Sodium in PDB 3k6a: Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis

The structure of Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis, PDB code: 3k6a was solved by C.Chang, L.Bigelow, A.Joachimiak, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.132, 66.310, 74.332, 92.15, 103.64, 119.98
R / Rfree (%)	17.7 / 21.6

The binding sites of Sodium atom in the Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis (pdb code 3k6a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis, PDB code: 3k6a:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis


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 Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na178 b:25.7 occ:1.00 O A:HOH276 2.1 29.7 1.0 O A:HOH248 2.2 8.5 1.0 OD1 A:ASP126 2.5 15.7 1.0 O A:HOH303 2.5 21.4 1.0 OG A:SER127 2.5 7.9 1.0 O A:ALA62 2.6 11.3 1.0 C A:ALA62 3.6 11.3 1.0 CG A:ASP126 3.7 13.3 1.0 CB A:SER127 3.8 9.5 1.0 N A:SER127 3.9 10.2 1.0 O A:HOH343 4.0 26.2 1.0 CA A:ALA62 4.1 10.0 1.0 C A:ASP126 4.2 11.2 1.0 O A:ARG124 4.2 8.5 1.0 N A:ASP126 4.2 10.8 1.0 CB A:ALA62 4.3 10.1 1.0 CA A:SER127 4.3 8.9 1.0 OD2 A:ASP126 4.4 16.6 1.0 O A:CYS67 4.4 10.8 1.0 CA A:ASP126 4.6 11.3 1.0 O A:HOH254 4.6 31.5 1.0 N A:ASP63 4.6 12.4 1.0 O A:HOH275 4.8 44.5 1.0 OD1 A:ASP63 4.8 18.4 1.0 O A:ASP126 4.8 11.8 1.0 CB A:ASP126 4.8 11.6 1.0 CA A:ASP63 4.9 13.9 1.0 O A:HOH307 5.0 27.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis


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 Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Na178 b:48.6 occ:1.00 O D:HOH283 2.3 21.6 1.0 O D:HOH248 2.4 12.7 1.0 O D:HOH181 2.4 34.8 1.0 O D:ARG124 2.8 11.4 1.0 OD1 D:ASP126 3.3 18.0 1.0 OG D:SER127 3.5 12.6 1.0 O D:ALA62 3.6 15.0 1.0 N D:ASP126 3.6 12.1 1.0 C D:ARG124 3.7 11.4 1.0 N D:SER127 3.9 12.0 1.0 OD1 D:ASP63 3.9 13.8 1.0 CB D:SER127 4.0 11.9 1.0 CA D:GLY125 4.0 11.6 1.0 C D:ALA62 4.0 14.6 1.0 CB D:ALA62 4.1 14.5 1.0 N D:GLY125 4.2 11.1 1.0 O D:HOH264 4.2 33.5 1.0 C D:GLY125 4.2 12.2 1.0 CG D:ASP126 4.4 15.2 1.0 CA D:ALA62 4.5 14.4 1.0 CA D:ASP126 4.6 12.8 1.0 CA D:SER127 4.6 12.3 1.0 CG D:ARG124 4.6 12.5 1.0 C D:ASP126 4.6 12.5 1.0 N D:ASP63 4.7 14.8 1.0 CB D:ARG124 4.8 11.2 1.0 CA D:ASP63 4.8 15.4 1.0 CA D:ARG124 4.9 11.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis


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 Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ E:Na178 b:37.9 occ:1.00 O E:HOH324 2.3 29.9 1.0 O E:HOH234 2.3 22.4 1.0 OD1 E:ASP126 2.4 20.1 1.0 OG E:SER127 2.5 11.5 1.0 O E:ALA62 2.7 13.2 1.0 C E:ALA62 3.6 13.6 1.0 CG E:ASP126 3.6 18.1 1.0 CB E:SER127 3.8 13.0 1.0 N E:SER127 3.9 14.0 1.0 CA E:ALA62 4.0 13.4 1.0 N E:ASP126 4.2 15.1 1.0 CB E:ALA62 4.2 13.1 1.0 O E:ARG124 4.3 11.9 1.0 C E:ASP126 4.3 15.1 1.0 O E:CYS67 4.3 13.7 1.0 OD2 E:ASP126 4.3 22.2 1.0 CA E:SER127 4.3 13.0 1.0 O E:HOH267 4.4 28.8 1.0 OD1 E:ASP66 4.5 23.5 1.0 CA E:ASP126 4.5 15.5 1.0 N E:ASP63 4.7 14.3 1.0 CB E:ASP126 4.7 16.4 1.0 CA E:ASP66 4.8 17.8 1.0 O E:ASP126 5.0 16.2 1.0

C.Chang, L.Bigelow, A.Joachimiak. Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis To Be Published.