Sodium in PDB 3sep: E. Coli (Lacz) Beta-Galactosidase (S796A)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A):
3.2.1.23;

The structure of E. Coli (Lacz) Beta-Galactosidase (S796A), PDB code: 3sep was solved by L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.00 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	152.342, 163.165, 203.401, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.1

The structure of E. Coli (Lacz) Beta-Galactosidase (S796A) also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (S796A) (pdb code 3sep). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (S796A), PDB code: 3sep:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3101 b:29.0 occ:1.00 OD1 A:ASN604 2.4 23.3 1.0 O A:PHE601 2.4 32.4 1.0 O A:HOH4266 2.4 26.6 1.0 OD2 A:ASP201 2.4 33.1 1.0 O A:HOH4696 2.8 44.8 1.0 CG A:ASP201 3.3 27.0 1.0 CG A:ASN604 3.4 23.9 1.0 CD1 A:PHE601 3.5 41.9 1.0 C A:PHE601 3.6 31.8 1.0 O A:HOH4695 3.6 40.1 1.0 OD1 A:ASP201 3.6 25.3 1.0 ND2 A:ASN604 3.7 20.8 1.0 CE1 A:PHE601 3.7 45.4 1.0 OH A:TYR100 3.9 30.7 1.0 NE1 A:TRP568 4.1 17.2 1.0 CG A:PHE601 4.2 35.7 1.0 CA A:CYS602 4.3 29.0 1.0 O A:HOH4050 4.3 22.4 1.0 N A:CYS602 4.3 32.5 1.0 CB A:ASP201 4.5 22.7 1.0 O A:ASP201 4.5 20.3 1.0 CZ A:PHE601 4.5 41.5 1.0 CA A:PHE601 4.6 30.4 1.0 NE2 A:HIS540 4.6 22.5 1.0 C A:CYS602 4.7 26.8 1.0 CB A:ASN604 4.7 19.3 1.0 CB A:PHE601 4.7 31.3 1.0 CE2 A:TRP568 4.9 17.6 1.0 CD2 A:PHE601 5.0 32.3 1.0 CZ A:TYR100 5.0 33.7 1.0 CZ2 A:TRP568 5.0 20.0 1.0

Sodium binding site 2 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3102 b:17.9 occ:1.00 O A:HOH4527 2.3 27.6 1.0 O A:PHE556 2.4 15.1 1.0 O A:LEU562 2.4 16.8 1.0 O A:TYR559 2.4 18.5 1.0 O A:HOH4374 2.5 34.0 1.0 O A:PRO560 3.1 14.1 1.0 C A:TYR559 3.3 16.9 1.0 C A:LEU562 3.4 16.2 1.0 C A:PHE556 3.5 18.1 1.0 C A:PRO560 3.6 17.5 1.0 CA A:PRO560 3.7 16.0 1.0 N A:PRO560 3.9 17.4 1.0 O A:HOH4272 4.0 23.9 1.0 N A:LEU562 4.0 13.6 1.0 CA A:LEU562 4.1 16.0 1.0 CA A:PHE556 4.2 17.5 1.0 O A:HOH4616 4.3 40.0 1.0 N A:GLN563 4.4 14.6 1.0 O A:HOH4528 4.4 33.1 1.0 CB A:LEU562 4.4 12.7 1.0 N A:TYR559 4.4 14.5 1.0 CA A:TYR559 4.4 16.8 1.0 CA A:GLN563 4.4 14.3 1.0 N A:ARG561 4.5 13.6 1.0 N A:ARG557 4.6 14.4 1.0 O A:HOH4872 4.6 40.5 1.0 CG A:GLN563 4.7 10.6 1.0 CA A:ARG557 4.7 19.4 1.0 C A:ARG557 4.8 18.5 1.0 CD1 A:LEU350 4.8 17.1 1.0 CB A:PHE556 4.8 18.5 1.0 C A:ARG561 4.9 18.6 1.0 O A:ARG557 4.9 19.4 1.0 O A:ALA555 5.0 16.6 1.0 CB A:TYR559 5.0 14.2 1.0

