Sodium in PDB 1tg7: Native Structure of Beta-Galactosidase From Penicillium Sp.

All present enzymatic activity of Native Structure of Beta-Galactosidase From Penicillium Sp.:
3.2.1.23;

The structure of Native Structure of Beta-Galactosidase From Penicillium Sp., PDB code: 1tg7 was solved by A.L.Rojas, R.A.P.Nagem, K.N.Neustroev, M.Arand, M.Adamska, E.V.Eneyskaya, A.A.Kulminskaya, R.C.Garratt, A.M.Golubev, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.30 / 1.90
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	110.960, 110.960, 161.050, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.5

The binding sites of Sodium atom in the Native Structure of Beta-Galactosidase From Penicillium Sp. (pdb code 1tg7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Native Structure of Beta-Galactosidase From Penicillium Sp., PDB code: 1tg7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Native Structure of Beta-Galactosidase From Penicillium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Native Structure of Beta-Galactosidase From Penicillium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na9001 b:16.6 occ:1.00 O A:HOH8170 2.7 44.1 1.0 O A:ASN917 2.7 24.0 1.0 O A:THR919 2.8 37.4 1.0 O6 A:NAG7001 2.8 26.9 1.0 O5 A:NAG7001 2.8 18.4 1.0 C6 A:NAG7001 3.5 21.4 1.0 ND2 A:ASN917 3.7 18.6 1.0 C5 A:NAG7001 3.7 18.7 1.0 C1 A:NAG7001 3.8 17.4 1.0 C A:ASN917 3.8 25.6 1.0 CG A:ASN917 3.9 18.6 1.0 C A:THR919 3.9 36.7 1.0 OD1 A:ASN917 4.0 18.7 1.0 C A:SER918 4.2 34.1 1.0 N A:THR919 4.3 34.4 1.0 O A:HOH9645 4.3 27.8 1.0 O A:SER918 4.4 35.0 1.0 CA A:SER918 4.5 33.1 1.0 N A:SER918 4.6 29.3 1.0 CB A:ASN917 4.7 20.9 1.0 O A:SER920 4.7 39.5 1.0 CA A:THR919 4.7 36.3 1.0 N A:SER920 4.8 37.5 1.0 CA A:ASN917 4.8 23.4 1.0 CA A:SER920 4.9 38.6 1.0

Sodium binding site 2 out of 3 in the Native Structure of Beta-Galactosidase From Penicillium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Native Structure of Beta-Galactosidase From Penicillium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na9002 b:18.4 occ:1.00 O A:LYS499 2.7 22.0 1.0 O A:ALA597 2.8 20.9 1.0 O A:HOH9520 2.8 22.2 1.0 O A:HOH8052 2.9 39.9 1.0 O A:HOH9877 2.9 31.9 1.0 O A:HOH8389 3.5 53.1 1.0 C A:ALA597 3.8 20.2 1.0 O A:HOH9492 3.8 22.1 1.0 C A:LYS499 3.9 22.3 1.0 CA A:SER598 4.1 20.7 1.0 N A:SER598 4.4 20.3 1.0 CD1 A:PHE500 4.5 21.7 1.0 CA A:PHE500 4.5 25.0 1.0 O A:HOH9762 4.5 35.4 1.0 O A:HOH9468 4.7 20.6 1.0 N A:PHE500 4.7 23.1 1.0 CA A:ALA597 4.9 20.9 1.0 N A:LYS499 4.9 20.4 1.0 C A:SER598 4.9 20.9 1.0 CB A:SER598 5.0 20.6 1.0 CB A:ALA597 5.0 21.0 1.0 CA A:LYS499 5.0 22.2 1.0

Sodium binding site 3 out of 3 in the Native Structure of Beta-Galactosidase From Penicillium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Native Structure of Beta-Galactosidase From Penicillium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na9003 b:23.6 occ:1.00 O7 A:NAG7001 2.7 18.0 1.0 O A:HOH9645 2.8 27.8 1.0 O A:PRO945 2.8 15.1 1.0 O A:HOH9852 2.9 34.1 1.0 O A:HOH8158 3.5 48.4 1.0 C A:PRO945 3.7 15.3 1.0 O A:HOH8232 3.9 43.3 1.0 C7 A:NAG7001 3.9 17.8 1.0 CG2 A:THR947 3.9 15.7 1.0 CA A:PRO945 4.0 15.3 1.0 O A:HOH9626 4.1 22.9 1.0 O A:HOH8117 4.3 38.8 1.0 CB A:PRO945 4.4 15.6 1.0 O A:HOH9772 4.6 32.8 1.0 C2 A:NAG7001 4.6 17.2 1.0 O A:HOH9975 4.7 40.5 1.0 ND2 A:ASN917 4.7 18.6 1.0 OG1 A:THR947 4.7 15.7 1.0 N2 A:NAG7001 4.8 16.9 1.0 O A:HOH8170 4.8 44.1 1.0 C8 A:NAG7001 4.8 15.2 1.0 N A:GLN946 4.9 13.8 1.0 CB A:THR947 5.0 15.5 1.0

A.L.Rojas, R.A.P.Nagem, K.N.Neustroev, M.Arand, M.Adamska, E.V.Eneyskaya, A.A.Kulminskaya, R.C.Garratt, A.M.Golubev, I.Polikarpov. Crystal Structures of Beta-Galactosidase From Penicillium Sp. and Its Complex with Galactose J.Mol.Biol. V. 343 1281 2004.
ISSN: ISSN 0022-2836
PubMed: 15491613
DOI: 10.1016/J.JMB.2004.09.012