Sodium in PDB 3oec: Crystal Structure of Carveol Dehydrogenase From Mycobacterium Thermoresistibile

All present enzymatic activity of Crystal Structure of Carveol Dehydrogenase From Mycobacterium Thermoresistibile:
1.1.1.234;

The structure of Crystal Structure of Carveol Dehydrogenase From Mycobacterium Thermoresistibile, PDB code: 3oec 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)	45.74 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.860, 120.570, 134.560, 90.00, 94.05, 90.00
R / Rfree (%)	17.6 / 23.3

The binding sites of Sodium atom in the Crystal Structure of Carveol Dehydrogenase From Mycobacterium Thermoresistibile (pdb code 3oec). 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 Carveol Dehydrogenase From Mycobacterium Thermoresistibile, PDB code: 3oec:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Carveol Dehydrogenase From Mycobacterium Thermoresistibile


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 Carveol Dehydrogenase From Mycobacterium Thermoresistibile within 5.0Å range: probe atom residue distance (Å) B Occ A:Na300 b:18.9 occ:1.00 O A:HOH686 2.4 13.5 1.0 O A:LEU255 2.5 9.3 1.0 O A:SER250 2.5 16.4 1.0 O A:THR253 2.6 8.2 1.0 OG1 A:THR253 2.6 11.4 1.0 C A:THR253 3.2 7.7 1.0 C A:LEU255 3.6 9.9 1.0 C A:SER250 3.6 17.8 1.0 CB A:THR253 3.6 8.9 1.0 O A:ILE257 3.8 10.8 1.0 CA A:THR253 3.9 8.9 1.0 CA A:PRO256 4.0 12.1 1.0 N A:ILE257 4.0 11.9 1.0 N A:LEU254 4.1 7.1 1.0 C A:LEU254 4.1 8.6 1.0 CA A:SER250 4.1 17.3 1.0 N A:THR253 4.1 10.1 1.0 O A:LEU254 4.2 9.0 1.0 N A:PRO256 4.2 11.7 1.0 N A:LEU255 4.3 7.2 1.0 CA A:LEU254 4.4 7.6 1.0 C A:PRO256 4.5 12.5 1.0 CB A:SER250 4.6 18.4 1.0 NH2 A:ARG294 4.6 31.1 1.0 CA A:LEU255 4.6 8.3 1.0 O D:HOH347 4.7 22.0 1.0 C A:ILE257 4.7 12.2 1.0 N A:GLN251 4.8 18.3 1.0 CG2 A:THR253 5.0 9.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Carveol Dehydrogenase From Mycobacterium Thermoresistibile


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 Carveol Dehydrogenase From Mycobacterium Thermoresistibile within 5.0Å range: probe atom residue distance (Å) B Occ B:Na300 b:20.8 occ:1.00 O B:SER250 2.4 21.4 1.0 O B:HOH306 2.4 13.7 1.0 OG1 B:THR253 2.5 10.1 1.0 O B:THR253 2.5 9.6 1.0 O B:LEU255 2.6 11.3 1.0 C B:THR253 3.2 10.3 1.0 C B:SER250 3.5 21.9 1.0 CB B:THR253 3.6 11.1 1.0 O B:ILE257 3.7 11.3 1.0 C B:LEU255 3.7 11.1 1.0 CA B:THR253 3.8 11.3 1.0 CA B:SER250 4.0 21.9 1.0 N B:THR253 4.0 14.4 1.0 N B:ILE257 4.1 12.0 1.0 N B:LEU254 4.2 9.1 1.0 CA B:PRO256 4.2 12.0 1.0 C B:LEU254 4.2 9.1 1.0 O B:LEU254 4.3 9.1 1.0 CB B:SER250 4.4 22.7 1.0 N B:PRO256 4.4 11.8 1.0 CA B:LEU254 4.5 9.2 1.0 N B:LEU255 4.5 10.3 1.0 N B:GLN251 4.6 22.9 1.0 C B:PRO256 4.7 12.2 1.0 C B:ILE257 4.7 12.6 1.0 NH2 B:ARG294 4.7 38.3 1.0 CA B:LEU255 4.8 9.8 1.0 O C:HOH808 4.8 24.6 1.0 OG B:SER250 4.9 24.0 1.0 CG2 B:THR253 4.9 9.8 1.0 CA B:GLN251 5.0 22.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Carveol Dehydrogenase From Mycobacterium Thermoresistibile


