Sodium in PDB 1v8z: X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus

All present enzymatic activity of X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus:
4.2.1.20;

The structure of X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus, PDB code: 1v8z was solved by Y.Hioki, K.Ogasahara, S.J.Lee, J.Ma, M.Ishida, Y.Yamagata, Y.Matsuura, M.Ota, S.Kuramitsu, K.Yutani, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.30 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.835, 110.530, 159.999, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 26.3

The binding sites of Sodium atom in the X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus (pdb code 1v8z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus, PDB code: 1v8z:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na389 b:78.4 occ:1.00 O A:HOH454 2.1 68.4 1.0 O A:HOH455 2.1 52.2 1.0 O A:HOH410 2.3 54.6 1.0 O A:GLY303 2.4 49.1 1.0 O A:GLY227 2.5 47.3 1.0 O A:TYR301 3.1 52.8 1.0 C A:GLY227 3.3 38.9 1.0 C A:GLY303 3.6 50.6 1.0 O A:SER263 3.7 36.5 1.0 CA A:GLY227 3.8 37.6 1.0 OG A:SER265 3.8 64.8 1.0 OG A:SER263 4.1 53.7 1.0 C A:TYR301 4.1 54.9 1.0 N A:GLY303 4.2 52.3 1.0 O A:HOH405 4.2 30.1 1.0 O A:VAL226 4.2 38.3 1.0 N A:GLY228 4.3 43.6 1.0 CB A:TYR301 4.4 51.5 1.0 CA A:GLY303 4.5 40.3 1.0 CB A:SER265 4.5 46.7 1.0 N A:VAL304 4.6 44.4 1.0 CA A:VAL304 4.7 44.4 1.0 N A:GLY227 4.7 38.2 1.0 CA A:TYR301 4.7 52.6 1.0 CB A:VAL304 4.7 41.5 1.0 CA A:GLY228 4.8 33.6 1.0 CD2 A:TYR301 4.8 59.4 1.0 C A:VAL226 4.8 37.5 1.0 OE2 A:GLU251 4.8 48.9 1.0 C A:SER263 4.9 39.5 1.0 N A:TYR301 4.9 56.0 1.0 N A:SER265 5.0 40.5 1.0

Sodium binding site 2 out of 3 in the X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na389 b:41.5 occ:1.00 O B:HOH483 2.3 25.6 1.0 O B:HOH404 2.4 33.9 1.0 O B:HOH474 2.4 45.1 1.0 O B:GLY303 2.5 24.8 1.0 O B:GLY227 2.5 26.9 1.0 C B:GLY227 3.4 14.2 1.0 O B:TYR301 3.5 30.5 1.0 C B:GLY303 3.6 23.7 1.0 OG B:SER265 3.8 43.1 1.0 O B:HOH415 3.8 31.1 1.0 O B:SER263 3.9 39.9 1.0 CA B:GLY227 3.9 22.1 1.0 O B:VAL226 3.9 31.1 1.0 CB B:SER265 4.2 25.8 1.0 N B:GLY303 4.3 30.8 1.0 CB B:VAL304 4.3 25.8 1.0 OE2 B:GLU251 4.4 27.8 1.0 CA B:GLY303 4.4 23.0 1.0 N B:VAL304 4.5 30.7 1.0 CA B:VAL304 4.5 28.5 1.0 N B:GLY228 4.5 27.7 1.0 C B:VAL226 4.6 27.9 1.0 C B:TYR301 4.6 33.0 1.0 N B:GLY227 4.6 37.4 1.0 OG B:SER263 4.7 43.7 1.0 N B:SER265 4.7 27.8 1.0 CG2 B:VAL304 4.7 32.5 1.0 CA B:GLY228 4.9 22.3 1.0 CB B:TYR301 4.9 29.5 1.0 C B:SER263 5.0 38.4 1.0

Sodium binding site 3 out of 3 in the X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Crystal Structure of the Tryptophan Synthase B2 Subunit From Hyperthermophile, Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na389 b:41.1 occ:1.00 O C:HOH419 2.2 33.8 1.0 O C:HOH461 2.3 43.4 1.0 O C:GLY303 2.4 29.6 1.0 O C:GLY227 2.4 25.1 1.0 O C:HOH405 2.5 30.5 1.0 C C:GLY227 3.3 27.7 1.0 O C:TYR301 3.5 28.0 1.0 C C:GLY303 3.6 20.9 1.0 CA C:GLY227 3.7 24.1 1.0 OG C:SER265 3.9 36.8 1.0 O C:SER263 3.9 32.5 1.0 O C:VAL226 3.9 31.6 1.0 O C:HOH408 3.9 34.6 1.0 CB C:SER265 4.3 32.0 1.0 N C:GLY228 4.3 22.4 1.0 N C:GLY303 4.4 28.8 1.0 CB C:VAL304 4.4 31.0 1.0 N C:VAL304 4.4 21.9 1.0 CA C:GLY303 4.5 22.9 1.0 CA C:VAL304 4.5 28.3 1.0 N C:GLY227 4.5 29.3 1.0 OE2 C:GLU251 4.5 35.6 1.0 C C:VAL226 4.5 32.8 1.0 C C:TYR301 4.6 34.3 1.0 OG C:SER263 4.6 42.4 1.0 N C:SER265 4.7 34.0 1.0 CA C:GLY228 4.8 19.5 1.0 CB C:TYR301 4.9 29.5 1.0 CD2 C:TYR301 5.0 30.2 1.0 CG2 C:VAL304 5.0 43.2 1.0

Y.Hioki, K.Ogasahara, S.J.Lee, J.Ma, M.Ishida, Y.Yamagata, Y.Matsuura, M.Ota, M.Ikeguchi, S.Kuramitsu, K.Yutani. The Crystal Structure of the Tryptophan Synthase Beta Subunit From the Hyperthermophile Pyrococcus Furiosus. Investigation of Stabilization Factors Eur.J.Biochem. V. 271 2624 2004.
ISSN: ISSN 0014-2956
PubMed: 15206928
DOI: 10.1111/J.1432-1033.2004.04191.X