Sodium in PDB 4dcc: Crystal Structure of Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088)

The structure of Crystal Structure of Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088), PDB code: 4dcc was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, K.N.Allen, D.Dunaway-Mariano, S.C.Almo, Enzyme Functioninitiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.65
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.252, 75.424, 131.270, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21

The structure of Crystal Structure of Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088) (pdb code 4dcc). 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 Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088), PDB code: 4dcc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088)


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 Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:29.0 occ:1.00 OD2 A:ASP12 2.2 35.7 1.0 OD1 A:ASP176 2.2 30.5 1.0 O A:HOH521 2.3 29.5 1.0 O A:GLY14 2.4 25.3 1.0 O A:HOH598 2.5 47.0 1.0 O A:HOH567 2.8 53.2 1.0 CG A:ASP176 3.3 31.9 1.0 CG A:ASP12 3.3 25.4 1.0 C A:GLY14 3.3 21.5 1.0 OD2 A:ASP176 3.6 38.8 1.0 CA A:GLY14 3.9 23.3 1.0 OD1 A:ASP175 4.0 29.9 1.0 O A:HOH523 4.0 42.0 1.0 OD1 A:ASP12 4.1 36.4 1.0 O A:HOH583 4.1 32.6 1.0 CB A:ASP12 4.2 22.5 1.0 N A:GLY14 4.2 24.5 1.0 N A:GLY15 4.4 24.9 1.0 N A:ASP176 4.4 24.7 1.0 O A:HOH522 4.4 47.9 1.0 CL A:CL301 4.6 43.9 1.0 CB A:ASP176 4.6 27.9 1.0 CG A:ASP175 4.7 34.6 1.0 CA A:GLY15 4.7 25.3 1.0 N A:VAL16 4.7 23.1 1.0 CG2 A:VAL16 4.8 24.4 1.0 OD2 A:ASP175 4.9 26.4 1.0 CA A:ASP176 4.9 25.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088)


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 Had Family Enzyme Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:34.5 occ:1.00 O A:GLU135 2.2 26.4 1.0 O A:PHE138 2.4 26.9 1.0 O A:HOH563 2.4 29.5 0.5 O A:HOH516 2.4 43.4 1.0 O A:HOH517 2.5 39.7 1.0 O A:HOH590 2.8 50.7 1.0 O A:HOH563 2.9 29.2 0.5 C A:GLU135 3.4 27.2 1.0 C A:PHE138 3.5 26.3 1.0 CA A:GLU135 4.1 25.4 1.0 NH2 A:ARG103 4.1 66.0 1.0 O A:GLU139 4.1 26.9 1.0 CA A:GLU139 4.2 23.3 1.0 NH1 A:ARG103 4.2 50.2 1.0 N A:GLU139 4.2 24.3 1.0 O A:HOH515 4.3 39.0 0.5 CB A:GLU135 4.4 33.3 1.0 C A:GLU139 4.4 25.1 1.0 N A:PHE138 4.4 23.8 1.0 N A:ASP136 4.4 24.9 1.0 CZ A:ARG103 4.5 65.0 1.0 CA A:PHE138 4.6 23.9 1.0 CA A:ASP136 4.7 23.8 1.0 C A:ASP136 4.9 29.4 1.0

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, K.N.Allen, D.Dunaway-Mariano, J.A.Gerlt, S.C.Almo. Crystal Structure of Protein Bt-2542 From Bacteroides Thetaiotaomicron (Target Efi-501088) To Be Published.