Sodium binding site 3 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3103 b:41.7 occ:1.00 O A:PRO932 2.7 22.6 1.0 O A:LEU967 2.7 24.6 1.0 O A:THR970 2.7 33.6 1.0 O A:HOH4199 3.0 28.1 1.0 O A:HOH4475 3.1 36.7 1.0 O A:HOH4582 3.3 45.8 1.0 CZ A:PHE931 3.4 29.8 1.0 CE2 A:PHE931 3.7 33.9 1.0 C A:PRO932 3.7 21.2 1.0 C A:LEU967 3.8 23.5 1.0 C A:THR970 3.8 35.2 1.0 CE1 A:PHE931 3.8 31.4 1.0 CA A:MET968 3.9 29.8 1.0 O A:MET968 3.9 34.2 1.0 C A:MET968 4.0 32.9 1.0 CB A:PRO932 4.1 25.9 1.0 CD A:PRO932 4.2 25.2 1.0 N A:PRO932 4.3 25.9 1.0 CA A:PRO932 4.3 25.0 1.0 N A:THR970 4.3 32.0 1.0 CD2 A:PHE931 4.3 33.0 1.0 N A:MET968 4.3 27.1 1.0 CD1 A:PHE931 4.4 32.9 1.0 N A:GLU969 4.6 30.9 1.0 CG A:PHE931 4.6 31.2 1.0 CA A:THR970 4.7 32.9 1.0 CG A:PRO932 4.7 26.4 1.0 N A:SER971 4.7 35.1 1.0 CA A:SER971 4.7 33.9 1.0 N A:SER933 4.7 21.8 1.0 C A:PHE931 5.0 28.1 1.0

Sodium binding site 4 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3101 b:21.0 occ:1.00 O B:HOH4280 2.4 20.9 1.0 OD1 B:ASN604 2.4 18.5 1.0 OD2 B:ASP201 2.4 19.2 1.0 O B:PHE601 2.5 18.6 1.0 O B:HOH4820 2.8 36.5 1.0 CG B:ASP201 3.3 17.4 1.0 CG B:ASN604 3.4 18.2 1.0 CD1 B:PHE601 3.5 32.8 1.0 CE1 B:PHE601 3.6 38.6 1.0 O B:HOH4818 3.6 33.6 1.0 C B:PHE601 3.7 19.1 1.0 OD1 B:ASP201 3.7 20.1 1.0 ND2 B:ASN604 3.8 15.9 1.0 OH B:TYR100 3.8 20.8 1.0 NE1 B:TRP568 4.1 15.9 1.0 CG B:PHE601 4.2 27.9 1.0 CA B:CYS602 4.4 15.8 1.0 O B:HOH4068 4.4 17.5 1.0 N B:CYS602 4.4 17.7 1.0 CZ B:PHE601 4.4 34.7 1.0 CB B:ASP201 4.5 14.9 1.0 NE2 B:HIS540 4.5 17.4 1.0 CA B:PHE601 4.7 19.0 1.0 O B:ASP201 4.7 15.3 1.0 CB B:PHE601 4.7 20.7 1.0 CB B:ASN604 4.7 13.2 1.0 C B:CYS602 4.8 16.0 1.0 CE2 B:TRP568 4.8 20.4 1.0 CD2 B:PHE601 4.9 21.3 1.0 CZ2 B:TRP568 4.9 9.3 1.0 CZ B:TYR100 4.9 22.7 1.0 CE2 B:PHE601 5.0 33.2 1.0

Sodium binding site 5 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3102 b:21.9 occ:1.00 O B:HOH4968 2.2 32.5 1.0 O B:PHE556 2.4 15.9 1.0 O B:TYR559 2.4 18.1 1.0 O B:LEU562 2.4 18.0 1.0 O B:HOH4395 2.6 27.4 1.0 O B:PRO560 3.2 14.8 1.0 C B:TYR559 3.4 15.6 1.0 C B:LEU562 3.4 15.1 1.0 C B:PHE556 3.5 13.9 1.0 C B:PRO560 3.7 14.7 1.0 CA B:PRO560 3.7 15.6 1.0 O B:HOH4287 3.8 22.5 1.0 N B:PRO560 3.9 15.6 1.0 O B:HOH4680 4.0 38.6 1.0 N B:LEU562 4.1 13.3 1.0 CA B:LEU562 4.2 14.9 1.0 CA B:PHE556 4.3 16.7 1.0 O B:HOH4707 4.3 26.5 1.0 N B:GLN563 4.3 14.7 1.0 CA B:GLN563 4.4 17.0 1.0 CB B:LEU562 4.5 14.0 1.0 CA B:TYR559 4.5 15.8 1.0 N B:ARG557 4.5 14.3 1.0 N B:TYR559 4.5 19.8 1.0 N B:ARG561 4.6 16.0 1.0 CD1 B:LEU350 4.7 12.1 1.0 CA B:ARG557 4.7 14.8 1.0 CG B:GLN563 4.7 13.8 1.0 C B:ARG557 4.8 16.0 1.0 CB B:PHE556 4.9 13.9 1.0 O B:ARG557 4.9 15.3 1.0 C B:ARG561 4.9 11.3 1.0

