Sodium in PDB 8wch: Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L- Pyroglutamate

Protein crystallography data

The structure of Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L- Pyroglutamate, PDB code: 8wch was solved by B.E.Clifton, P.Laurino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.30 / 1.52
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 122.204, 122.204, 125.908, 90, 90, 90
R / Rfree (%) 15 / 18.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L- Pyroglutamate (pdb code 8wch). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L- Pyroglutamate, PDB code: 8wch:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8wch

Go back to Sodium Binding Sites List in 8wch
Sodium binding site 1 out of 2 in the Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L- Pyroglutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L- Pyroglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:27.0
occ:1.00
O A:ILE54 2.3 25.8 1.0
O A:ASP69 2.3 29.5 1.0
O A:ASN57 2.4 29.7 1.0
O A:LEU66 2.4 26.5 1.0
O A:ALA67 2.4 27.6 1.0
O A:ILE55 2.5 26.3 1.0
C A:ALA67 3.1 27.4 1.0
C A:ILE55 3.1 24.8 1.0
C A:ILE54 3.4 23.6 1.0
CA A:ALA67 3.4 28.0 1.0
C A:ASN57 3.5 30.4 1.0
C A:ASP69 3.5 29.6 1.0
CA A:ILE55 3.5 24.1 1.0
C A:LEU66 3.5 24.8 1.0
N A:ILE55 3.9 23.4 1.0
N A:ALA67 3.9 25.8 1.0
O A:HOH671 4.0 27.8 1.0
N A:ASP69 4.1 28.2 1.0
N A:LYS68 4.1 26.0 1.0
N A:ASN57 4.1 28.1 1.0
N A:ASN56 4.2 22.7 1.0
CA A:SER58 4.2 31.6 1.0
N A:SER58 4.3 30.5 1.0
C A:LYS68 4.3 29.4 1.0
N A:ALA70 4.4 30.6 1.0
CA A:ASP69 4.4 31.2 1.0
CA A:ALA70 4.4 31.0 1.0
CA A:ASN57 4.5 30.8 1.0
N A:HIS59 4.5 33.1 1.0
C A:ASN56 4.6 27.3 1.0
N A:GLY71 4.6 28.2 1.0
CA A:ILE54 4.7 22.8 1.0
O A:LYS68 4.7 32.5 1.0
CA A:LEU66 4.8 23.9 1.0
CA A:LYS68 4.8 28.5 1.0
CB A:ALA67 4.8 29.9 1.0
CA A:ASN56 4.8 26.3 1.0
CD2 A:HIS59 4.8 31.6 1.0
C A:SER58 4.9 31.8 1.0
O A:ASP53 4.9 28.5 1.0
CB A:ILE55 4.9 24.2 1.0

Sodium binding site 2 out of 2 in 8wch

Go back to Sodium Binding Sites List in 8wch
Sodium binding site 2 out of 2 in the Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L- Pyroglutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L- Pyroglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:33.9
occ:1.00
O B:ILE54 2.3 29.8 1.0
O B:ASP69 2.3 39.7 1.0
O B:LEU66 2.4 32.2 1.0
O B:ASN57 2.4 35.9 1.0
O B:ALA67 2.4 35.7 1.0
O B:ILE55 2.5 31.5 1.0
C B:ALA67 3.1 35.0 1.0
C B:ILE55 3.1 28.1 1.0
C B:ILE54 3.4 28.1 1.0
C B:ASP69 3.5 40.2 1.0
C B:LEU66 3.5 32.6 1.0
C B:ASN57 3.5 37.8 1.0
CA B:ALA67 3.5 35.2 1.0
CA B:ILE55 3.5 28.5 1.0
N B:ILE55 3.8 25.5 1.0
N B:ALA67 3.9 31.0 1.0
N B:ASN57 4.1 36.6 1.0
N B:ASP69 4.1 40.3 1.0
N B:LYS68 4.1 38.3 1.0
O B:HOH643 4.1 32.5 1.0
N B:ASN56 4.2 29.8 1.0
CA B:SER58 4.3 39.4 1.0
N B:SER58 4.3 38.3 1.0
N B:ALA70 4.3 41.5 1.0
C B:LYS68 4.4 43.7 1.0
CA B:ASP69 4.4 42.4 1.0
CA B:ALA70 4.4 39.2 1.0
CA B:ASN57 4.4 36.2 1.0
N B:HIS59 4.5 41.9 1.0
C B:ASN56 4.6 33.7 1.0
N B:GLY71 4.6 34.6 1.0
CA B:ILE54 4.6 27.9 1.0
O B:LYS68 4.7 43.6 1.0
CA B:LEU66 4.8 32.7 1.0
CA B:LYS68 4.8 40.2 1.0
O B:ASP53 4.8 29.7 1.0
CA B:ASN56 4.9 31.1 1.0
CD2 B:HIS59 4.9 35.1 1.0
C B:SER58 4.9 40.6 1.0
CB B:ALA67 4.9 32.5 1.0
CB B:ILE55 4.9 28.3 1.0

Reference:

B.E.Clifton, P.Laurino. Crystal Structure of SAR11_0655 Bound to A Co-Purified Ligand, L-Pyroglutamate To Be Published.
Page generated: Wed Oct 9 14:15:47 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy