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

Enzymatic activity of 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;

Protein crystallography data

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

Sodium Binding Sites:

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 1v8z

Go back to Sodium Binding Sites List in 1v8z
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 1v8z

Go back to Sodium Binding Sites List in 1v8z
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 1v8z

Go back to Sodium Binding Sites List in 1v8z
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

Reference:

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
Page generated: Sun Aug 17 08:00:29 2025

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