Atomistry » Sodium » PDB 1b7s-1c82 » 1bw9
Atomistry »
  Sodium »
    PDB 1b7s-1c82 »
      1bw9 »

Sodium in PDB 1bw9: Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate

Enzymatic activity of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate

All present enzymatic activity of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate:
1.4.1.20;

Protein crystallography data

The structure of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate, PDB code: 1bw9 was solved by J.L.Vanhooke, J.B.Thoden, N.M.W.Brunhuber, J.L.Blanchard, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.300, 110.200, 113.400, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1bw9:

The structure of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate also contains other interesting chemical elements:

Potassium (K) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate (pdb code 1bw9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate, PDB code: 1bw9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1bw9

Go back to Sodium Binding Sites List in 1bw9
Sodium binding site 1 out of 2 in the Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na851

b:12.1
occ:1.00
O B:HOH1319 2.3 49.3 1.0
O B:ASP409 2.6 9.7 1.0
O B:HOH1100 2.7 15.6 1.0
O B:HOH1227 2.9 24.1 1.0
C B:ASP409 3.6 8.2 1.0
O B:HOH924 3.8 13.7 1.0
CB B:ASP409 4.1 12.4 1.0
O B:HOH1249 4.1 32.2 1.0
CA B:ASP409 4.1 6.9 1.0
O B:GLY410 4.4 7.7 1.0
N B:GLY410 4.7 8.5 1.0
O B:HOH1114 4.7 13.7 1.0
C B:GLY410 4.7 7.6 1.0
CG B:ASP409 5.0 0.0 1.0

Sodium binding site 2 out of 2 in 1bw9

Go back to Sodium Binding Sites List in 1bw9
Sodium binding site 2 out of 2 in the Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na852

b:9.0
occ:1.00
O B:GLY618 2.6 19.5 1.0
O B:HOH1008 2.6 15.1 1.0
O B:HOH1083 2.7 14.8 1.0
O B:HOH1326 2.7 48.7 1.0
NE2 B:GLN600 2.9 33.6 1.0
C B:GLY618 3.7 14.1 1.0
CD B:GLN600 3.9 38.4 1.0
O B:HOH1286 4.1 46.4 1.0
CA B:HIS619 4.2 14.0 1.0
OE1 B:GLN600 4.4 39.9 1.0
O B:HOH971 4.4 22.7 1.0
N B:HIS619 4.4 11.9 1.0
O B:HOH1300 4.4 45.7 1.0
OG1 B:THR620 4.5 15.0 1.0
ND1 B:HIS619 4.6 20.7 1.0
O B:HOH1314 4.7 42.4 1.0
C B:HIS619 4.7 14.5 1.0
N B:LEU601 4.7 7.0 1.0
CA B:GLY618 4.7 20.1 1.0
O B:LEU601 4.7 8.9 1.0
CA B:GLN600 4.8 7.3 1.0
CB B:GLN600 4.9 12.5 1.0
N B:THR620 4.9 9.2 1.0

Reference:

J.L.Vanhooke, J.B.Thoden, N.M.Brunhuber, J.S.Blanchard, H.M.Holden. Phenylalanine Dehydrogenase From Rhodococcus Sp. M4: High-Resolution X-Ray Analyses of Inhibitory Ternary Complexes Reveal Key Features in the Oxidative Deamination Mechanism. Biochemistry V. 38 2326 1999.
ISSN: ISSN 0006-2960
PubMed: 10029526
DOI: 10.1021/BI982244Q
Page generated: Tue Dec 15 05:22:16 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy