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Sodium in PDB 8fha: Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin

Protein crystallography data

The structure of Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin, PDB code: 8fha was solved by S.Jin, P.G.Young, C.J.Squire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.03 / 1.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.051, 104.712, 52.587, 90, 91.81, 90
R / Rfree (%) 16.6 / 21.2

Other elements in 8fha:

The structure of Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin (pdb code 8fha). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin, PDB code: 8fha:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8fha

Go back to Sodium Binding Sites List in 8fha
Sodium binding site 1 out of 6 in the Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:25.2
occ:1.00
 O A:THR12 2.3 20.0 1.0
OG A:SER143 2.4 22.3 1.0
O A:HOH336 2.4 34.4 1.0
O A:HOH348 2.4 39.3 1.0
O A:HOH323 2.4 29.8 1.0
O A:HOH308 2.4 21.5 1.0
CB A:SER143 3.1 19.5 1.0
C A:THR12 3.4 16.7 1.0
N A:THR12 3.8 15.6 1.0
OG1 A:THR13 4.0 23.7 1.0
CA A:THR12 4.3 15.7 1.0
OD2 A:ASP141 4.3 21.0 1.0
CB A:SER11 4.3 23.3 1.0
N A:THR13 4.4 16.7 1.0
OD1 A:ASP141 4.4 22.9 1.0
CA A:SER143 4.5 16.1 1.0
OG A:SER11 4.6 26.2 1.0
CA A:THR13 4.7 17.8 1.0
C A:SER11 4.7 17.9 1.0
CG A:ASP141 4.8 20.6 1.0
OG1 A:THR12 4.8 16.0 1.0
C A:SER143 4.8 14.0 1.0
CD2 A:HIS45 4.9 26.2 1.0
O A:HOH349 4.9 43.8 1.0
O A:SER143 5.0 15.0 1.0
CB A:THR13 5.0 20.6 1.0
CA A:SER11 5.0 20.0 1.0

Sodium binding site 2 out of 6 in 8fha

Go back to Sodium Binding Sites List in 8fha
Sodium binding site 2 out of 6 in the Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:39.8
occ:1.00
 OD1 B:ASP90 2.4 31.9 1.0
O B:HOH351 2.4 32.2 1.0
CG B:ASP90 3.2 27.0 1.0
O B:GLY89 3.4 17.3 1.0
OD2 B:ASP90 3.7 35.8 1.0
C B:GLY89 3.7 17.5 1.0
ND1 B:HIS45 4.0 24.5 1.0
CB B:HIS45 4.0 17.2 1.0
CA B:GLY89 4.2 19.0 1.0
N B:ASP90 4.2 18.2 1.0
CA B:HIS45 4.3 16.1 1.0
CB B:ASP90 4.4 22.0 1.0
CG B:HIS45 4.4 21.2 1.0
CA B:ASP90 4.6 18.4 1.0
N B:GLY89 4.6 18.7 1.0
C B:HIS45 5.0 16.4 1.0
N B:TYR46 5.0 16.3 1.0

Sodium binding site 3 out of 6 in 8fha

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Sodium binding site 3 out of 6 in the Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:28.0
occ:1.00
 O B:THR12 2.3 20.8 1.0
OG B:SER143 2.4 21.3 1.0
O B:HOH354 2.4 37.2 1.0
O B:HOH326 2.4 31.9 1.0
O B:HOH312 2.4 21.0 1.0
CB B:SER143 3.1 18.6 1.0
C B:THR12 3.4 17.2 1.0
N B:THR12 3.8 16.1 1.0
OG1 B:THR13 4.0 24.9 1.0
CA B:THR12 4.2 15.7 1.0
OD2 B:ASP141 4.2 24.9 1.0
CB B:SER11 4.3 21.4 1.0
N B:THR13 4.4 18.0 1.0
O B:HOH329 4.4 40.9 1.0
CA B:SER143 4.5 13.8 1.0
OD1 B:ASP141 4.5 21.0 1.0
OG B:SER11 4.6 23.1 1.0
CA B:THR13 4.7 17.6 1.0
C B:SER11 4.7 16.6 1.0
OG1 B:THR12 4.8 15.4 1.0
CD2 B:HIS45 4.8 24.0 1.0
CG B:ASP141 4.8 19.8 1.0
C B:SER143 4.8 13.0 1.0
O B:SER143 4.9 13.5 1.0
CB B:THR13 5.0 21.8 1.0
CA B:SER11 5.0 18.7 1.0

