Sodium in PDB 3i3e: E. Coli (Lacz) Beta-Galactosidase (M542A)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (M542A):
3.2.1.23;

The structure of E. Coli (Lacz) Beta-Galactosidase (M542A), PDB code: 3i3e was solved by M.L.Dugdale, D.Dymianiw, B.Minhas, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.70 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	149.701, 168.417, 200.709, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.1

The structure of E. Coli (Lacz) Beta-Galactosidase (M542A) also contains other interesting chemical elements:

Magnesium

(Mg)

15 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (M542A) (pdb code 3i3e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (M542A), PDB code: 3i3e:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3101 b:36.5 occ:1.00 OD1 A:ASN604 2.2 20.7 1.0 O A:PHE601 2.2 22.8 1.0 O A:HOH4170 2.4 22.2 1.0 O A:HOH4278 2.4 34.7 1.0 O A:HOH7434 2.5 35.4 1.0 O A:HOH7338 2.5 31.0 1.0 CG A:ASN604 3.3 20.7 1.0 C A:PHE601 3.4 23.9 1.0 OD2 A:ASP201 3.5 21.6 1.0 ND2 A:ASN604 3.7 22.6 1.0 NE2 A:HIS540 3.8 16.3 1.0 CA A:PHE601 4.2 25.9 1.0 NE1 A:TRP568 4.2 12.3 1.0 CE1 A:HIS540 4.2 16.8 1.0 OH A:TYR100 4.3 27.1 1.0 CB A:PHE601 4.4 27.5 1.0 N A:CYS602 4.4 21.3 1.0 CB A:ASN604 4.5 20.0 1.0 O A:HOH7309 4.5 40.7 1.0 CA A:CYS602 4.6 20.3 1.0 O A:HOH7435 4.6 38.8 1.0 CG A:ASP201 4.6 20.9 1.0 O A:HOH4052 4.7 17.9 1.0 C A:CYS602 4.9 19.2 1.0 OD1 A:ASP201 4.9 21.0 1.0 O A:HOH4300 5.0 43.1 1.0 N A:MET603 5.0 18.3 1.0

Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3102 b:9.9 occ:1.00 O A:PHE556 2.2 8.8 1.0 O A:TYR559 2.3 13.3 1.0 O A:LEU562 2.3 5.7 1.0 O A:HOH4652 2.4 19.7 1.0 O A:HOH4410 2.6 17.6 1.0 C A:TYR559 3.3 8.9 1.0 O A:PRO560 3.4 7.2 1.0 C A:LEU562 3.4 7.0 1.0 C A:PHE556 3.4 8.9 1.0 C A:PRO560 3.7 7.2 1.0 CA A:PRO560 3.8 6.9 1.0 N A:LEU562 4.0 5.7 1.0 N A:PRO560 4.0 7.6 1.0 O A:HOH5118 4.0 47.9 1.0 O A:HOH4286 4.1 18.8 1.0 CA A:PHE556 4.1 7.3 1.0 CA A:LEU562 4.2 6.7 1.0 N A:GLN563 4.3 6.5 1.0 CA A:GLN563 4.3 7.5 1.0 CB A:LEU562 4.3 5.9 1.0 N A:ARG557 4.4 7.7 1.0 CA A:TYR559 4.4 8.4 1.0 N A:TYR559 4.5 9.4 1.0 N A:ARG561 4.6 6.7 1.0 CG A:GLN563 4.6 7.6 1.0 CA A:ARG557 4.6 8.3 1.0 C A:ARG557 4.8 8.0 1.0 CB A:PHE556 4.8 7.7 1.0 C A:ARG561 4.9 7.2 1.0 O A:ARG557 4.9 9.6 1.0 O A:ALA555 4.9 6.8 1.0 CD1 A:LEU350 4.9 6.5 1.0

Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3103 b:29.4 occ:1.00 O A:PRO932 2.7 13.6 1.0 O A:THR970 2.8 21.8 1.0 O A:LEU967 2.9 16.6 1.0 O A:HOH4207 3.2 14.5 1.0 CZ A:PHE931 3.6 28.2 1.0 C A:PRO932 3.6 14.8 1.0 CE1 A:PHE931 3.8 28.5 1.0 O A:HOH7324 3.8 34.4 1.0 CB A:PRO932 3.8 16.7 1.0 C A:THR970 3.9 23.3 1.0 CE2 A:PHE931 3.9 27.3 1.0 O A:MET968 4.0 20.3 1.0 CA A:PRO932 4.1 16.6 1.0 CD A:PRO932 4.1 15.5 1.0 C A:LEU967 4.1 16.3 1.0 N A:PRO932 4.1 17.5 1.0 C A:MET968 4.2 21.3 1.0 CD1 A:PHE931 4.3 26.4 1.0 CA A:MET968 4.4 20.0 1.0 CD2 A:PHE931 4.4 25.7 1.0 CG A:PRO932 4.5 16.9 1.0 N A:THR970 4.5 23.4 1.0 CG A:PHE931 4.6 23.8 1.0 CA A:SER971 4.7 22.8 1.0 N A:SER971 4.7 22.5 1.0 N A:MET968 4.7 17.2 1.0 N A:SER933 4.7 13.5 1.0 C A:PHE931 4.8 18.6 1.0 CA A:THR970 4.8 23.1 1.0 N A:GLU969 4.9 20.7 1.0

Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3104 b:28.2 occ:1.00 O A:DMS8425 2.3 45.5 1.0 O A:LEU670 2.4 20.6 1.0 O A:GLU650 2.5 18.7 1.0 O A:SER647 2.6 15.4 1.0 O A:HOH6122 2.9 35.5 1.0 S A:DMS8425 3.4 46.3 1.0 C A:LEU670 3.5 21.6 1.0 N A:GLU650 3.5 16.6 1.0 C A:GLU650 3.5 18.6 1.0 N A:LEU670 3.8 20.9 1.0 C A:SER647 3.8 17.0 1.0 CA A:GLU650 4.0 17.0 1.0 CA A:LEU670 4.0 21.2 1.0 C1 A:DMS8425 4.1 46.5 1.0 N A:ASN649 4.2 18.2 1.0 C A:ASP648 4.2 18.5 1.0 CB A:LEU670 4.2 22.2 1.0 CA A:ASP648 4.3 19.5 1.0 OG A:SER647 4.3 12.8 1.0 CB A:GLU650 4.4 15.8 1.0 N A:ASP648 4.5 17.9 1.0 N A:ASP671 4.6 23.1 1.0 C A:ASN649 4.6 17.4 1.0 O A:ASP648 4.7 18.5 1.0 N A:LEU651 4.7 18.8 1.0 C A:PRO669 4.7 20.8 1.0 CA A:ASN649 4.7 16.7 1.0 CB A:SER647 4.8 15.5 1.0 CA A:SER647 4.9 15.5 1.0 C2 A:DMS8425 4.9 45.5 1.0 CA A:ASP671 5.0 25.3 1.0 OE1 A:GLU650 5.0 13.2 1.0

Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3101 b:26.2 occ:1.00 O B:PHE601 2.1 17.6 1.0 OD1 B:ASN604 2.3 17.4 1.0 O B:HOH4170 2.3 15.6 1.0 O B:HOH4278 2.4 31.6 1.0 O B:HOH7211 2.4 25.2 1.0 O B:HOH7216 2.4 31.0 1.0 CG B:ASN604 3.2 18.7 1.0 C B:PHE601 3.3 18.7 1.0 OD2 B:ASP201 3.6 19.7 1.0 ND2 B:ASN604 3.7 20.6 1.0 NE2 B:HIS540 3.8 13.1 1.0 CA B:PHE601 4.0 21.2 1.0 CB B:PHE601 4.1 23.4 1.0 CE1 B:HIS540 4.2 13.2 1.0 OH B:TYR100 4.2 19.4 1.0 N B:CYS602 4.3 18.5 1.0 O B:HOH7279 4.4 42.7 1.0 NE1 B:TRP568 4.5 9.0 1.0 CA B:CYS602 4.5 18.2 1.0 CB B:ASN604 4.5 18.4 1.0 CG B:ASP201 4.6 18.8 1.0 O B:HOH7191 4.6 25.9 1.0 O B:HOH4052 4.8 14.0 1.0 C B:CYS602 4.8 17.9 1.0 OD1 B:ASP201 4.8 19.9 1.0 N B:MET603 4.9 15.3 1.0

Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3102 b:12.4 occ:1.00 O B:PHE556 2.2 4.5 1.0 O B:TYR559 2.2 12.7 1.0 O B:LEU562 2.3 8.8 1.0 O B:HOH4652 2.4 19.7 1.0 O B:HOH4410 2.6 20.1 1.0 C B:TYR559 3.3 10.3 1.0 C B:LEU562 3.3 7.3 1.0 O B:PRO560 3.3 7.3 1.0 C B:PHE556 3.4 7.2 1.0 C B:PRO560 3.6 8.6 1.0 CA B:PRO560 3.7 8.1 1.0 N B:PRO560 3.9 10.4 1.0 N B:LEU562 3.9 4.2 1.0 O B:HOH4286 3.9 16.6 1.0 CA B:PHE556 4.1 5.5 1.0 CA B:LEU562 4.1 6.4 1.0 N B:GLN563 4.2 6.6 1.0 O B:HOH5118 4.3 56.2 1.0 CB B:LEU562 4.3 5.5 1.0 CA B:GLN563 4.3 6.6 1.0 CA B:TYR559 4.4 10.4 1.0 N B:ARG557 4.4 6.7 1.0 N B:ARG561 4.5 5.8 1.0 N B:TYR559 4.5 10.1 1.0 CA B:ARG557 4.7 9.5 1.0 CD1 B:LEU350 4.7 6.0 1.0 CG B:GLN563 4.7 5.5 1.0 CB B:PHE556 4.7 5.7 1.0 C B:ARG557 4.8 9.7 1.0 C B:ARG561 4.8 6.5 1.0 O B:ARG557 4.9 11.2 1.0 O B:ALA555 4.9 7.5 1.0 CB B:TYR559 5.0 10.2 1.0

Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3103 b:30.8 occ:1.00 O B:THR970 2.5 21.8 1.0 O B:LEU967 2.6 16.9 1.0 O B:PRO932 2.7 15.1 1.0 O B:HOH4558 3.1 34.7 1.0 O B:HOH4207 3.2 15.4 1.0 O B:HOH4763 3.3 33.5 1.0 C B:PRO932 3.6 15.9 1.0 C B:THR970 3.7 22.8 1.0 CZ B:PHE931 3.7 29.3 1.0 C B:LEU967 3.8 16.7 1.0 O B:MET968 3.8 21.9 1.0 CB B:PRO932 3.9 16.6 1.0 CE2 B:PHE931 4.0 28.8 1.0 CE1 B:PHE931 4.0 27.4 1.0 C B:MET968 4.0 22.9 1.0 CA B:PRO932 4.1 16.2 1.0 CD B:PRO932 4.1 17.3 1.0 N B:PRO932 4.1 17.9 1.0 CA B:MET968 4.1 21.3 1.0 N B:THR970 4.2 22.4 1.0 N B:MET968 4.4 18.2 1.0 CD2 B:PHE931 4.5 26.4 1.0 CD1 B:PHE931 4.5 25.6 1.0 CG B:PRO932 4.5 15.0 1.0 CA B:THR970 4.5 22.7 1.0 N B:SER971 4.6 21.5 1.0 CA B:SER971 4.6 21.1 1.0 N B:SER933 4.7 15.2 1.0 CG B:PHE931 4.7 24.4 1.0 N B:GLU969 4.8 21.5 1.0 C B:PHE931 4.8 17.1 1.0 CA B:LEU967 5.0 15.6 1.0

Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3104 b:28.7 occ:1.00 O B:DMS8425 2.2 49.1 1.0 O B:SER647 2.4 16.3 1.0 O B:HOH7217 2.6 43.2 1.0 O B:GLU650 2.8 17.4 1.0 O B:LEU670 2.9 23.4 1.0 N B:GLU650 3.1 14.6 1.0 O B:HOH5010 3.3 45.5 1.0 N B:ASN649 3.4 16.9 1.0 S B:DMS8425 3.4 49.7 1.0 C B:SER647 3.4 17.1 1.0 C B:ASP648 3.5 18.5 1.0 CA B:ASP648 3.6 18.6 1.0 C B:GLU650 3.6 17.4 1.0 C1 B:DMS8425 3.7 49.1 1.0 CA B:GLU650 3.8 15.2 1.0 N B:ASP648 3.9 16.4 1.0 C B:LEU670 4.0 22.7 1.0 C B:ASN649 4.1 15.3 1.0 CA B:ASN649 4.1 15.3 1.0 O B:ASP648 4.1 18.9 1.0 CB B:GLU650 4.2 14.8 1.0 N B:LEU670 4.4 23.5 1.0 OE1 B:GLU650 4.5 14.1 1.0 OG B:SER647 4.5 15.8 1.0 O B:HOH5124 4.6 37.0 1.0 CA B:LEU670 4.6 23.4 1.0 C2 B:DMS8425 4.6 48.2 1.0 CA B:SER647 4.7 16.9 1.0 CB B:LEU670 4.7 23.5 1.0 CB B:SER647 4.7 17.4 1.0 N B:LEU651 4.9 18.7 1.0

Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3101 b:35.1 occ:1.00 O C:PHE601 2.2 17.9 1.0 OD1 C:ASN604 2.2 20.5 1.0 O C:HOH4278 2.3 32.7 1.0 O C:HOH4170 2.3 23.0 1.0 O C:HOH7268 2.4 35.3 1.0 O C:HOH7262 2.5 26.6 1.0 CG C:ASN604 3.0 18.5 1.0 ND2 C:ASN604 3.3 20.6 1.0 C C:PHE601 3.4 19.0 1.0 OD2 C:ASP201 3.5 17.4 1.0 NE2 C:HIS540 3.8 17.1 1.0 CA C:PHE601 4.2 20.9 1.0 CE1 C:HIS540 4.2 14.8 1.0 NE1 C:TRP568 4.2 9.3 1.0 CB C:PHE601 4.2 23.6 1.0 OH C:TYR100 4.3 20.8 1.0 CB C:ASN604 4.4 19.0 1.0 O C:HOH7252 4.4 32.4 1.0 N C:CYS602 4.4 18.4 1.0 CA C:CYS602 4.5 18.6 1.0 O C:HOH7263 4.6 43.8 1.0 O C:HOH4052 4.6 15.7 1.0 CG C:ASP201 4.6 16.6 1.0 C C:CYS602 4.9 18.5 1.0 OD1 C:ASP201 4.9 19.3 1.0 N C:MET603 5.0 17.3 1.0 CD1 C:TRP568 5.0 11.3 1.0

Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3102 b:9.7 occ:1.00 O C:TYR559 2.3 10.7 1.0 O C:PHE556 2.3 7.2 1.0 O C:LEU562 2.3 5.4 1.0 O C:HOH4410 2.6 15.0 1.0 O C:HOH4652 2.7 18.3 1.0 O C:PRO560 3.2 7.8 1.0 C C:TYR559 3.3 9.2 1.0 C C:LEU562 3.3 6.0 1.0 C C:PHE556 3.5 8.1 1.0 C C:PRO560 3.6 8.8 1.0 CA C:PRO560 3.7 8.3 1.0 N C:PRO560 3.9 8.1 1.0 N C:LEU562 3.9 5.7 1.0 O C:HOH4286 4.0 15.8 1.0 CA C:LEU562 4.2 5.2 1.0 CA C:PHE556 4.2 7.4 1.0 N C:GLN563 4.2 6.1 1.0 O C:HOH4580 4.3 45.2 1.0 CA C:GLN563 4.3 5.7 1.0 CB C:LEU562 4.3 4.9 1.0 CA C:TYR559 4.4 10.0 1.0 N C:ARG561 4.5 7.0 1.0 N C:ARG557 4.5 8.7 1.0 N C:TYR559 4.5 10.3 1.0 CG C:GLN563 4.6 8.2 1.0 CA C:ARG557 4.7 9.6 1.0 C C:ARG557 4.8 9.4 1.0 CB C:PHE556 4.8 7.0 1.0 C C:ARG561 4.8 7.1 1.0 CD1 C:LEU350 4.9 6.1 1.0 O C:ARG557 4.9 9.9 1.0 O C:ALA555 4.9 8.2 1.0 CB C:TYR559 5.0 10.4 1.0

M.L.Dugdale, D.L.Dymianiw, B.K.Minhas, I.D'angelo, R.E.Huber. Role of Met-542 As A Guide For the Conformational Changes of Phe-601 That Occur During the Reaction of β-Galactosidase (Escherichia Coli). Biochem.Cell Biol. V. 88 861 2010.
ISSN: ISSN 0829-8211
PubMed: 20921997
DOI: 10.1139/O10-009