:ASP138 4.0 58.0 1.0
N F:ASP138 4.1 47.9 1.0
CA F:GLY54 4.1 45.4 1.0
CB F:ALA58 4.1 57.4 1.0
O F:THR137 4.2 46.5 1.0
CA F:ALA58 4.3 52.2 1.0
CG2 F:THR137 4.3 49.8 1.0
C F:THR137 4.3 48.8 1.0
C F:LEU57 4.5 43.5 1.0
O F:ASP138 4.6 44.0 1.0
C F:ASP138 4.6 47.2 1.0
OD1 F:ASN141 4.7 58.3 1.0
OD2 F:ASP138 4.7 66.0 1.0
CA F:LEU57 4.8 47.6 1.0
CD2 F:HIS61 4.9 62.5 1.0
CE1 F:PHE142 5.0 52.4 1.0

Sodium binding site 10 out of 10 in 6grj

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Sodium binding site 10 out of 10 in the Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of the Ahlb Pore of the Tripartite Alpha-Pore Forming Toxin, Ahl, From Aeromonas Hydrophila. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na406

b:63.4
occ:1.00
 NE H:ARG241 3.2 59.1 1.0
CE I:LYS247 3.2 0.1 1.0
CD2 H:LEU238 3.3 96.1 1.0
NH2 H:ARG241 3.3 67.3 1.0
O H:LEU238 3.3 91.2 1.0
CZ H:ARG241 3.7 61.8 1.0
CG1 I:VAL159 3.9 55.0 1.0
CD I:LYS247 3.9 0.6 1.0
CA H:LEU238 3.9 95.4 1.0
CB H:LEU238 4.0 93.3 1.0
C H:LEU238 4.1 94.7 1.0
CD2 I:LEU163 4.1 74.8 1.0
CB H:ARG241 4.1 66.2 1.0
CG H:LEU238 4.2 92.4 1.0
CG I:LEU163 4.2 73.3 1.0
CD H:ARG241 4.3 58.3 1.0
NZ I:LYS247 4.3 0.8 1.0
CG H:ARG241 4.4 57.8 1.0
CD1 I:LEU163 4.4 74.4 1.0
CG I:LYS247 4.7 0.2 1.0
CD1 H:LEU238 4.9 96.4 1.0
NH1 H:ARG241 5.0 53.1 1.0

Reference:

J.S.Wilson, A.M.Churchill-Angus, S.P.Davies, S.E.Sedelnikova, S.B.Tzokov, J.B.Rafferty, P.A.Bullough, C.Bisson, P.J.Baker. Identification and Structural Analysis of the Tripartite Alpha-Pore Forming Toxin of Aeromonas Hydrophila. Nat Commun V. 10 2900 2019.
ISSN: ESSN 2041-1723
PubMed: 31263098
DOI: 10.1038/S41467-019-10777-X
Page generated: Tue Oct 8 09:06:33 2024

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