Sodium in PDB 3oib: Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak

The structure of Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak, PDB code: 3oib was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.12 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.590, 64.490, 83.600, 90.00, 111.99, 90.00
R / Rfree (%)	15.2 / 20

The structure of Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak also contains other interesting chemical elements:

Iodine

(I)

30 atoms

The binding sites of Sodium atom in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak (pdb code 3oib). 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 A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak, PDB code: 3oib:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:16.8 occ:1.00 O A:HOH815 3.0 20.9 1.0 O A:HOH840 3.0 31.1 1.0 NH1 A:ARG321 3.3 9.5 1.0 CD A:ARG321 3.6 8.7 1.0 CG2 A:VAL318 4.1 7.7 1.0 CD1 A:TRP25 4.1 11.6 1.0 O A:HOH635 4.3 11.8 1.0 CZ A:ARG321 4.3 10.2 1.0 NE A:ARG321 4.4 9.6 1.0 CA A:VAL318 4.6 8.3 1.0 CB A:ARG321 4.6 9.1 1.0 NE1 A:TRP25 4.6 11.8 1.0 CB A:VAL318 4.8 9.5 1.0 CG A:ARG321 4.8 9.4 1.0 CG A:TRP25 4.8 13.5 1.0 OE2 A:GLU325 4.8 27.5 1.0 CG1 A:VAL318 4.9 10.1 1.0 O A:HOH662 5.0 21.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:20.4 occ:1.00 O B:HOH698 2.8 23.5 1.0 O B:HOH796 3.2 22.7 1.0 NH1 B:ARG321 3.4 12.7 1.0 CD B:ARG321 3.7 9.6 1.0 CD1 B:TRP25 4.1 14.5 1.0 CG2 B:VAL318 4.2 8.1 1.0 O B:HOH731 4.4 13.1 1.0 CZ B:ARG321 4.4 12.1 1.0 NE B:ARG321 4.5 9.8 1.0 NE1 B:TRP25 4.6 13.5 1.0 CB B:ARG321 4.6 10.4 1.0 CA B:VAL318 4.7 8.2 1.0 CG B:TRP25 4.7 14.2 1.0 OE2 B:GLU325 4.8 30.2 1.0 CG B:ARG321 4.8 8.4 1.0 CB B:VAL318 4.9 8.7 1.0

J.Abendroth, A.S.Gardberg, J.I.Robinson, J.S.Christensen, B.L.Staker, P.J.Myler, L.J.Stewart, T.E.Edwards. Sad Phasing Using Iodide Ions in A High-Throughput Structural Genomics Environment. J Struct Funct Genomics 2011.
PubMed: 21359836
DOI: 10.1007/S10969-011-9101-7