Sodium in PDB 8ey3: Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37

The structure of Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37, PDB code: 8ey3 was solved by K.Michalska, L.Stols, W.Eschenfeldt, C.W.Goulding, C.S.Hayes, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Centerfor 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)	29.15 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	27.386, 35.753, 50.34, 90, 90, 90
R / Rfree (%)	10.3 / 11

The structure of Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37 also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Sodium atom in the Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37 (pdb code 8ey3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37, PDB code: 8ey3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:16.4 occ:0.78 O A:HOH259 2.3 20.3 0.9 O A:HOH290 2.4 18.9 0.8 O A:ASP42 2.4 17.1 1.0 OG A:SER44 2.6 16.9 1.0 H A:SER44 2.9 17.9 1.0 HG A:SER44 3.1 20.3 1.0 HB2 A:SER44 3.4 19.3 1.0 N A:SER44 3.5 14.9 1.0 CB A:SER44 3.5 16.1 1.0 C A:ASP42 3.6 15.4 1.0 HB3 A:SER51 3.7 18.7 1.0 HA A:PHE43 3.7 18.1 1.0 CA A:SER44 4.1 15.1 1.0 HB3 A:ASP42 4.2 20.6 1.0 O A:HOH236 4.2 27.6 0.8 C A:PHE43 4.2 14.3 1.0 CA A:PHE43 4.3 15.0 1.0 HB3 A:SER44 4.3 19.3 1.0 O A:HOH335 4.4 25.6 0.5 N A:PHE43 4.4 14.9 1.0 OE2 A:GLU54 4.4 21.4 1.0 O A:HOH222 4.5 17.5 0.8 HA A:ASP42 4.6 19.1 1.0 CB A:SER51 4.6 15.6 1.0 CA A:ASP42 4.6 15.9 1.0 HA A:SER44 4.7 18.1 1.0 HG A:SER51 4.7 19.5 1.0 HB2 A:SER51 4.8 18.7 1.0 CB A:ASP42 4.9 17.1 1.0 OE1 A:GLU54 4.9 19.7 1.0 CD A:GLU54 5.0 19.6 1.0

Sodium binding site 2 out of 3 in the Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:15.1 occ:0.34 O A:HOH292 2.1 28.2 1.0 O A:CYS12 2.3 17.0 1.0 O A:HOH291 2.4 30.8 0.8 O A:HOH326 2.4 19.5 0.6 O A:HOH213 2.4 20.1 0.6 O A:HOH295 2.4 19.6 0.6 O A:HOH314 3.2 14.0 0.5 C A:CYS12 3.4 15.7 1.0 HA3 A:GLY13 3.5 19.2 1.0 O A:HOH331 3.8 27.4 0.7 O A:HOH319 3.9 29.6 0.8 HA A:CYS12 4.0 18.6 1.0 HE2 A:PHE59 4.1 24.4 1.0 O A:HOH243 4.1 20.5 0.6 N A:GLY13 4.2 15.6 1.0 CA A:GLY13 4.2 16.0 1.0 CA A:CYS12 4.3 15.4 1.0 O A:HOH315 4.4 22.7 0.8 O A:HOH275 4.5 18.0 0.8 HB2 A:CYS12 4.5 18.9 1.0 O A:HOH262 4.5 28.0 0.6 O A:HOH276 4.8 28.4 0.7 O A:HOH245 4.8 21.2 0.5 OD1 A:ASN60 4.8 28.4 1.0 C A:GLY13 4.8 15.9 1.0 CE2 A:PHE59 4.9 20.4 1.0 HD2 A:PHE59 4.9 22.7 1.0 H A:ASN14 4.9 18.4 1.0 H A:GLY13 5.0 18.7 1.0 HD21 A:ASN14 5.0 19.4 1.0 CB A:CYS12 5.0 15.7 1.0 HA2 A:GLY13 5.0 19.2 1.0

Sodium binding site 3 out of 3 in the Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:20.0 occ:0.65 O A:ALA39 2.3 18.0 1.0 O A:HOH249 2.3 24.4 0.7 O A:HOH296 2.5 34.2 0.8 HA A:ALA39 3.3 19.2 1.0 C A:ALA39 3.4 16.0 1.0 HD3 A:PRO41 3.9 19.0 0.5 CA A:ALA39 3.9 16.0 1.0 HD3 A:PRO41 4.1 18.6 0.5 HB1 A:ALA39 4.3 19.8 1.0 HA A:ASP40 4.3 18.4 1.0 O A:SER38 4.4 16.2 0.9 HD2 A:PRO41 4.5 19.0 0.5 N A:ASP40 4.5 15.3 1.0 CD A:PRO41 4.6 15.8 0.5 CB A:ALA39 4.7 16.5 1.0 O A:HOH333 4.7 26.3 0.5 HD2 A:PRO41 4.7 18.6 0.5 CD A:PRO41 4.8 15.5 0.5 CA A:ASP40 5.0 15.3 1.0

K.Michalska, L.Stols, W.Eschenfeldt, C.W.Goulding, C.S.Hayes, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Center For Structural Genomics Of Infectious Diseases(Csgid). Contact-Dependent Growth Inhibition (Cdi) Immunity Protein From E. Coli O32:H37 To Be Published.