Sodium in PDB 3u0a: Crystal Structure of An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum

The structure of Crystal Structure of An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum, PDB code: 3u0a was solved by T.L.Arakaki, B.L.Staker, M.C.Clifton, B.Sankaran, Seattle Structuralgenomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	102.130, 138.160, 81.180, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 29

The binding sites of Sodium atom in the Crystal Structure of An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum (pdb code 3u0a). 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 An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum, PDB code: 3u0a:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum


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 An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na285 b:16.2 occ:1.00 O3 B:SO4283 2.0 47.1 1.0 S B:SO4283 3.3 51.4 1.0 O2 B:SO4283 3.7 46.1 1.0 N A:SER84 3.7 45.1 1.0 N A:GLY83 3.7 45.8 1.0 N A:PHE85 3.8 43.2 1.0 O4 B:SO4283 3.9 32.1 1.0 CA A:GLY82 4.0 44.8 1.0 C A:GLY82 4.2 45.3 1.0 CB A:SER84 4.3 44.6 1.0 CB A:PHE85 4.3 41.9 1.0 CA A:SER84 4.4 44.6 1.0 O A:PHE85 4.4 42.7 1.0 CD1 A:PHE85 4.4 42.4 1.0 O1 B:SO4283 4.4 40.2 1.0 CA A:PHE85 4.5 42.4 1.0 C A:SER84 4.6 43.7 1.0 CA A:GLY83 4.6 46.5 1.0 C A:GLY83 4.7 46.0 1.0 NH1 A:ARG80 4.8 41.8 1.0 CG A:PHE85 4.9 41.8 1.0 N A:GLY82 4.9 44.1 1.0 OG A:SER84 5.0 45.6 1.0 C A:PHE85 5.0 42.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum


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 An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na286 b:12.2 occ:1.00 O A:HOH312 2.4 4.6 1.0 O A:VAL49 2.7 43.8 1.0 O A:VAL46 2.8 42.4 1.0 C A:VAL49 3.6 43.6 1.0 CG1 A:VAL46 3.6 42.1 1.0 CA A:PRO51 3.7 45.3 1.0 C A:VAL46 3.8 41.9 1.0 CB A:VAL49 3.8 42.1 1.0 N A:PRO51 3.9 45.4 1.0 C A:ASP50 4.1 44.9 1.0 O A:ASP50 4.1 44.3 1.0 CB A:PRO51 4.1 46.0 1.0 CG1 A:VAL49 4.1 42.4 1.0 CA A:VAL49 4.1 42.7 1.0 CA A:VAL46 4.3 41.3 1.0 O A:TYR53 4.4 43.0 1.0 N A:VAL49 4.5 42.5 1.0 CD A:PRO51 4.6 46.2 1.0 CB A:VAL46 4.6 41.4 1.0 N A:ASP50 4.6 44.1 1.0 CG A:PRO51 4.7 46.6 1.0 O A:HOH304 4.9 3.5 1.0 CA A:ASP50 4.9 45.0 1.0 C A:PRO51 4.9 45.7 1.0 N A:ARG47 5.0 41.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum


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 An Acyl-Coa Thioesterase II TESB2 From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ B:Na288 b:19.6 occ:1.00 O3 B:SO4282 1.7 39.7 1.0 S B:SO4282 3.0 52.4 1.0 OG B:SER84 3.1 44.3 1.0 O1 B:SO4282 3.3 43.8 1.0 CB B:SER84 3.9 43.4 1.0 O2 B:SO4282 3.9 34.3 1.0 NH1 A:ARG271 3.9 44.7 1.0 NH2 A:ARG271 4.0 43.6 1.0 O4 B:SO4282 4.1 39.3 1.0 N B:SER84 4.4 44.1 1.0 CZ A:ARG271 4.4 43.9 1.0 CA B:SER84 4.8 43.4 1.0 O B:HOH300 4.9 19.5 1.0

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003