Sodium in PDB 5ubu: 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.

The structure of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica., PDB code: 5ubu was solved by G.Minasov, L.Shuvalova, K.Flores, I.Dubrovska, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.81 / 2.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.884, 137.884, 204.281, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22

The binding sites of Sodium atom in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. (pdb code 5ubu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica., PDB code: 5ubu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:31.6 occ:1.00 OD2 A:ASP217 2.2 40.2 1.0 OD1 A:ASN190 2.2 36.4 1.0 OD1 A:ASP192 2.3 40.8 1.0 O A:HOH632 2.6 17.6 0.5 OD2 A:ASP192 2.7 38.4 1.0 CG A:ASP192 2.8 38.2 1.0 O A:HOH552 3.1 20.4 0.5 O A:HOH632 3.1 60.2 0.5 CG A:ASN190 3.1 33.9 1.0 NA A:NA402 3.2 25.4 1.0 ND2 A:ASN190 3.4 33.8 1.0 CG A:ASP217 3.4 37.0 1.0 ND2 A:ASN82 3.6 31.2 1.0 NE2 A:HIS219 3.9 38.2 1.0 OD1 A:ASP217 3.9 37.9 1.0 CE1 A:HIS219 3.9 36.7 1.0 OE2 A:GLU226 4.0 38.2 1.0 OD1 A:ASN82 4.2 31.7 1.0 CG A:ASN82 4.3 31.3 1.0 CB A:ASP192 4.3 37.4 1.0 OE1 A:GLU226 4.4 38.0 1.0 OD2 A:ASP313 4.5 40.8 1.0 CB A:ASP217 4.5 36.0 1.0 CB A:ASN190 4.6 33.8 1.0 CA A:GLY168 4.6 31.1 1.0 CD A:GLU226 4.6 37.0 1.0 CG2 A:THR169 4.7 28.6 1.0 OD1 A:ASP313 4.7 41.3 1.0 C A:GLY168 4.8 29.9 1.0 O A:GLY168 4.8 29.4 1.0

Sodium binding site 2 out of 8 in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:25.4 occ:1.00 OE1 A:GLU233 2.2 42.1 1.0 OE2 A:GLU233 2.3 40.4 1.0 OD1 A:ASP217 2.3 37.9 1.0 NE2 A:HIS219 2.3 38.2 1.0 CD A:GLU233 2.5 38.5 1.0 O A:HOH632 2.7 17.6 0.5 OD2 A:ASP217 2.9 40.2 1.0 CG A:ASP217 2.9 37.0 1.0 CD2 A:HIS219 3.2 38.0 1.0 NA A:NA401 3.2 31.6 1.0 CE1 A:HIS219 3.4 36.7 1.0 O A:HOH632 3.5 60.2 0.5 OE2 A:GLU226 3.7 38.2 1.0 CG A:GLU233 4.0 38.1 1.0 CB A:ALA60 4.1 30.1 1.0 OD1 A:ASN82 4.1 31.7 1.0 O A:HOH560 4.4 31.1 1.0 CG A:HIS219 4.4 37.5 1.0 O A:HOH552 4.4 20.4 0.5 CB A:ASP217 4.4 36.0 1.0 ND1 A:HIS219 4.5 36.6 1.0 OD1 A:ASP192 4.5 40.8 1.0 N A:ALA231 4.8 34.6 1.0 CD A:GLU226 4.9 37.0 1.0 CB A:GLU233 4.9 37.5 1.0 O A:ASP217 4.9 34.0 1.0

Sodium binding site 3 out of 8 in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:22.5 occ:1.00 OE1 B:GLU233 2.2 51.7 1.0 OE2 B:GLU233 2.2 51.1 1.0 OD1 B:ASP217 2.3 50.5 1.0 O B:HOH556 2.3 18.1 0.5 NE2 B:HIS219 2.3 47.0 1.0 CD B:GLU233 2.5 49.9 1.0 OD2 B:ASP217 2.9 49.9 1.0 CG B:ASP217 2.9 48.0 1.0 NA B:NA402 3.2 26.1 1.0 CD2 B:HIS219 3.2 46.5 1.0 CE1 B:HIS219 3.4 45.6 1.0 O B:HOH579 3.5 39.1 0.5 OE2 B:GLU226 3.7 45.6 1.0 O B:HOH579 3.8 8.2 0.5 CG B:GLU233 4.0 50.0 1.0 CB B:ALA60 4.1 45.8 1.0 OD1 B:ASN82 4.1 52.8 1.0 O B:HOH556 4.2 15.8 0.5 CG B:HIS219 4.4 45.5 1.0 CB B:ASP217 4.4 46.8 1.0 ND1 B:HIS219 4.5 45.2 1.0 OD1 B:ASP192 4.5 48.9 1.0 O B:HOH535 4.6 29.4 1.0 N B:ALA231 4.8 43.9 1.0 CB B:GLU233 4.9 49.8 1.0 CD B:GLU226 4.9 44.2 1.0 O B:ASP217 4.9 44.6 1.0 CG B:ASN82 5.0 50.1 1.0

Sodium binding site 4 out of 8 in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:26.1 occ:1.00 OD2 B:ASP217 2.2 49.9 1.0 OD1 B:ASN190 2.2 48.9 1.0 OD1 B:ASP192 2.3 48.9 1.0 O B:HOH556 2.5 18.1 0.5 O B:HOH579 2.7 8.2 0.5 OD2 B:ASP192 2.7 46.5 1.0 CG B:ASP192 2.8 46.5 1.0 O B:HOH556 2.9 15.8 0.5 CG B:ASN190 3.1 46.1 1.0 NA B:NA401 3.2 22.5 1.0 CG B:ASP217 3.4 48.0 1.0 ND2 B:ASN190 3.4 46.2 1.0 ND2 B:ASN82 3.6 50.8 1.0 NE2 B:HIS219 3.9 47.0 1.0 OD1 B:ASP217 3.9 50.5 1.0 CE1 B:HIS219 4.0 45.6 1.0 OE2 B:GLU226 4.0 45.6 1.0 OD1 B:ASN82 4.2 52.8 1.0 CG B:ASN82 4.2 50.1 1.0 CB B:ASP192 4.3 45.8 1.0 O B:HOH579 4.4 39.1 0.5 OE1 B:GLU226 4.4 43.7 1.0 OD2 B:ASP313 4.5 54.3 1.0 CB B:ASP217 4.5 46.8 1.0 CB B:ASN190 4.6 45.3 1.0 CA B:GLY168 4.6 42.0 1.0 CD B:GLU226 4.7 44.2 1.0 CG2 B:THR169 4.7 41.9 1.0 OD1 B:ASP313 4.8 54.8 1.0 C B:GLY168 4.8 41.4 1.0 O B:GLY168 4.8 41.1 1.0

Sodium binding site 5 out of 8 in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:35.3 occ:1.00 OD2 C:ASP217 2.2 44.3 1.0 OD1 C:ASN190 2.2 45.1 1.0 OD1 C:ASP192 2.3 45.1 1.0 OD2 C:ASP192 2.7 44.0 1.0 CG C:ASP192 2.8 43.1 1.0 O C:HOH593 2.9 59.1 0.5 O C:HOH593 2.9 51.1 0.5 O C:HOH547 3.1 22.9 0.5 CG C:ASN190 3.1 42.7 1.0 NA C:NA402 3.2 31.8 1.0 ND2 C:ASN190 3.4 42.2 1.0 CG C:ASP217 3.4 42.0 1.0 ND2 C:ASN82 3.6 38.1 1.0 NE2 C:HIS219 3.9 44.8 1.0 OD1 C:ASP217 3.9 44.1 1.0 CE1 C:HIS219 3.9 43.6 1.0 OE2 C:GLU226 4.0 47.1 1.0 OD1 C:ASN82 4.2 40.5 1.0 CG C:ASN82 4.3 39.1 1.0 CB C:ASP192 4.3 42.2 1.0 OE1 C:GLU226 4.4 45.1 1.0 OD2 C:ASP313 4.5 45.6 1.0 CB C:ASP217 4.5 40.6 1.0 CB C:ASN190 4.6 40.9 1.0 CA C:GLY168 4.6 29.7 1.0 CD C:GLU226 4.6 45.1 1.0 CG2 C:THR169 4.7 30.4 1.0 C C:GLY168 4.8 29.1 1.0 OD1 C:ASP313 4.8 47.3 1.0 O C:GLY168 4.8 28.1 1.0