Sodium binding site 4 out of 6 in 8fha

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Sodium binding site 4 out of 6 in the Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:19.7
occ:1.00
 O C:THR12 2.3 17.4 1.0
OG C:SER143 2.3 16.9 1.0
O C:HOH362 2.4 29.9 1.0
O C:HOH307 2.4 19.6 1.0
CB C:SER143 3.2 15.0 1.0
C C:THR12 3.4 15.0 1.0
N C:THR12 3.8 15.3 1.0
OG1 C:THR13 4.0 24.5 1.0
OD2 C:ASP141 4.2 20.5 1.0
CA C:THR12 4.2 14.0 1.0
CB C:SER11 4.3 18.9 1.0
N C:THR13 4.4 15.1 1.0
O C:HOH336 4.4 25.9 1.0
OD1 C:ASP141 4.5 19.5 1.0
CA C:SER143 4.5 15.1 1.0
O C:HOH364 4.5 29.0 1.0
CA C:THR13 4.7 14.8 1.0
C C:SER11 4.7 15.6 1.0
CG C:ASP141 4.8 19.4 1.0
OG1 C:THR12 4.8 15.3 1.0
C C:SER143 4.8 14.0 1.0
OG C:SER11 4.8 22.9 1.0
O C:SER143 4.9 13.8 1.0
CD2 C:HIS45 4.9 21.5 1.0
CA C:SER11 5.0 17.0 1.0
CB C:THR13 5.0 18.6 1.0

Sodium binding site 5 out of 6 in 8fha

Go back to Sodium Binding Sites List in 8fha
Sodium binding site 5 out of 6 in the Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:28.0
occ:1.00
 O C:SER33 2.3 30.2 1.0
O C:GLY37 2.3 23.6 1.0
OD2 C:ASP17 2.4 34.1 1.0
OD1 C:ASP36 2.4 29.2 1.0
O C:HOH321 2.4 33.0 1.0
CG C:ASP17 3.3 30.3 1.0
C C:SER33 3.4 28.1 1.0
OD1 C:ASP17 3.5 32.6 1.0
C C:GLY37 3.5 23.1 1.0
CG C:ASP36 3.5 28.5 1.0
CA C:VAL34 4.0 25.1 1.0
OD2 C:ASP36 4.0 32.9 1.0
N C:VAL34 4.2 25.1 1.0
CA C:VAL38 4.2 18.4 1.0
N C:VAL38 4.3 18.3 1.0
OG C:SER33 4.3 36.4 1.0
N C:GLY37 4.3 21.9 1.0
C C:ASP36 4.4 24.4 1.0
CB C:SER33 4.4 35.4 1.0
CA C:SER33 4.5 31.0 1.0
CA C:GLY37 4.5 24.2 1.0
C C:VAL34 4.6 24.8 1.0
N C:ASP36 4.6 22.1 1.0
O C:ASP36 4.6 28.2 1.0
CB C:ASP36 4.7 26.0 1.0
CB C:ASP17 4.7 26.6 1.0
CA C:ASP36 4.8 23.5 1.0
N C:ALA39 4.9 18.1 1.0
N C:GLY35 5.0 25.0 1.0

Sodium binding site 6 out of 6 in 8fha

Go back to Sodium Binding Sites List in 8fha
Sodium binding site 6 out of 6 in the Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Intramolecular Ester Bond-Containing Repeat Domain 1 From Suipraoptans Intestinalis Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:22.7
occ:1.00
 O D:THR12 2.3 19.0 1.0
OG D:SER143 2.4 17.9 1.0
O D:HOH324 2.4 20.4 1.0
O D:HOH341 2.4 32.8 1.0
O D:HOH329 2.4 30.9 1.0
O D:HOH356 2.4 30.3 1.0
CB D:SER143 3.1 15.2 1.0
C D:THR12 3.5 17.2 1.0
N D:THR12 3.8 15.7 1.0
OG1 D:THR13 4.1 23.6 1.0
CA D:THR12 4.3 15.8 1.0
CB D:SER11 4.3 21.6 1.0
OD2 D:ASP141 4.4 22.6 1.0
O D:HOH358 4.4 32.6 1.0
N D:THR13 4.5 16.4 1.0
CA D:SER143 4.5 14.0 1.0
OD1 D:ASP141 4.5 21.4 1.0
OG D:SER11 4.7 23.9 1.0
OG1 D:THR12 4.7 15.6 1.0
C D:SER11 4.8 16.5 1.0
CA D:THR13 4.8 17.0 1.0
C D:SER143 4.8 13.4 1.0
CG D:ASP141 4.9 19.7 1.0
O D:SER143 4.9 14.4 1.0
CA D:SER11 5.0 19.0 1.0

Reference:

S.Jin, P.G.Young, C.J.Squire. Intramolecular Ester Bond-Containing Repeat Domain From Suipraoptans Intestinalis Adhesin To Be Published.
Page generated: Mon Aug 18 14:09:05 2025

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