Sodium in PDB 2hcj: Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline

The structure of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline, PDB code: 2hcj was solved by S.Mui, S.E.Heffron, A.Aorora, K.Abel, E.Bergmann, F.Jurnak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.92 / 2.12
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.110, 69.110, 157.330, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.4

The structure of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline (pdb code 2hcj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline, PDB code: 2hcj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1001 b:40.8 occ:1.00 OD1 B:ASP109 2.4 36.1 1.0 O B:THR108 2.9 38.6 1.0 C B:THR108 3.3 34.4 1.0 CG B:ASP109 3.6 34.6 1.0 N B:ASP109 3.7 32.0 1.0 CB B:THR108 3.7 36.2 1.0 CA B:ASP109 3.8 30.8 1.0 OG1 B:THR108 4.1 39.5 1.0 CA B:THR108 4.1 31.6 1.0 CB B:ASP109 4.3 34.8 1.0 OD2 B:ASP109 4.6 40.7 1.0 CG2 B:THR108 5.0 30.1 1.0 O B:HOH2036 5.0 36.3 1.0

Sodium binding site 2 out of 3 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:63.2 occ:1.00 OE2 B:GLU348 2.5 62.7 1.0 CD B:GLU348 3.6 62.5 1.0 CE2 B:PHE323 3.9 31.4 1.0 OE1 B:GLU348 4.1 64.5 1.0 CE B:MET349 4.2 54.2 1.0 CZ B:PHE323 4.4 34.3 1.0 CG B:GLU348 4.7 53.7 1.0

Sodium binding site 3 out of 3 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1003 b:53.7 occ:1.00 OD2 B:ASP196 2.5 34.2 1.0 O B:HOH2048 3.3 48.1 1.0 CG B:ASP196 3.7 35.2 1.0 CA B:GLY193 3.7 29.4 1.0 O B:ALA192 3.7 35.2 1.0 OH A:TYR39 3.7 54.0 1.0 CG2 B:THR71 3.8 31.3 1.0 N B:GLY193 3.8 30.9 1.0 C B:ALA192 3.8 32.3 1.0 CB B:THR71 4.0 25.1 1.0 O B:HOH2063 4.2 28.9 1.0 CB B:ALA192 4.3 28.6 1.0 CZ A:TYR39 4.4 50.3 1.0 CB B:ASP196 4.4 29.8 1.0 CE2 A:TYR39 4.5 52.5 1.0 OD1 B:ASP196 4.5 34.5 1.0 CD B:PRO72 4.6 32.8 1.0 O B:LEU189 4.7 31.3 1.0 CA B:ALA192 4.7 31.3 1.0 OG1 B:THR71 4.8 28.7 1.0 C B:GLY193 4.9 30.5 1.0

S.E.Heffron, S.Mui, A.Aorora, K.Abel, E.Bergmann, F.Jurnak. Molecular Complementarity Between Tetracycline and the Gtpase Active Site of Elongation Factor Tu. Acta Crystallogr.,Sect.D V. 62 1392 2006.
ISSN: ISSN 0907-4449
PubMed: 17057344
DOI: 10.1107/S0907444906035426