Sodium in PDB 3zmd: Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor

The structure of Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor, PDB code: 3zmd was solved by C.E.M.Stevenson, H.Kock, S.Mootien, S.C.Davies, M.J.Bibb, D.M.Lawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.68 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.648, 120.483, 144.290, 90.00, 90.00, 90.00
R / Rfree (%)	21.477 / 24.282

The structure of Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor (pdb code 3zmd). 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 Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor, PDB code: 3zmd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor


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 Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:31.3 occ:1.00 OD1 A:ASP58 2.7 36.9 1.0 O A:SER55 2.7 33.7 1.0 O A:HOH2034 2.7 61.8 1.0 O A:SER53 2.8 33.2 1.0 OE2 D:GLU56 2.8 62.1 1.0 CL A:CL303 3.5 43.7 1.0 C A:SER55 3.7 35.7 1.0 C A:SER53 3.7 33.4 1.0 CD D:GLU56 3.8 60.1 1.0 CG A:ASP58 3.9 34.1 1.0 N A:SER55 4.1 32.8 1.0 N A:ASP58 4.1 30.9 1.0 OE1 D:GLU56 4.2 62.0 1.0 C A:GLU54 4.2 34.5 1.0 CA A:GLU54 4.5 34.8 1.0 N A:GLU54 4.5 32.3 1.0 CA A:SER55 4.5 35.3 1.0 CA A:ASP58 4.5 30.1 1.0 N A:GLU56 4.5 37.9 1.0 N A:GLY57 4.6 35.0 1.0 CA A:SER53 4.6 32.1 1.0 O A:LEU52 4.6 31.1 1.0 O A:HOH2040 4.7 38.5 1.0 OD2 A:ASP58 4.7 36.5 1.0 CA A:GLU56 4.7 40.7 1.0 O A:GLU54 4.7 35.7 1.0 N D:GLY57 4.8 39.2 1.0 CB A:ASP58 4.8 31.9 1.0 C A:GLU56 4.9 35.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor


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 Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:25.0 occ:1.00 O B:SER53 2.7 33.2 1.0 O B:SER55 2.7 31.7 1.0 OD1 B:ASP58 2.8 29.7 1.0 CL B:CL303 3.0 40.7 1.0 C B:SER55 3.6 34.6 1.0 C B:SER53 3.6 31.8 1.0 N B:SER55 4.0 31.5 1.0 CG B:ASP58 4.0 31.1 1.0 C B:GLU54 4.1 32.9 1.0 CA B:GLU54 4.2 33.0 1.0 N B:ASP58 4.3 28.4 1.0 N B:GLU54 4.3 31.1 1.0 O B:HOH2043 4.4 44.4 1.0 CA B:SER55 4.4 34.1 1.0 N B:GLU56 4.5 35.9 1.0 O B:GLU54 4.5 33.7 1.0 CA B:SER53 4.6 30.1 1.0 O B:LEU52 4.6 31.2 1.0 N B:GLY57 4.7 35.2 1.0 CA B:ASP58 4.7 28.0 1.0 CA B:GLU56 4.7 39.3 1.0 OD2 B:ASP58 4.8 34.9 1.0 C B:GLU56 4.9 36.0 1.0 CB B:ASP58 5.0 28.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor


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 Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:28.3 occ:1.00 OD1 C:ASP58 2.7 31.9 1.0 O C:SER55 2.8 31.1 1.0 O C:SER53 2.8 30.9 1.0 C C:SER55 3.7 33.2 1.0 C C:SER53 3.8 29.7 1.0 CG C:ASP58 3.9 30.1 1.0 N C:SER55 4.1 31.0 1.0 N C:ASP58 4.2 29.0 1.0 C C:GLU54 4.4 31.7 1.0 CA C:SER55 4.5 32.9 1.0 N C:GLU56 4.6 35.1 1.0 N C:GLU54 4.6 29.5 1.0 CA C:ASP58 4.6 27.5 1.0 CA C:GLU54 4.6 31.5 1.0 OD2 C:ASP58 4.6 31.8 1.0 CA C:GLU56 4.7 36.4 1.0 CA C:SER53 4.7 29.6 1.0 N C:GLY57 4.7 32.8 1.0 O C:LEU52 4.7 27.8 1.0 CB C:ASP58 4.9 28.0 1.0 O C:GLU54 4.9 32.2 1.0 C C:GLU56 4.9 33.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor


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 Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:34.0 occ:1.00 OD1 D:ASP58 2.6 42.2 1.0 OE2 A:GLU56 2.6 67.0 1.0 O D:SER55 2.7 38.8 1.0 O D:SER53 2.9 37.9 1.0 CL A:CL303 3.4 43.7 1.0 CD A:GLU56 3.7 60.4 1.0 C D:SER55 3.7 39.3 1.0 C D:SER53 3.8 37.1 1.0 CG D:ASP58 3.8 37.7 1.0 N D:SER55 4.1 35.7 1.0 N D:ASP58 4.1 36.3 1.0 OE1 A:GLU56 4.1 66.3 1.0 C D:GLU54 4.3 38.7 1.0 CA D:ASP58 4.5 34.6 1.0 O A:HOH2038 4.5 44.0 1.0 CA D:SER55 4.5 38.5 1.0 CA D:GLU54 4.5 38.1 1.0 N D:GLU56 4.6 41.0 1.0 N D:GLU54 4.6 35.5 1.0 N D:GLY57 4.6 39.2 1.0 O D:LEU52 4.6 33.0 1.0 N A:GLY57 4.6 35.0 1.0 OD2 D:ASP58 4.6 40.7 1.0 CA D:SER53 4.7 33.9 1.0 CA D:GLU56 4.7 44.0 1.0 CB D:ASP58 4.8 35.2 1.0 O D:GLU54 4.8 38.7 1.0 C D:GLU56 4.9 40.1 1.0 CG A:GLU56 4.9 52.0 1.0 CA A:GLY57 4.9 34.3 1.0

C.E.M.Stevenson, H.Kock, S.Mootien, S.C.Davies, M.J.Bibb, D.M.Lawson. Crystal Structure of Absc, A Marr Family Transcriptional Regulator From Streptomyces Coelicolor To Be Published.