Sodium in PDB 3dyo: E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg:
3.2.1.23;

The structure of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg, PDB code: 3dyo was solved by D.H.Juers, R.E.Huber, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	152.010, 162.520, 204.010, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg also contains other interesting chemical elements:

Magnesium

(Mg)

14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg (pdb code 3dyo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 18 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg, PDB code: 3dyo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3101 b:21.6 occ:1.00 O6 A:IPT2001 2.3 20.0 1.0 O A:PHE601 2.3 16.0 1.0 O A:HOH4272 2.3 25.7 1.0 OD2 A:ASP201 2.3 21.4 1.0 OD1 A:ASN604 2.4 21.4 1.0 C6 A:IPT2001 3.2 19.1 1.0 CG A:ASP201 3.2 23.4 1.0 CG A:ASN604 3.4 20.6 1.0 OD1 A:ASP201 3.4 21.0 1.0 C A:PHE601 3.5 21.2 1.0 ND2 A:ASN604 3.7 16.7 1.0 OH A:TYR100 3.7 16.1 1.0 NE1 A:TRP568 4.0 14.4 1.0 CA A:CYS602 4.1 18.4 1.0 O4 A:IPT2001 4.1 21.7 1.0 N A:CYS602 4.3 20.4 1.0 C5 A:IPT2001 4.3 23.0 1.0 O A:HOH4051 4.4 22.9 1.0 C4 A:IPT2001 4.5 25.2 1.0 CB A:ASP201 4.5 15.4 1.0 CA A:PHE601 4.5 16.6 1.0 CB A:PHE601 4.5 18.8 1.0 C A:CYS602 4.5 21.2 1.0 O A:ASP201 4.6 15.5 1.0 NE2 A:HIS540 4.7 14.4 1.0 CE2 A:TRP568 4.8 13.7 1.0 CB A:ASN604 4.8 13.7 1.0 CZ A:TYR100 4.8 18.9 1.0 CZ2 A:TRP568 4.9 15.9 1.0 O A:CYS602 4.9 18.9 1.0 CD1 A:TRP568 5.0 19.3 1.0

Sodium binding site 2 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3102 b:15.2 occ:1.00 O A:LEU562 2.3 12.6 1.0 O A:TYR559 2.3 18.0 1.0 O A:PHE556 2.3 13.5 1.0 O A:HOH4388 2.3 33.7 1.0 O A:HOH4575 2.4 23.2 1.0 O A:PRO560 3.3 14.7 1.0 C A:TYR559 3.3 13.3 1.0 C A:LEU562 3.4 17.3 1.0 C A:PHE556 3.5 12.1 1.0 C A:PRO560 3.6 14.9 1.0 CA A:PRO560 3.8 15.3 1.0 O A:HOH4278 3.9 22.2 1.0 N A:PRO560 4.0 13.2 1.0 N A:LEU562 4.0 12.3 1.0 CA A:LEU562 4.2 13.2 1.0 CA A:PHE556 4.2 8.7 1.0 CA A:TYR559 4.3 12.1 1.0 N A:GLN563 4.3 12.3 1.0 N A:TYR559 4.4 12.5 1.0 CB A:LEU562 4.4 11.0 1.0 O A:HOH4702 4.4 34.4 1.0 CA A:GLN563 4.5 14.4 1.0 N A:ARG557 4.5 12.8 1.0 N A:ARG561 4.5 12.8 1.0 CG A:GLN563 4.6 11.6 1.0 CA A:ARG557 4.6 14.1 1.0 C A:ARG557 4.7 16.2 1.0 CD1 A:LEU350 4.7 14.9 1.0 O A:ARG557 4.8 13.5 1.0 CB A:PHE556 4.8 12.7 1.0 C A:ARG561 4.9 11.7 1.0 CB A:TYR559 4.9 12.6 1.0 O A:ALA555 5.0 14.1 1.0

