Atomistry » Sodium » PDB 8ezg-8fr5 » 8fha
Atomistry »
  Sodium »
    PDB 8ezg-8fr5 »
      8fha »

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

Go back to Sodium Binding Sites List in 8fha
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

Go back to Sodium Binding Sites List in 8fha
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: Wed Oct 9 11:50:17 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy