Sodium in PDB 3dym: E. Coli (Lacz) Beta-Galactosidase (H418E)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (H418E):
3.2.1.23;

The structure of E. Coli (Lacz) Beta-Galactosidase (H418E), PDB code: 3dym 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)	34.50 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	149.340, 167.160, 200.350, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of E. Coli (Lacz) Beta-Galactosidase (H418E) also contains other interesting chemical elements:

Magnesium

(Mg)

10 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 (H418E) (pdb code 3dym). 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 (H418E), PDB code: 3dym:
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 (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3101 b:30.5 occ:1.00 O A:HOH4273 2.1 30.7 1.0 OD1 A:ASN604 2.3 18.8 1.0 O A:PHE601 2.3 22.6 1.0 O A:HOH4167 2.4 31.8 1.0 OD2 A:ASP201 2.5 32.5 1.0 CG A:ASP201 3.3 29.3 1.0 CG A:ASN604 3.3 33.0 1.0 C A:PHE601 3.4 36.5 1.0 OD1 A:ASP201 3.5 29.6 1.0 ND2 A:ASN604 3.5 19.3 1.0 OH A:TYR100 3.6 34.5 1.0 CA A:CYS602 4.1 22.2 1.0 NE1 A:TRP568 4.1 21.3 1.0 N A:CYS602 4.2 23.5 1.0 O A:HOH4279 4.3 48.1 1.0 O A:HOH4051 4.3 27.2 1.0 ND2 A:ASN102 4.4 61.2 1.0 C A:CYS602 4.5 30.0 1.0 CA A:PHE601 4.5 26.3 1.0 CB A:ASP201 4.5 22.6 1.0 CB A:PHE601 4.6 24.4 1.0 CB A:ASN604 4.7 7.8 1.0 CZ A:TYR100 4.7 36.0 1.0 NE2 A:HIS540 4.7 19.8 1.0 O A:ASP201 4.7 19.6 1.0 CE2 A:TRP568 4.9 22.6 1.0 O A:CYS602 4.9 26.7 1.0 O A:HOH4578 4.9 46.9 1.0 CZ2 A:TRP568 4.9 19.1 1.0 CD2 A:PHE601 5.0 19.7 1.0

Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3102 b:14.6 occ:1.00 O A:TYR559 2.2 20.5 1.0 O A:PHE556 2.2 22.2 1.0 O A:LEU562 2.3 11.3 1.0 O A:HOH4556 2.5 28.1 1.0 O A:HOH4384 2.5 20.9 1.0 O A:PRO560 3.1 17.3 1.0 C A:TYR559 3.3 15.7 1.0 C A:PHE556 3.4 19.5 1.0 C A:LEU562 3.4 16.7 1.0 C A:PRO560 3.5 15.0 1.0 CA A:PRO560 3.6 7.2 1.0 N A:PRO560 3.9 16.2 1.0 N A:LEU562 3.9 9.3 1.0 O A:HOH4280 4.0 24.5 1.0 CA A:PHE556 4.2 10.9 1.0 CA A:LEU562 4.2 20.4 1.0 CA A:GLN563 4.3 14.1 1.0 N A:GLN563 4.4 12.2 1.0 CA A:TYR559 4.4 14.8 1.0 N A:ARG561 4.5 9.5 1.0 N A:TYR559 4.5 11.1 1.0 N A:ARG557 4.5 13.9 1.0 CB A:LEU562 4.5 20.1 1.0 CG A:GLN563 4.7 11.3 1.0 CA A:ARG557 4.7 7.7 1.0 C A:ARG557 4.7 12.6 1.0 O A:ARG557 4.7 12.0 1.0 CD1 A:LEU350 4.8 10.9 1.0 C A:ARG561 4.8 15.3 1.0 CB A:PHE556 4.8 9.5 1.0 O A:ALA555 4.9 17.2 1.0 O A:HOH4700 4.9 54.6 1.0

Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3103 b:27.9 occ:1.00 O A:HOH4631 2.2 27.8 1.0 O A:THR970 2.4 35.3 1.0 O A:PRO932 2.5 24.8 1.0 O A:HOH4203 2.6 20.3 1.0 O A:LEU967 2.6 24.1 1.0 C A:PRO932 3.5 28.4 1.0 O A:HOH4496 3.5 33.7 1.0 CZ A:PHE931 3.5 31.6 1.0 CE1 A:PHE931 3.6 33.7 1.0 C A:THR970 3.6 27.9 1.0 O A:MET968 3.7 29.9 1.0 C A:LEU967 3.7 17.7 1.0 CB A:PRO932 3.9 27.2 1.0 C A:MET968 3.9 33.9 1.0 CA A:PRO932 4.0 27.3 1.0 CA A:MET968 4.0 17.9 1.0 CE2 A:PHE931 4.1 30.5 1.0 N A:PRO932 4.1 30.0 1.0 CD1 A:PHE931 4.2 36.2 1.0 N A:THR970 4.2 25.2 1.0 CD A:PRO932 4.2 22.4 1.0 CG A:PRO932 4.3 31.8 1.0 N A:MET968 4.4 19.0 1.0 N A:SER971 4.5 24.5 1.0 CA A:THR970 4.5 15.9 1.0 CD2 A:PHE931 4.6 24.6 1.0 CA A:SER971 4.6 29.6 1.0 N A:SER933 4.6 14.7 1.0 CG A:PHE931 4.7 21.6 1.0 N A:GLU969 4.7 17.4 1.0 C A:PHE931 4.9 35.4 1.0 C A:GLU969 4.9 36.2 1.0 CA A:LEU967 4.9 18.5 1.0 CA A:SER933 4.9 19.9 1.0

Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3104 b:32.2 occ:1.00 O A:DMS8425 2.1 39.2 1.0 O A:LEU670 2.3 15.6 1.0 O A:SER647 2.5 20.2 1.0 O A:GLU650 2.5 28.3 1.0 S A:DMS8425 3.2 60.0 1.0 N A:GLU650 3.4 18.2 1.0 C A:LEU670 3.5 26.5 1.0 C A:GLU650 3.5 25.6 1.0 C A:SER647 3.7 26.3 1.0 C2 A:DMS8425 3.7 70.2 1.0 CA A:GLU650 3.9 17.5 1.0 N A:LEU670 3.9 26.6 1.0 C A:ASP648 4.1 27.6 1.0 CB A:GLU650 4.1 15.4 1.0 OD1 A:ASP671 4.1 0.0 1.0 N A:ASN649 4.2 22.5 1.0 CA A:LEU670 4.2 26.2 1.0 CA A:ASP648 4.2 18.6 1.0 CB A:LEU670 4.2 35.1 1.0 OG A:SER647 4.3 18.6 1.0 N A:ASP648 4.4 18.4 1.0 C A:ASN649 4.5 20.7 1.0 N A:ASP671 4.6 19.6 1.0 O A:ASP648 4.6 22.2 1.0 N A:LEU651 4.7 25.9 1.0 CB A:SER647 4.7 16.1 1.0 CA A:ASN649 4.7 18.4 1.0 C1 A:DMS8425 4.8 37.1 1.0 CA A:ASP671 4.8 31.7 1.0 CA A:SER647 4.8 18.7 1.0 C A:PRO669 4.9 26.4 1.0 CB A:PRO669 5.0 45.9 1.0 OE1 A:GLU650 5.0 20.2 1.0

Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3101 b:29.1 occ:1.00 O B:HOH4182 2.2 32.9 1.0 O B:HOH4284 2.3 30.7 1.0 O B:PHE601 2.3 21.9 1.0 OD2 B:ASP201 2.3 25.9 1.0 OD1 B:ASN604 2.4 27.2 1.0 CG B:ASP201 3.3 25.7 1.0 CG B:ASN604 3.4 21.9 1.0 C B:PHE601 3.4 16.4 1.0 OD1 B:ASP201 3.5 27.8 1.0 OH B:TYR100 3.6 30.6 1.0 ND2 B:ASN604 3.6 14.2 1.0 O B:HOH4290 4.0 42.2 1.0 NE1 B:TRP568 4.1 18.1 1.0 N B:CYS602 4.2 14.7 1.0 CA B:CYS602 4.3 19.1 1.0 CB B:PHE601 4.3 23.6 1.0 CA B:PHE601 4.4 23.3 1.0 ND2 B:ASN102 4.5 49.1 1.0 O B:HOH4065 4.5 21.2 1.0 NE2 B:HIS540 4.5 19.0 1.0 CB B:ASP201 4.6 30.4 1.0 CZ B:TYR100 4.7 31.2 1.0 CB B:ASN604 4.8 12.8 1.0 C B:CYS602 4.8 23.7 1.0 O B:ASP201 4.9 22.6 1.0 CE2 B:TRP568 4.9 24.7 1.0 CD2 B:PHE601 5.0 22.8 1.0

Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3102 b:19.3 occ:1.00 O B:LEU562 2.2 18.1 1.0 O B:TYR559 2.2 15.6 1.0 O B:PHE556 2.3 8.9 1.0 O B:HOH4587 2.6 28.6 1.0 O B:HOH4404 2.7 22.9 1.0 C B:TYR559 3.3 12.2 1.0 C B:LEU562 3.3 24.0 1.0 O B:PRO560 3.3 13.3 1.0 C B:PHE556 3.4 23.4 1.0 C B:PRO560 3.6 28.4 1.0 CA B:PRO560 3.7 19.5 1.0 N B:PRO560 3.9 19.1 1.0 N B:LEU562 3.9 11.5 1.0 O B:HOH4291 4.0 18.7 1.0 CA B:LEU562 4.1 9.1 1.0 CA B:PHE556 4.1 12.7 1.0 N B:GLN563 4.2 14.5 1.0 CB B:LEU562 4.2 8.9 1.0 CA B:GLN563 4.4 13.1 1.0 CA B:TYR559 4.4 7.8 1.0 N B:TYR559 4.4 12.4 1.0 N B:ARG561 4.5 7.3 1.0 O B:HOH4716 4.5 62.6 1.0 N B:ARG557 4.5 13.3 1.0 CG B:GLN563 4.6 11.5 1.0 CB B:PHE556 4.7 11.2 1.0 O B:ARG557 4.7 16.2 1.0 CA B:ARG557 4.7 16.7 1.0 C B:ARG557 4.7 21.3 1.0 CD1 B:LEU350 4.7 13.7 1.0 O B:ALA555 4.8 14.6 1.0 CB B:TYR559 4.8 10.9 1.0 C B:ARG561 4.9 10.9 1.0

Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3103 b:25.6 occ:1.00 O B:PRO932 2.3 22.6 1.0 O B:LEU967 2.5 22.2 1.0 O B:HOH4218 2.6 22.4 1.0 O B:THR970 2.7 39.8 1.0 O B:HOH4659 3.0 46.3 1.0 CZ B:PHE931 3.3 39.3 1.0 C B:PRO932 3.4 27.2 1.0 CE1 B:PHE931 3.6 23.1 1.0 C B:LEU967 3.7 25.1 1.0 CE2 B:PHE931 3.7 39.6 1.0 C B:THR970 3.7 36.9 1.0 O B:HOH4522 3.8 30.9 1.0 CA B:MET968 4.0 21.3 1.0 CB B:PRO932 4.0 24.8 1.0 CA B:PRO932 4.1 24.9 1.0 C B:MET968 4.1 33.9 1.0 CD B:PRO932 4.1 23.0 1.0 O B:MET968 4.1 28.9 1.0 N B:PRO932 4.2 26.0 1.0 N B:THR970 4.2 27.6 1.0 CD1 B:PHE931 4.2 20.0 1.0 CD2 B:PHE931 4.3 24.1 1.0 N B:MET968 4.3 18.4 1.0 N B:SER933 4.4 16.8 1.0 CG B:PRO932 4.5 20.8 1.0 CA B:THR970 4.5 32.2 1.0 CG B:PHE931 4.6 25.6 1.0 CA B:SER933 4.6 15.4 1.0 N B:SER971 4.6 30.4 1.0 C B:PHE931 4.7 24.9 1.0 CA B:SER971 4.7 29.8 1.0 N B:GLU969 4.8 34.0 1.0 O B:HOH4678 4.8 52.6 1.0 CA B:LEU967 4.8 20.4 1.0

Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3104 b:39.7 occ:1.00 O B:DMS8425 2.2 44.9 1.0 O B:LEU670 2.4 22.4 1.0 O B:SER647 2.4 21.4 1.0 O B:GLU650 2.5 28.3 1.0 O B:HOH4671 2.6 38.5 1.0 S B:DMS8425 3.2 55.2 1.0 N B:GLU650 3.4 21.3 1.0 C B:LEU670 3.5 25.0 1.0 C B:GLU650 3.6 27.9 1.0 C B:SER647 3.6 21.8 1.0 N B:LEU670 3.6 32.7 1.0 C2 B:DMS8425 3.6 33.5 1.0 CA B:LEU670 3.9 26.9 1.0 CA B:GLU650 4.0 17.9 1.0 CB B:LEU670 4.0 31.6 1.0 CA B:ASP648 4.0 23.2 1.0 N B:ASN649 4.0 21.6 1.0 C B:ASP648 4.1 28.6 1.0 CB B:GLU650 4.2 15.0 1.0 OG B:SER647 4.2 18.7 1.0 N B:ASP648 4.3 15.9 1.0 C B:ASN649 4.6 32.9 1.0 C B:PRO669 4.6 35.2 1.0 N B:ASP671 4.6 15.6 1.0 C1 B:DMS8425 4.7 30.6 1.0 CB B:SER647 4.7 28.1 1.0 CA B:ASN649 4.7 16.9 1.0 CA B:SER647 4.8 19.4 1.0 N B:LEU651 4.8 25.0 1.0 CA B:ASP671 4.8 18.3 1.0 OE1 B:GLU650 4.8 25.2 1.0 O B:ASP648 4.8 24.7 1.0 CB B:PRO669 4.9 54.0 1.0 O B:HOH4753 4.9 41.8 1.0 CA B:PRO669 5.0 47.8 1.0

Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3101 b:30.0 occ:1.00 O C:HOH4190 2.2 41.9 1.0 OD1 C:ASN604 2.4 21.1 1.0 OD2 C:ASP201 2.4 31.3 1.0 O C:HOH4289 2.5 33.0 1.0 O C:PHE601 2.5 25.8 1.0 CG C:ASP201 3.3 37.1 1.0 CG C:ASN604 3.4 19.4 1.0 C C:PHE601 3.6 21.6 1.0 OD1 C:ASP201 3.7 27.7 1.0 ND2 C:ASN604 3.7 27.0 1.0 OH C:TYR100 3.8 26.5 1.0 O C:HOH4295 4.0 45.4 1.0 NE1 C:TRP568 4.0 20.8 1.0 ND2 C:ASN102 4.2 57.8 1.0 O C:HOH4072 4.3 20.5 1.0 CA C:CYS602 4.4 22.9 1.0 CB C:PHE601 4.4 22.2 1.0 N C:CYS602 4.4 19.4 1.0 CB C:ASP201 4.4 23.2 1.0 CA C:PHE601 4.5 20.8 1.0 NE2 C:HIS540 4.6 20.3 1.0 O C:HOH4596 4.6 51.3 1.0 CB C:ASN604 4.8 13.3 1.0 CE2 C:TRP568 4.8 19.1 1.0 O C:ASP201 4.8 17.8 1.0 CZ2 C:TRP568 4.9 17.1 1.0 CZ C:TYR100 4.9 34.6 1.0 CD2 C:PHE601 4.9 28.0 1.0 C C:CYS602 4.9 27.8 1.0 CG C:ASN102 5.0 61.0 1.0 CD1 C:TRP568 5.0 24.4 1.0

Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3102 b:18.7 occ:1.00 O C:PHE556 2.2 16.9 1.0 O C:TYR559 2.3 18.5 1.0 O C:LEU562 2.3 12.5 1.0 O C:HOH4575 2.4 25.9 1.0 O C:HOH4401 2.6 25.1 1.0 O C:PRO560 3.2 18.4 1.0 C C:TYR559 3.3 15.6 1.0 C C:LEU562 3.4 11.5 1.0 C C:PHE556 3.4 19.6 1.0 C C:PRO560 3.6 24.1 1.0 CA C:PRO560 3.7 13.5 1.0 O C:HOH4296 4.0 21.7 1.0 N C:PRO560 4.0 17.9 1.0 N C:LEU562 4.0 8.9 1.0 CA C:PHE556 4.2 16.5 1.0 CA C:LEU562 4.2 8.6 1.0 CB C:LEU562 4.3 9.3 1.0 N C:GLN563 4.3 15.2 1.0 N C:TYR559 4.4 13.1 1.0 CA C:TYR559 4.4 9.5 1.0 CA C:GLN563 4.4 11.6 1.0 N C:ARG557 4.5 16.7 1.0 N C:ARG561 4.6 8.1 1.0 CG C:GLN563 4.7 14.5 1.0 CA C:ARG557 4.7 11.0 1.0 C C:ARG557 4.8 19.8 1.0 CD1 C:LEU350 4.8 12.4 1.0 CB C:PHE556 4.8 18.6 1.0 O C:ARG557 4.8 21.6 1.0 CB C:TYR559 4.9 16.2 1.0 O C:ALA555 4.9 17.0 1.0 C C:ARG561 4.9 14.5 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