Sodium binding site 3 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3103 b:33.2 occ:1.00 O A:HOH4649 2.4 31.6 1.0 O A:PRO932 2.5 19.9 1.0 O A:LEU967 2.6 21.6 1.0 O A:HOH4202 2.6 22.3 1.0 O A:THR970 2.8 32.6 1.0 O A:HOH4510 3.2 32.0 1.0 CZ A:PHE931 3.4 29.6 1.0 C A:PRO932 3.6 19.5 1.0 CE1 A:PHE931 3.7 21.9 1.0 C A:LEU967 3.7 19.7 1.0 O A:MET968 3.7 27.1 1.0 C A:THR970 3.8 31.7 1.0 C A:MET968 3.9 31.3 1.0 CA A:MET968 3.9 24.3 1.0 CE2 A:PHE931 4.0 23.0 1.0 CA A:PRO932 4.3 17.9 1.0 N A:MET968 4.3 21.0 1.0 CB A:PRO932 4.3 24.4 1.0 N A:THR970 4.3 23.2 1.0 N A:PRO932 4.3 21.3 1.0 CD A:PRO932 4.4 22.5 1.0 CD1 A:PHE931 4.4 24.5 1.0 CG A:PRO932 4.6 25.6 1.0 N A:SER933 4.6 19.9 1.0 CD2 A:PHE931 4.6 25.7 1.0 O A:HOH4817 4.6 57.6 1.0 N A:SER971 4.7 25.4 1.0 CA A:SER971 4.7 27.5 1.0 CA A:THR970 4.7 26.7 1.0 N A:GLU969 4.7 23.9 1.0 CG A:PHE931 4.8 21.4 1.0 CA A:LEU967 4.9 22.9 1.0 CA A:SER933 4.9 21.0 1.0

Sodium binding site 4 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3105 b:46.7 occ:1.00 O A:HOH4557 2.1 28.3 0.5 O A:HOH4464 2.2 34.1 1.0 O A:ASN597 2.4 27.4 1.0 O A:HOH4428 2.4 41.9 1.0 O A:HOH4219 2.7 43.1 1.0 C A:ASN597 3.6 31.2 1.0 N A:ASN597 4.0 22.7 1.0 O A:HOH4658 4.0 56.2 1.0 OE2 A:GLU797 4.1 57.4 1.0 OE1 A:GLU797 4.1 64.6 1.0 OD1 A:ASN597 4.3 24.4 1.0 CD A:GLU797 4.3 44.3 1.0 OD1 A:ASP598 4.4 36.4 1.0 CA A:ASN597 4.4 26.4 1.0 N A:ASP598 4.6 24.9 1.0 CG A:ASN597 4.6 33.2 1.0 O A:HOH4701 4.6 48.2 1.0 CA A:ASP598 4.6 20.2 1.0 ND2 A:ASN597 4.7 25.0 1.0

Sodium binding site 5 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3101 b:17.8 occ:1.00 OD2 B:ASP201 2.3 13.3 1.0 O6 B:IPT2001 2.4 16.4 1.0 O B:PHE601 2.4 14.9 1.0 O B:HOH4297 2.4 18.6 1.0 OD1 B:ASN604 2.5 15.8 1.0 C6 B:IPT2001 3.1 16.2 1.0 CG B:ASP201 3.2 18.9 1.0 CG B:ASN604 3.4 18.6 1.0 OD1 B:ASP201 3.5 15.9 1.0 C B:PHE601 3.5 16.8 1.0 ND2 B:ASN604 3.6 15.5 1.0 OH B:TYR100 3.6 12.9 1.0 O4 B:IPT2001 4.1 19.9 1.0 NE1 B:TRP568 4.1 15.1 1.0 CA B:CYS602 4.2 10.5 1.0 C5 B:IPT2001 4.3 26.5 1.0 N B:CYS602 4.3 12.8 1.0 O B:HOH4076 4.3 18.6 1.0 C4 B:IPT2001 4.4 20.7 1.0 CB B:ASP201 4.4 13.7 1.0 NE2 B:HIS540 4.6 13.8 1.0 CA B:PHE601 4.6 15.0 1.0 CB B:PHE601 4.6 11.6 1.0 O B:ASP201 4.6 13.8 1.0 C B:CYS602 4.7 12.2 1.0 CZ B:TYR100 4.7 15.1 1.0 CE2 B:TRP568 4.8 16.9 1.0 CB B:ASN604 4.9 12.2 1.0 CZ2 B:TRP568 4.9 12.8 1.0