Sodium binding site 6 out of 8 in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:31.8 occ:1.00 OE1 C:GLU233 2.2 50.1 1.0 OE2 C:GLU233 2.2 50.7 1.0 OD1 C:ASP217 2.2 44.1 1.0 NE2 C:HIS219 2.3 44.8 1.0 CD C:GLU233 2.5 48.1 1.0 OD2 C:ASP217 2.9 44.3 1.0 CG C:ASP217 2.9 42.0 1.0 O C:HOH593 2.9 51.1 0.5 CD2 C:HIS219 3.2 44.5 1.0 NA C:NA401 3.2 35.3 1.0 O C:HOH593 3.3 59.1 0.5 CE1 C:HIS219 3.4 43.6 1.0 OE2 C:GLU226 3.7 47.1 1.0 CG C:GLU233 4.0 48.2 1.0 CB C:ALA60 4.1 39.9 1.0 OD1 C:ASN82 4.1 40.5 1.0 CG C:HIS219 4.4 43.7 1.0 O C:HOH515 4.4 30.8 1.0 CB C:ASP217 4.4 40.6 1.0 O C:HOH547 4.4 22.9 0.5 ND1 C:HIS219 4.4 42.9 1.0 OD1 C:ASP192 4.5 45.1 1.0 N C:ALA231 4.8 45.7 1.0 CB C:GLU233 4.9 47.4 1.0 CD C:GLU226 4.9 45.1 1.0 O C:ASP217 4.9 39.6 1.0

Sodium binding site 7 out of 8 in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:34.1 occ:1.00 OE1 D:GLU233 2.2 50.5 1.0 OE2 D:GLU233 2.3 48.8 1.0 OD1 D:ASP217 2.3 47.5 1.0 NE2 D:HIS219 2.3 44.6 1.0 CD D:GLU233 2.5 47.3 1.0 O D:HOH551 2.7 24.6 0.5 OD2 D:ASP217 2.9 47.9 1.0 CG D:ASP217 2.9 45.8 1.0 NA D:NA402 3.2 37.6 1.0 CD2 D:HIS219 3.2 45.0 1.0 CE1 D:HIS219 3.4 43.1 1.0 OE2 D:GLU226 3.7 50.6 1.0 CG D:GLU233 4.0 46.4 1.0 CB D:ALA60 4.1 40.1 1.0 OD1 D:ASN82 4.2 45.5 1.0 O D:HOH551 4.3 10.0 0.5 CG D:HIS219 4.4 44.8 1.0 ND1 D:HIS219 4.4 43.7 1.0 CB D:ASP217 4.4 45.2 1.0 OD1 D:ASP192 4.5 47.1 1.0 O D:HOH535 4.6 32.0 1.0 N D:ALA231 4.8 38.0 1.0 CD D:GLU226 4.9 47.4 1.0 CB D:GLU233 4.9 46.0 1.0 O D:ASP217 4.9 44.0 1.0

Sodium binding site 8 out of 8 in the 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na402 b:37.6 occ:1.00 OD2 D:ASP217 2.2 47.9 1.0 OD1 D:ASP192 2.3 47.1 1.0 OD1 D:ASN190 2.3 46.5 1.0 O D:HOH551 2.5 24.6 0.5 OD2 D:ASP192 2.7 44.8 1.0 CG D:ASP192 2.8 44.7 1.0 CG D:ASN190 3.2 43.7 1.0 NA D:NA401 3.2 34.1 1.0 CG D:ASP217 3.4 45.8 1.0 ND2 D:ASN190 3.4 44.9 1.0 O D:HOH551 3.4 10.0 0.5 ND2 D:ASN82 3.6 46.2 1.0 NE2 D:HIS219 3.9 44.6 1.0 OD1 D:ASP217 3.9 47.5 1.0 CE1 D:HIS219 3.9 43.1 1.0 OE2 D:GLU226 4.0 50.6 1.0 OD1 D:ASN82 4.2 45.5 1.0 CG D:ASN82 4.3 45.1 1.0 CB D:ASP192 4.3 44.7 1.0 OE1 D:GLU226 4.4 49.9 1.0 OD2 D:ASP313 4.5 61.0 1.0 CB D:ASP217 4.5 45.2 1.0 CB D:ASN190 4.6 44.1 1.0 CA D:GLY168 4.6 40.8 1.0 CD D:GLU226 4.6 47.4 1.0 CG2 D:THR169 4.7 38.5 1.0 OD1 D:ASP313 4.8 59.0 1.0 C D:GLY168 4.8 40.0 1.0 O D:GLY168 4.8 39.5 1.0

G.Minasov, L.Shuvalova, K.Flores, I.Dubrovska, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.75 Angstrom Resolution Crystal Structure of Acetamidase From Yersinia Enterocolitica. To Be Published.