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 Carveol Dehydrogenase From Mycobacterium Thermoresistibile within 5.0Å range: probe atom residue distance (Å) B Occ C:Na300 b:22.2 occ:1.00 O C:HOH736 2.3 22.1 1.0 O C:SER250 2.5 16.9 1.0 O C:LEU255 2.5 14.0 1.0 OG1 C:THR253 2.7 12.5 1.0 O C:THR253 2.7 10.8 1.0 O C:HOH605 2.8 27.9 1.0 C C:THR253 3.4 12.6 1.0 O C:ILE257 3.6 10.5 1.0 C C:SER250 3.6 17.7 1.0 C C:LEU255 3.7 14.6 1.0 CB C:THR253 3.7 12.7 1.0 N C:ILE257 3.9 11.3 1.0 CA C:THR253 4.0 12.6 1.0 CA C:SER250 4.1 16.8 1.0 CA C:PRO256 4.1 13.3 1.0 O C:LEU254 4.1 14.2 1.0 C C:LEU254 4.2 13.6 1.0 N C:THR253 4.2 14.0 1.0 N C:LEU254 4.3 12.2 1.0 N C:PRO256 4.4 14.4 1.0 C C:PRO256 4.4 12.6 1.0 CB C:SER250 4.5 16.2 1.0 N C:LEU255 4.5 13.8 1.0 C C:ILE257 4.5 11.8 1.0 CA C:LEU254 4.5 13.0 1.0 NH2 C:ARG294 4.7 18.7 0.5 N C:GLN251 4.7 20.0 1.0 CA C:LEU255 4.8 13.4 1.0 CA C:ILE257 4.8 11.4 1.0 OG C:SER250 4.9 20.4 1.0 O C:HOH351 5.0 16.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Carveol Dehydrogenase From Mycobacterium Thermoresistibile


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 Carveol Dehydrogenase From Mycobacterium Thermoresistibile within 5.0Å range: probe atom residue distance (Å) B Occ D:Na300 b:17.6 occ:1.00 O D:HOH763 2.3 10.6 1.0 OG1 D:THR253 2.6 11.4 1.0 O D:SER250 2.6 17.8 1.0 O D:LEU255 2.6 11.1 1.0 O D:THR253 2.7 10.3 1.0 O D:HOH764 2.7 23.1 1.0 C D:THR253 3.4 11.0 1.0 CB D:THR253 3.6 11.7 1.0 O D:ILE257 3.6 10.9 1.0 C D:SER250 3.7 17.3 1.0 C D:LEU255 3.7 10.2 1.0 CA D:THR253 3.9 11.3 1.0 N D:ILE257 4.0 10.8 1.0 CA D:PRO256 4.0 11.9 1.0 CA D:SER250 4.1 16.7 1.0 N D:THR253 4.1 13.9 1.0 N D:LEU254 4.3 8.9 1.0 C D:LEU254 4.3 10.1 1.0 O D:LEU254 4.3 11.9 1.0 N D:PRO256 4.4 11.7 1.0 C D:PRO256 4.5 11.3 1.0 CB D:SER250 4.5 17.0 1.0 N D:LEU255 4.6 9.1 1.0 CA D:LEU254 4.6 10.0 1.0 C D:ILE257 4.6 11.0 1.0 CA D:LEU255 4.8 9.6 1.0 N D:GLN251 4.8 18.6 1.0 NH1 D:ARG294 4.9 17.3 0.5 CG2 D:THR253 5.0 11.5 1.0 CA D:ILE257 5.0 10.7 1.0 OG D:SER250 5.0 19.9 1.0

D.H.Haft, P.G.Pierce, S.J.Mayclin, A.Sullivan, A.S.Gardberg, J.Abendroth, D.W.Begley, I.Q.Phan, B.L.Staker, P.J.Myler, V.M.Marathias, D.D.Lorimer, T.E.Edwards. Mycofactocin-Associated Mycobacterial Dehydrogenases with Non-Exchangeable Nad Cofactors. Sci Rep V. 7 41074 2017.
ISSN: ESSN 2045-2322
PubMed: 28120876
DOI: 10.1038/SREP41074