Sodium binding site 6 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3102 b:15.0 occ:1.00 O B:TYR559 2.2 14.9 1.0 O B:PHE556 2.2 12.6 1.0 O B:LEU562 2.3 13.9 1.0 O B:HOH4633 2.3 28.7 1.0 O B:HOH4419 2.6 23.6 1.0 C B:TYR559 3.2 13.6 1.0 O B:PRO560 3.3 14.0 1.0 C B:LEU562 3.4 13.7 1.0 C B:PHE556 3.4 13.9 1.0 C B:PRO560 3.6 16.8 1.0 CA B:PRO560 3.7 14.4 1.0 N B:PRO560 3.8 14.3 1.0 N B:LEU562 4.0 11.8 1.0 O B:HOH4303 4.1 20.7 1.0 CA B:PHE556 4.1 11.6 1.0 CB B:LEU562 4.1 11.5 1.0 CA B:LEU562 4.2 13.2 1.0 N B:TYR559 4.3 13.2 1.0 CA B:TYR559 4.3 12.9 1.0 O B:HOH4813 4.3 26.8 1.0 N B:GLN563 4.4 11.0 1.0 N B:ARG557 4.5 14.5 1.0 CA B:GLN563 4.5 12.1 1.0 N B:ARG561 4.5 13.0 1.0 CA B:ARG557 4.7 8.5 1.0 O B:HOH4775 4.7 32.1 1.0 C B:ARG557 4.7 11.6 1.0 CG B:GLN563 4.7 13.0 1.0 CB B:PHE556 4.8 10.6 1.0 O B:ARG557 4.8 13.1 1.0 CB B:TYR559 4.8 14.7 1.0 O B:ALA555 4.9 13.0 1.0 CD1 B:LEU350 4.9 16.7 1.0 C B:ARG561 5.0 9.9 1.0

Sodium binding site 7 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3103 b:31.9 occ:1.00 O B:PRO932 2.5 21.0 1.0 O B:LEU967 2.7 23.1 1.0 O B:THR970 2.7 25.9 1.0 O B:HOH4226 3.0 20.1 1.0 O B:HOH4715 3.2 37.0 1.0 CZ B:PHE931 3.4 17.2 1.0 CE1 B:PHE931 3.5 19.6 1.0 C B:PRO932 3.6 19.0 1.0 O B:HOH4556 3.6 33.6 1.0 C B:THR970 3.8 27.7 1.0 C B:LEU967 3.8 20.6 1.0 O B:MET968 3.8 26.5 1.0 CE2 B:PHE931 3.9 13.2 1.0 CA B:MET968 4.0 19.1 1.0 C B:MET968 4.0 30.0 1.0 CD B:PRO932 4.1 15.0 1.0 N B:PRO932 4.1 13.5 1.0 CD1 B:PHE931 4.2 21.1 1.0 CA B:PRO932 4.2 15.4 1.0 CB B:PRO932 4.2 18.2 1.0 N B:THR970 4.2 24.8 1.0 N B:MET968 4.4 20.0 1.0 CD2 B:PHE931 4.5 15.0 1.0 CA B:SER971 4.5 28.3 1.0 CG B:PRO932 4.6 17.1 1.0 N B:SER971 4.6 23.5 1.0 CG B:PHE931 4.6 16.4 1.0 CA B:THR970 4.6 22.2 1.0 N B:SER933 4.7 14.4 1.0 N B:GLU969 4.8 24.6 1.0 C B:PHE931 4.8 14.3 1.0 CA B:SER933 4.8 11.2 1.0 CA B:LEU967 4.9 15.2 1.0

Sodium binding site 8 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3104 b:29.3 occ:1.00 O B:DMS8425 2.1 42.4 1.0 O B:LEU670 2.4 22.9 1.0 O B:GLU650 2.4 20.4 1.0 O B:SER647 2.5 21.4 1.0 O B:HOH4837 2.6 35.8 1.0 O B:HOH4725 3.0 45.1 1.0 S B:DMS8425 3.2 50.9 1.0 N B:GLU650 3.3 16.3 1.0 C B:GLU650 3.4 21.3 1.0 C B:LEU670 3.5 24.4 1.0 C B:SER647 3.7 24.2 1.0 N B:LEU670 3.7 31.8 1.0 CA B:GLU650 3.8 17.5 1.0 C2 B:DMS8425 3.9 43.1 1.0 CB B:GLU650 4.0 16.6 1.0 CA B:LEU670 4.0 32.6 1.0 N B:ASN649 4.0 14.2 1.0 C B:ASP648 4.1 21.6 1.0 CA B:ASP648 4.1 26.8 1.0 CB B:LEU670 4.2 33.5 1.0 OG B:SER647 4.2 20.5 1.0 N B:ASP648 4.4 19.9 1.0 C B:ASN649 4.5 19.6 1.0 CB B:SER647 4.5 24.0 1.0 CA B:ASN649 4.6 15.9 1.0 O B:ASP648 4.6 22.7 1.0 N B:LEU651 4.6 20.0 1.0 N B:ASP671 4.6 19.0 1.0 OE1 B:GLU650 4.7 21.7 1.0 C1 B:DMS8425 4.7 41.7 1.0 C B:PRO669 4.8 39.0 1.0 CA B:SER647 4.8 20.3 1.0 CA B:ASP671 4.9 21.8 1.0