Sodium binding site 6 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3103 b:48.4 occ:1.00 O B:LEU967 2.6 24.3 1.0 O B:PRO932 2.8 18.2 1.0 O B:THR970 2.8 26.8 1.0 O B:HOH4216 3.1 18.2 1.0 O B:HOH4632 3.3 43.0 1.0 O B:HOH4510 3.3 31.9 1.0 CZ B:PHE931 3.5 19.8 1.0 C B:LEU967 3.8 21.9 1.0 C B:PRO932 3.8 20.4 1.0 CE2 B:PHE931 3.8 16.7 1.0 C B:THR970 3.8 26.0 1.0 CE1 B:PHE931 3.8 23.3 1.0 C B:MET968 3.9 28.5 1.0 CA B:MET968 3.9 25.4 1.0 O B:MET968 3.9 29.1 1.0 N B:THR970 4.2 25.3 1.0 CB B:PRO932 4.2 21.1 1.0 CD B:PRO932 4.2 20.5 1.0 N B:MET968 4.3 22.9 1.0 N B:PRO932 4.3 21.6 1.0 CA B:PRO932 4.3 20.3 1.0 CD2 B:PHE931 4.4 22.5 1.0 CD1 B:PHE931 4.5 22.4 1.0 N B:GLU969 4.5 26.2 1.0 CA B:THR970 4.6 25.5 1.0 N B:SER971 4.6 25.7 1.0 CA B:SER971 4.6 24.9 1.0 CG B:PRO932 4.6 22.8 1.0 CG B:PHE931 4.7 19.0 1.0 N B:SER933 4.9 18.9 1.0 O B:HOH4652 4.9 38.4 1.0 C B:GLU969 5.0 25.4 1.0 CA B:LEU967 5.0 24.9 1.0

Sodium binding site 7 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3104 b:35.5 occ:1.00 O B:HOH4870 2.5 36.5 1.0 O B:GLU650 2.8 23.3 1.0 O B:SER647 2.8 28.2 1.0 O B:LEU670 3.0 27.8 1.0 O B:HOH4641 3.1 40.9 1.0 N B:GLU650 3.2 19.4 1.0 C B:GLU650 3.6 25.9 1.0 N B:ASN649 3.7 22.9 1.0 C B:ASP648 3.7 23.1 1.0 CA B:GLU650 3.8 20.7 1.0 C B:SER647 3.9 27.3 1.0 CA B:ASP648 3.9 26.6 1.0 C B:LEU670 4.1 28.1 1.0 O B:ASP648 4.1 23.1 1.0 C B:ASN649 4.1 18.8 1.0 CA B:ASN649 4.2 19.9 1.0 N B:LEU670 4.2 33.0 1.0 CB B:GLU650 4.3 20.7 1.0 N B:ASP648 4.4 26.0 1.0 CA B:LEU670 4.6 32.3 1.0 OG B:SER647 4.7 21.9 1.0 O B:HOH4683 4.7 48.9 1.0 OE1 B:GLU650 4.8 23.6 1.0 CB B:LEU670 4.8 30.7 1.0 N B:LEU651 4.8 26.3 1.0

Sodium binding site 8 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3101 b:23.1 occ:1.00 O C:HOH4300 2.2 25.8 1.0 OD1 C:ASN604 2.4 16.9 1.0 OD2 C:ASP201 2.4 20.5 1.0 O C:PHE601 2.6 19.9 1.0 O C:HOH4846 2.9 28.9 1.0 CG C:ASP201 3.3 19.2 1.0 CG C:ASN604 3.4 18.0 1.0 O C:HOH4848 3.5 40.3 1.0 CD1 C:PHE601 3.6 37.6 1.0 C C:PHE601 3.7 19.0 1.0 OD1 C:ASP201 3.7 17.0 1.0 ND2 C:ASN604 3.8 15.8 1.0 CE1 C:PHE601 3.8 35.4 1.0 OH C:TYR100 3.8 20.9 1.0 NE1 C:TRP568 4.1 15.6 1.0 O C:HOH4081 4.3 11.8 1.0 CG C:PHE601 4.3 28.2 1.0 CA C:CYS602 4.3 18.3 1.0 N C:CYS602 4.4 17.6 1.0 CB C:ASP201 4.5 14.4 1.0 O C:ASP201 4.6 18.5 1.0 CZ C:PHE601 4.6 31.6 1.0 NE2 C:HIS540 4.6 11.6 1.0 CB C:ASN604 4.7 14.2 1.0 CA C:PHE601 4.7 20.2 1.0 CB C:PHE601 4.8 20.4 1.0 C C:CYS602 4.8 18.7 1.0 CE2 C:TRP568 4.9 19.6 1.0 CZ C:TYR100 4.9 20.5 1.0 CZ2 C:TRP568 4.9 18.6 1.0

