Sodium in PDB 4gfi: Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop)

The structure of Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop), PDB code: 4gfi was solved by M.W.Vetting, J.T.Bouvier, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.83 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.901, 77.274, 215.825, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.3

The structure of Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop) also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop) (pdb code 4gfi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop), PDB code: 4gfi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop)


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 Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.4 occ:1.00 OE2 A:GLU201 2.3 20.3 1.0 OD2 A:ASP224 2.3 26.7 1.0 O A:HOH501 2.3 19.4 1.0 OD2 A:ASP175 2.3 23.1 1.0 O A:GLU403 2.4 21.8 1.0 OXT A:GLU403 2.5 19.6 1.0 C A:GLU403 2.9 17.8 1.0 CG A:ASP175 3.2 20.6 1.0 CD A:GLU201 3.3 23.5 1.0 CG A:ASP224 3.3 20.3 1.0 OD1 A:ASP175 3.5 18.7 1.0 NZ A:LYS148 3.6 19.1 1.0 ND2 A:ASN177 3.6 22.7 1.0 CB A:ASP224 3.7 18.1 1.0 OE1 A:GLU201 3.9 22.8 1.0 ND2 A:ASN244 4.0 16.7 1.0 NZ A:LYS246 4.0 43.1 1.0 NZ A:LYS150 4.0 17.2 1.0 CB A:GLU201 4.2 26.0 1.0 CG A:GLU201 4.3 29.9 1.0 O A:HOH616 4.4 31.1 1.0 CA A:GLU403 4.4 19.5 1.0 CE A:LYS148 4.4 18.6 1.0 OD1 A:ASP224 4.4 22.3 1.0 CB A:ASP175 4.5 17.6 1.0 CG A:ASN177 4.5 25.1 1.0 OE1 A:GLU225 4.6 19.2 1.0 CE A:LYS246 4.7 32.9 1.0 O A:HOH513 4.8 18.5 1.0 OD1 A:ASN177 4.8 20.1 1.0 CG A:ASN244 5.0 24.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop)


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 Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:9.9 occ:1.00 OD2 B:ASP224 2.2 12.4 1.0 OE2 B:GLU201 2.4 12.9 1.0 O B:HOH501 2.4 11.8 1.0 OD2 B:ASP175 2.4 13.2 1.0 OXT B:GLU403 2.4 10.5 1.0 O B:GLU403 2.5 10.0 1.0 C B:GLU403 2.8 14.7 1.0 CG B:ASP224 3.3 11.7 1.0 CG B:ASP175 3.3 11.9 1.0 CD B:GLU201 3.4 16.1 1.0 OD1 B:ASP175 3.6 12.5 1.0 CB B:ASP224 3.7 9.3 1.0 NZ B:LYS148 3.8 9.1 1.0 ND2 B:ASN177 3.8 10.5 1.0 OE1 B:GLU201 4.0 14.7 1.0 ND2 B:ASN244 4.0 11.9 1.0 NZ B:LYS150 4.2 10.1 1.0 NZ B:LYS246 4.2 18.2 1.0 CB B:GLU201 4.3 11.8 1.0 O B:HOH566 4.3 19.4 1.0 CA B:GLU403 4.3 13.8 1.0 OD1 B:ASP224 4.4 14.2 1.0 CG B:GLU201 4.4 15.6 1.0 CE B:LYS148 4.5 9.6 1.0 CB B:ASP175 4.6 9.5 1.0 OE1 B:GLU225 4.6 12.5 1.0 O B:HOH512 4.6 12.5 1.0 CE B:LYS246 4.7 19.2 1.0 CG B:ASN177 4.7 14.4 1.0 OD1 B:ASN177 5.0 11.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop)


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 Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:17.2 occ:1.00 OD2 C:ASP224 2.3 20.4 1.0 O C:HOH501 2.3 16.4 1.0 OE2 C:GLU201 2.3 16.0 1.0 OD2 C:ASP175 2.3 21.3 1.0 O C:GLU403 2.4 18.9 1.0 OXT C:GLU403 2.5 19.1 1.0 C C:GLU403 2.8 20.5 1.0 CG C:ASP175 3.2 19.9 1.0 CG C:ASP224 3.3 22.0 1.0 CD C:GLU201 3.4 27.7 1.0 OD1 C:ASP175 3.5 17.5 1.0 CB C:ASP224 3.7 16.9 1.0 NZ C:LYS148 3.7 18.8 1.0 ND2 C:ASN177 3.8 17.7 1.0 OE1 C:GLU201 4.0 28.4 1.0 ND2 C:ASN244 4.1 20.6 1.0 NZ C:LYS150 4.2 19.5 1.0 NZ C:LYS246 4.2 25.8 1.0 CB C:GLU201 4.3 20.1 1.0 CG C:GLU201 4.3 23.6 1.0 CA C:GLU403 4.4 21.6 1.0 O C:HOH548 4.4 29.5 1.0 OD1 C:ASP224 4.4 21.4 1.0 CB C:ASP175 4.5 21.7 1.0 CE C:LYS148 4.6 18.6 1.0 OE1 C:GLU225 4.6 17.6 1.0 CG C:ASN177 4.6 20.7 1.0 O C:HOH508 4.7 17.6 1.0 CE C:LYS246 4.8 27.1 1.0 OD1 C:ASN177 4.8 19.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:11.6 occ:1.00 OD2 D:ASP224 2.3 16.7 1.0 OD2 D:ASP175 2.3 16.5 1.0 OE2 D:GLU201 2.3 10.8 1.0 O D:HOH502 2.4 12.7 1.0 OXT D:GLU403 2.4 12.6 1.0 O D:GLU403 2.5 12.9 1.0 C D:GLU403 2.9 15.1 1.0 CG D:ASP175 3.2 12.6 1.0 CG D:ASP224 3.3 11.5 1.0 CD D:GLU201 3.3 15.7 1.0 OD1 D:ASP175 3.4 11.3 1.0 NZ D:LYS148 3.7 8.1 1.0 CB D:ASP224 3.7 13.5 1.0 ND2 D:ASN177 3.8 9.8 1.0 ND2 D:ASN244 4.0 8.6 1.0 OE1 D:GLU201 4.0 17.3 1.0 NZ D:LYS150 4.0 10.7 1.0 NZ D:LYS246 4.0 33.6 1.0 CB D:GLU201 4.2 13.0 1.0 CG D:GLU201 4.3 17.5 1.0 CA D:GLU403 4.4 15.3 1.0 OD1 D:ASP224 4.5 10.1 1.0 CE D:LYS148 4.5 9.6 1.0 CB D:ASP175 4.5 9.3 1.0 O D:HOH573 4.5 20.7 1.0 CG D:ASN177 4.6 12.2 1.0 OE1 D:GLU225 4.6 11.5 1.0 O D:HOH510 4.7 9.7 1.0 CE D:LYS246 4.8 21.9 1.0 OD1 D:ASN177 4.8 9.3 1.0

M.W.Vetting, J.T.Bouvier, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of Efi-502318, An Enolase Family Member From Agrobacterium Tumefaciens with Homology to Dipeptide Epimerases (Bound Sodium, L-Ala-L-Glu with Ordered Loop) To Be Published.