Sodium binding site 9 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3105 b:48.5 occ:1.00 O B:HOH4612 2.0 14.3 0.5 O B:ASN597 2.1 15.6 1.0 O B:HOH4462 2.3 27.3 1.0 O B:HOH4504 2.5 39.7 1.0 O B:HOH4244 2.6 31.0 1.0 C B:ASN597 3.4 21.7 1.0 OE1 B:GLU797 3.6 0.0 1.0 N B:ASN597 3.7 17.0 1.0 O B:HOH4833 3.8 43.3 1.0 O B:HOH4948 4.0 44.5 1.0 CA B:ASN597 4.1 17.1 1.0 OD1 B:ASN597 4.2 15.9 1.0 OD1 B:ASP598 4.3 22.5 1.0 CD B:GLU797 4.4 37.8 1.0 N B:ASP598 4.4 17.2 1.0 OE2 B:GLU797 4.4 41.8 1.0 CG B:ASN597 4.4 18.6 1.0 O B:HOH4774 4.5 37.1 1.0 CA B:ASP598 4.5 14.3 1.0 CB B:PRO596 4.8 18.5 1.0 C B:PRO596 4.8 20.9 1.0 ND2 B:ASN597 4.8 12.9 1.0 CB B:ASN597 4.9 23.1 1.0 CA B:PRO596 5.0 16.5 1.0

Sodium binding site 10 out of 18 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3101 b:15.0 occ:1.00 O C:HOH4300 2.3 18.9 1.0 O6 C:IPT2001 2.3 18.4 1.0 O C:PHE601 2.4 14.0 1.0 OD2 C:ASP201 2.4 15.6 1.0 OD1 C:ASN604 2.4 13.0 1.0 C6 C:IPT2001 3.2 14.3 1.0 CG C:ASP201 3.3 21.2 1.0 CG C:ASN604 3.4 14.8 1.0 C C:PHE601 3.5 17.8 1.0 OD1 C:ASP201 3.5 15.7 1.0 ND2 C:ASN604 3.6 13.3 1.0 OH C:TYR100 3.6 15.5 1.0 NE1 C:TRP568 4.1 16.8 1.0 O4 C:IPT2001 4.1 18.6 1.0 CA C:CYS602 4.1 11.3 1.0 N C:CYS602 4.3 12.1 1.0 C5 C:IPT2001 4.3 14.7 1.0 O C:HOH4076 4.4 16.7 1.0 C4 C:IPT2001 4.4 18.5 1.0 CB C:PHE601 4.5 12.1 1.0 CB C:ASP201 4.5 12.1 1.0 CA C:PHE601 4.5 12.8 1.0 C C:CYS602 4.6 16.7 1.0 O C:ASP201 4.6 12.4 1.0 NE2 C:HIS540 4.7 14.1 1.0 CB C:ASN604 4.7 12.6 1.0 CZ C:TYR100 4.8 15.2 1.0 CE2 C:TRP568 4.9 16.4 1.0 CZ2 C:TRP568 4.9 17.2 1.0

D.H.Juers, B.Rob, M.L.Dugdale, N.Rahimzadeh, C.Giang, M.Lee, B.W.Matthews, R.E.Huber. Direct and Indirect Roles of His-418 in Metal Binding and in the Activity of Beta-Galactosidase (E. Coli). Protein Sci. V. 18 1281 2009.
ISSN: ISSN 0961-8368
PubMed: 19472413
DOI: 10.1002/PRO.140