Sodium in PDB 3u27: Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B

The structure of Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B, PDB code: 3u27 was solved by R.Wu, M.Gu, C.A.Kerfeld, A.Salmeen, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.42 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	100.854, 105.644, 101.551, 90.00, 90.06, 90.00
R / Rfree (%)	15.7 / 18.2

The structure of Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B (pdb code 3u27). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B, PDB code: 3u27:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B


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 Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B within 5.0Å range: probe atom residue distance (Å) B Occ C:Na305 b:31.2 occ:1.00 OD2 C:ASP104 2.1 41.2 1.0 O C:HOH599 2.2 27.2 1.0 OE2 C:GLU109 2.4 29.4 1.0 O C:HOH601 2.5 42.7 1.0 O C:HOH600 2.6 40.9 1.0 CG C:ASP104 2.8 34.4 1.0 OD1 C:ASP104 3.0 30.4 1.0 CD C:GLU109 3.2 30.8 1.0 CG C:GLU109 3.3 21.3 1.0 O C:HOH609 3.3 45.7 1.0 O C:ASP104 3.5 25.5 1.0 CB C:ASN108 3.6 24.2 1.0 OD1 C:ASN108 3.9 43.1 1.0 C C:ASP104 4.0 20.8 1.0 O F:HOH564 4.2 50.8 1.0 CB C:ASP104 4.2 18.1 1.0 CG C:ASN108 4.2 34.7 1.0 O C:HOH598 4.4 54.0 1.0 OD2 F:ASP61 4.4 40.3 1.0 OE1 C:GLU109 4.4 28.0 1.0 NE2 F:HIS33 4.5 19.6 1.0 NA C:NA306 4.6 36.9 1.0 O C:HOH417 4.6 21.8 1.0 CA C:ASP104 4.6 18.4 1.0 N C:PHE105 4.6 13.9 1.0 CB C:GLU109 4.7 20.8 1.0 OD1 F:ASP61 4.7 35.9 1.0 CA C:ASN108 4.8 24.7 1.0 CA C:PHE105 4.8 12.6 1.0 O C:HOH515 4.8 31.5 1.0 CE1 F:HIS33 4.9 19.3 1.0 C C:ASN108 4.9 27.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B


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 Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B within 5.0Å range: probe atom residue distance (Å) B Occ C:Na306 b:36.9 occ:1.00 O C:HOH608 2.0 56.9 1.0 O C:HOH609 2.1 45.7 1.0 O F:HOH564 2.5 50.8 1.0 OE2 C:GLU109 2.7 29.4 1.0 OE1 C:GLU109 2.8 28.0 1.0 CD C:GLU109 3.0 30.8 1.0 O C:HOH598 3.6 54.0 1.0 OD1 F:ASP61 4.0 35.9 1.0 OD2 F:ASP61 4.1 40.3 1.0 O C:HOH601 4.2 42.7 1.0 CG F:ASP61 4.4 33.9 1.0 CG C:GLU109 4.4 21.3 1.0 O F:HOH431 4.5 24.5 1.0 NA C:NA305 4.6 31.2 1.0 O C:HOH599 4.7 27.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:30.0 occ:1.00 OD2 A:ASP104 2.0 43.2 1.0 O A:HOH599 2.3 28.8 1.0 O A:HOH586 2.5 43.7 1.0 OE2 A:GLU109 2.5 30.3 1.0 O A:HOH609 2.5 43.2 1.0 CG A:ASP104 2.7 39.0 1.0 OD1 A:ASP104 2.9 29.1 1.0 CG A:GLU109 3.3 27.2 1.0 O A:ASP104 3.3 24.1 1.0 CD A:GLU109 3.3 35.0 1.0 CB A:ASN108 3.8 26.4 1.0 C A:ASP104 3.9 21.7 1.0 OD1 A:ASN108 4.0 42.6 1.0 CB A:ASP104 4.0 18.9 1.0 O1 A:GOL305 4.0 36.9 1.0 CG A:ASN108 4.4 37.4 1.0 O A:HOH436 4.4 23.6 1.0 NE2 E:HIS33 4.5 21.7 1.0 C1 A:GOL305 4.5 46.7 1.0 CA A:ASP104 4.5 18.3 1.0 OE1 A:GLU109 4.5 29.2 1.0 N A:PHE105 4.6 13.9 1.0 OD2 E:ASP61 4.6 41.8 1.0 O3 A:GOL305 4.6 54.6 1.0 O A:HOH608 4.6 35.4 1.0 CB A:GLU109 4.7 20.9 1.0 C2 A:GOL305 4.7 54.0 1.0 CA A:PHE105 4.7 15.7 1.0 OD1 E:ASP61 4.8 40.3 1.0 CE1 E:HIS33 4.9 20.4 1.0 CA A:ASN108 4.9 22.2 1.0 C A:ASN108 5.0 25.9 1.0

R.Wu, M.Gu, C.A.Kerfeld, A.Salmeen, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). Crystal Structure of Ethanolamine Utilization Protein Eutl From Leptotrichia Buccalis C-1013-B To Be Published.