Sodium binding site 9 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3102 b:22.9 occ:1.00 O C:PHE556 2.4 16.3 1.0 O C:LEU562 2.4 17.5 1.0 O C:TYR559 2.4 18.9 1.0 O C:HOH4418 2.6 31.6 1.0 O C:PRO560 3.1 16.0 1.0 C C:TYR559 3.3 15.8 1.0 C C:LEU562 3.4 16.4 1.0 C C:PHE556 3.5 16.7 1.0 C C:PRO560 3.6 15.2 1.0 O C:HOH4606 3.7 41.5 1.0 CA C:PRO560 3.7 16.4 1.0 N C:PRO560 3.9 15.7 1.0 O C:HOH4824 4.0 38.1 1.0 O C:HOH4307 4.0 20.5 1.0 N C:LEU562 4.0 13.0 1.0 CA C:LEU562 4.2 15.1 1.0 CA C:PHE556 4.2 16.8 1.0 N C:GLN563 4.3 14.3 1.0 CA C:GLN563 4.3 14.5 1.0 CB C:LEU562 4.4 13.5 1.0 CA C:TYR559 4.5 16.9 1.0 N C:ARG561 4.5 15.8 1.0 N C:TYR559 4.5 15.5 1.0 N C:ARG557 4.6 14.5 1.0 CD1 C:LEU350 4.7 14.2 1.0 CG C:GLN563 4.7 14.0 1.0 CA C:ARG557 4.7 18.1 1.0 C C:ARG557 4.8 18.6 1.0 CB C:PHE556 4.8 11.3 1.0 C C:ARG561 4.9 16.5 1.0 O C:ARG557 4.9 19.7 1.0 O C:ALA555 5.0 15.5 1.0

Sodium binding site 10 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3103 b:43.0 occ:1.00 O C:LEU967 2.5 23.1 1.0 O C:PRO932 2.6 21.0 1.0 O C:THR970 2.7 25.0 1.0 O C:HOH4681 3.0 46.9 1.0 O C:HOH4231 3.0 20.2 1.0 O C:HOH4540 3.4 29.2 1.0 CZ C:PHE931 3.5 19.9 1.0 C C:PRO932 3.6 20.9 1.0 C C:LEU967 3.7 21.5 1.0 C C:THR970 3.8 25.1 1.0 O C:MET968 3.9 24.0 1.0 CE1 C:PHE931 3.9 26.8 1.0 CE2 C:PHE931 3.9 15.8 1.0 CA C:MET968 3.9 23.1 1.0 C C:MET968 3.9 23.5 1.0 CB C:PRO932 4.0 18.3 1.0 CD C:PRO932 4.1 20.9 1.0 CA C:PRO932 4.2 18.2 1.0 N C:PRO932 4.2 22.7 1.0 N C:THR970 4.3 23.5 1.0 N C:MET968 4.3 20.5 1.0 CD1 C:PHE931 4.4 20.9 1.0 CD2 C:PHE931 4.4 23.5 1.0 CG C:PRO932 4.5 18.6 1.0 CA C:SER971 4.6 24.4 1.0 CA C:THR970 4.6 22.4 1.0 N C:SER971 4.6 23.1 1.0 N C:GLU969 4.6 20.9 1.0 CG C:PHE931 4.7 19.8 1.0 N C:SER933 4.7 19.4 1.0 CA C:LEU967 4.9 20.3 1.0 C C:PHE931 4.9 21.7 1.0

L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.E.Fraser, R.E.Huber. Ser-796 of Beta-Galactosidase (E. Coli) Plays A Key Role in Maintaining An Optimum Balance Between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Arch.Biochem.Biophys. V. 517 111 2012.
ISSN: ISSN 0003-9861
PubMed: 22155115
DOI: 10.1016/J.ABB.2011.11.017