Sodium in PDB 3iap: E. Coli (Lacz) Beta-Galactosidase (E416Q)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E416Q):
3.2.1.23;

The structure of E. Coli (Lacz) Beta-Galactosidase (E416Q), PDB code: 3iap was solved by S.Lo, M.L.Dugdale, N.Jeerh, T.Ku, N.J.Roth, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.38 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	151.230, 162.340, 202.060, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22

The structure of E. Coli (Lacz) Beta-Galactosidase (E416Q) also contains other interesting chemical elements:

Magnesium

(Mg)

8 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 (E416Q) (pdb code 3iap). 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 (E416Q), PDB code: 3iap:
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 (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3101 b:11.7 occ:1.00 O A:LEU562 2.2 10.1 1.0 O A:PHE556 2.3 11.0 1.0 O A:HOH4649 2.3 25.7 1.0 O A:TYR559 2.4 10.5 1.0 O A:HOH4227 2.6 24.4 1.0 O A:PRO560 3.2 8.2 1.0 C A:LEU562 3.2 10.2 1.0 C A:TYR559 3.4 9.9 1.0 C A:PHE556 3.4 9.2 1.0 C A:PRO560 3.6 8.6 1.0 CA A:PRO560 3.8 9.3 1.0 N A:LEU562 3.9 8.6 1.0 N A:PRO560 4.0 10.2 1.0 O A:HOH4097 4.0 11.8 1.0 CA A:LEU562 4.0 8.5 1.0 O A:HOH4193 4.0 34.1 1.0 CA A:PHE556 4.1 8.8 1.0 N A:GLN563 4.1 9.4 1.0 CA A:GLN563 4.2 9.7 1.0 CB A:LEU562 4.3 8.5 1.0 N A:ARG561 4.5 8.9 1.0 N A:ARG557 4.5 8.3 1.0 CA A:TYR559 4.5 10.1 1.0 CG A:GLN563 4.6 8.0 1.0 N A:TYR559 4.6 8.8 1.0 CB A:PHE556 4.7 9.3 1.0 CD1 A:LEU350 4.7 8.1 1.0 CA A:ARG557 4.7 8.9 1.0 C A:ARG561 4.8 8.8 1.0 C A:ARG557 4.9 9.3 1.0 O A:ARG557 4.9 9.9 1.0 O A:ALA555 5.0 9.1 1.0

Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3102 b:41.7 occ:1.00 O A:HOH4610 2.6 29.8 1.0 O A:LEU967 2.6 21.7 1.0 O A:HOH4213 2.6 37.9 1.0 O A:THR970 2.7 28.5 1.0 O A:PRO932 2.9 18.7 1.0 O A:HOH4455 3.4 19.6 1.0 O A:MET968 3.6 24.9 1.0 CZ A:PHE931 3.6 38.6 1.0 C A:THR970 3.7 28.1 1.0 C A:LEU967 3.8 21.2 1.0 C A:MET968 3.8 25.3 1.0 CE1 A:PHE931 3.9 39.0 1.0 CE2 A:PHE931 3.9 38.7 1.0 C A:PRO932 3.9 18.6 1.0 CD A:PRO932 4.1 20.9 1.0 CA A:MET968 4.1 24.6 1.0 N A:THR970 4.2 27.4 1.0 CB A:PRO932 4.2 20.0 1.0 N A:PRO932 4.3 21.3 1.0 CA A:PRO932 4.4 19.9 1.0 CD1 A:PHE931 4.4 36.1 1.0 N A:MET968 4.4 22.3 1.0 CD2 A:PHE931 4.4 36.6 1.0 N A:GLU969 4.5 25.7 1.0 CA A:THR970 4.5 27.3 1.0 CG A:PRO932 4.5 20.2 1.0 N A:SER971 4.5 28.6 1.0 CA A:SER971 4.6 29.4 1.0 CG A:PHE931 4.6 32.1 1.0 C A:GLU969 4.9 27.3 1.0 C A:PHE931 4.9 22.7 1.0 CA A:LEU967 5.0 20.5 1.0

Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3103 b:31.5 occ:1.00 O A:LEU670 2.6 20.7 1.0 O A:SER647 2.7 17.8 1.0 O A:GLU650 2.8 16.3 1.0 O A:HOH4686 3.0 36.2 1.0 O A:HOH4687 3.2 31.7 1.0 N A:GLU650 3.5 17.0 1.0 C A:LEU670 3.8 22.2 1.0 C A:GLU650 3.8 17.7 1.0 C A:SER647 3.8 18.1 1.0 C A:ASP648 3.9 18.6 1.0 CA A:ASP648 4.0 19.3 1.0 N A:ASN649 4.0 17.4 1.0 CA A:GLU650 4.1 16.5 1.0 N A:LEU670 4.1 24.8 1.0 N A:ASP648 4.4 18.8 1.0 CA A:LEU670 4.4 23.2 1.0 O A:ASP648 4.4 19.2 1.0 CB A:GLU650 4.4 16.5 1.0 O A:HOH4217 4.5 36.4 1.0 OG A:SER647 4.5 15.9 1.0 C A:ASN649 4.5 16.2 1.0 CA A:ASN649 4.6 16.8 1.0 CB A:LEU670 4.7 23.0 1.0 N A:ASP671 4.9 21.5 1.0 C A:PRO669 4.9 26.4 1.0

Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3104 b:50.6 occ:1.00 O A:HOH4947 2.4 28.9 1.0 OD1 A:ASN604 2.6 27.9 1.0 O3 A:BTB6001 2.8 48.3 1.0 O A:PHE601 2.8 52.1 1.0 OD2 A:ASP201 3.1 48.8 1.0 O A:HOH4370 3.5 43.3 1.0 NE1 A:TRP568 3.6 16.2 1.0 CG A:ASN604 3.8 26.7 1.0 OH A:TYR100 3.8 72.2 1.0 C3 A:BTB6001 4.0 47.2 1.0 CG A:ASP201 4.0 45.4 1.0 C A:PHE601 4.0 52.5 1.0 CZ2 A:TRP568 4.2 15.5 1.0 OD1 A:ASP201 4.3 46.8 1.0 CE2 A:TRP568 4.3 16.0 1.0 ND2 A:ASN102 4.4 82.7 1.0 O A:ASP201 4.4 43.1 1.0 CA A:CYS602 4.4 45.1 1.0 ND2 A:ASN604 4.5 24.9 1.0 O8 A:BTB6001 4.5 54.9 1.0 N A:CYS602 4.7 48.6 1.0 CD1 A:TRP568 4.7 13.0 1.0 NE2 A:HIS540 4.8 16.8 1.0 CB A:ASN604 4.9 25.2 1.0 C8 A:BTB6001 4.9 51.4 1.0 C A:CYS602 5.0 42.1 1.0

Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3101 b:13.8 occ:1.00 O B:PHE556 2.2 7.5 1.0 O B:LEU562 2.4 8.9 1.0 O B:TYR559 2.4 11.5 1.0 O B:HOH4468 2.5 22.8 1.0 O B:HOH4437 2.6 20.8 1.0 O B:PRO560 3.3 7.7 1.0 C B:TYR559 3.4 10.4 1.0 C B:PHE556 3.4 8.4 1.0 C B:LEU562 3.4 8.1 1.0 C B:PRO560 3.7 8.8 1.0 CA B:PRO560 3.8 9.0 1.0 N B:PRO560 4.0 10.0 1.0 O B:HOH4249 4.1 10.7 1.0 O B:HOH4642 4.1 24.8 1.0 N B:LEU562 4.2 8.4 1.0 CA B:PHE556 4.2 7.9 1.0 CA B:LEU562 4.3 8.2 1.0 N B:GLN563 4.4 9.2 1.0 CA B:GLN563 4.4 8.9 1.0 N B:ARG557 4.4 9.2 1.0 CA B:TYR559 4.5 11.1 1.0 CB B:LEU562 4.5 8.1 1.0 N B:TYR559 4.5 10.8 1.0 CA B:ARG557 4.6 10.2 1.0 CD1 B:LEU350 4.6 9.7 1.0 N B:ARG561 4.6 7.1 1.0 C B:ARG557 4.7 10.7 1.0 O B:ARG557 4.7 9.9 1.0 O B:HOH4572 4.7 33.6 1.0 CG B:GLN563 4.8 9.9 1.0 CB B:PHE556 4.8 6.4 1.0

Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3102 b:47.0 occ:1.00 O B:HOH4518 2.5 42.7 1.0 O B:HOH4415 2.7 24.7 1.0 O B:THR970 2.8 28.5 1.0 O B:LEU967 2.8 19.9 1.0 O B:PRO932 2.9 20.0 1.0 O B:HOH4183 3.4 17.1 1.0 O B:MET968 3.5 23.3 1.0 C B:THR970 3.8 28.8 1.0 CE2 B:PHE931 3.9 39.8 1.0 C B:MET968 3.9 24.0 1.0 C B:LEU967 3.9 19.7 1.0 CZ B:PHE931 3.9 41.2 1.0 C B:PRO932 3.9 20.6 1.0 CD B:PRO932 4.1 23.0 1.0 CA B:MET968 4.1 23.8 1.0 CB B:PRO932 4.1 22.9 1.0 N B:PRO932 4.3 23.8 1.0 CD2 B:PHE931 4.3 37.5 1.0 N B:THR970 4.3 28.3 1.0 CA B:PRO932 4.4 22.4 1.0 CE1 B:PHE931 4.4 41.5 1.0 N B:MET968 4.5 21.1 1.0 CG B:PRO932 4.5 23.1 1.0 N B:SER971 4.6 28.7 1.0 CA B:SER971 4.6 29.2 1.0 CA B:THR970 4.6 28.2 1.0 N B:GLU969 4.6 25.0 1.0 CG B:PHE931 4.7 34.0 1.0 CD1 B:PHE931 4.8 38.8 1.0 O B:SER971 4.8 29.4 1.0 C B:GLU969 4.9 27.7 1.0 C B:PHE931 4.9 25.6 1.0 C B:SER971 5.0 29.4 1.0

Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3103 b:34.4 occ:1.00 O B:DMS7016 2.3 85.2 1.0 O B:SER647 2.6 16.6 1.0 O B:LEU670 2.7 20.7 1.0 O B:GLU650 2.8 17.6 1.0 N B:GLU650 3.4 16.9 1.0 S B:DMS7016 3.5 85.5 1.0 C B:GLU650 3.7 18.2 1.0 C B:SER647 3.8 16.6 1.0 C B:LEU670 3.8 21.4 1.0 C B:ASP648 3.9 18.8 1.0 N B:ASN649 3.9 17.6 1.0 CA B:ASP648 3.9 19.0 1.0 CA B:GLU650 4.0 17.4 1.0 N B:LEU670 4.1 23.8 1.0 C1 B:DMS7016 4.2 85.6 1.0 N B:ASP648 4.3 17.4 1.0 CB B:GLU650 4.4 17.3 1.0 O B:ASP648 4.4 19.7 1.0 C B:ASN649 4.4 16.9 1.0 CA B:LEU670 4.4 22.3 1.0 CA B:ASN649 4.5 16.7 1.0 OG B:SER647 4.6 15.7 1.0 CB B:LEU670 4.7 21.6 1.0 N B:ASP671 4.9 21.8 1.0 N B:LEU651 5.0 18.7 1.0 OE1 B:GLU650 5.0 16.0 1.0 CB B:SER647 5.0 15.1 1.0 C B:PRO669 5.0 24.6 1.0

Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3104 b:87.1 occ:1.00 O B:PHE601 2.1 55.7 1.0 ND2 B:ASN604 2.6 31.1 1.0 O B:HOH4695 2.7 28.4 1.0 OD2 B:ASP201 2.9 52.3 1.0 C6 B:BTB6001 3.2 0.1 1.0 O6 B:BTB6001 3.3 0.8 1.0 C B:PHE601 3.3 55.9 1.0 OH B:TYR100 3.6 87.6 1.0 O B:HOH4242 3.8 26.5 1.0 CG B:ASN604 3.8 30.3 1.0 C5 B:BTB6001 4.0 0.1 1.0 CA B:CYS602 4.0 47.8 1.0 N B:CYS602 4.1 51.8 1.0 CG B:ASP201 4.1 50.4 1.0 OD1 B:ASN604 4.2 31.1 1.0 NE1 B:TRP568 4.3 14.8 1.0 CA B:PHE601 4.4 58.7 1.0 CB B:PHE601 4.5 59.0 1.0 C B:CYS602 4.6 44.7 1.0 ND2 B:ASN102 4.7 94.8 1.0 OD1 B:ASP201 4.8 54.8 1.0 NE2 B:HIS540 4.8 16.9 1.0 CZ B:TYR100 4.9 88.0 1.0 CD2 B:PHE601 5.0 59.3 1.0

Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3101 b:17.6 occ:1.00 O C:PHE556 2.3 8.6 1.0 O C:LEU562 2.3 7.4 1.0 O C:HOH4485 2.4 23.8 1.0 O C:TYR559 2.5 12.5 1.0 O C:HOH4337 2.5 17.2 1.0 O C:PRO560 3.3 9.5 1.0 C C:LEU562 3.4 7.5 1.0 C C:PHE556 3.5 8.9 1.0 C C:TYR559 3.5 9.6 1.0 C C:PRO560 3.7 9.4 1.0 CA C:PRO560 3.8 9.4 1.0 O C:HOH4654 3.9 31.6 1.0 O C:HOH4248 4.0 12.9 1.0 N C:PRO560 4.1 10.3 1.0 N C:LEU562 4.2 6.7 1.0 CA C:PHE556 4.2 8.5 1.0 CA C:LEU562 4.3 6.6 1.0 CA C:GLN563 4.3 9.1 1.0 N C:GLN563 4.3 8.6 1.0 N C:ARG557 4.5 9.4 1.0 CD1 C:LEU350 4.5 14.1 1.0 CB C:LEU562 4.6 6.1 1.0 CA C:TYR559 4.6 10.7 1.0 N C:TYR559 4.6 9.4 1.0 N C:ARG561 4.6 7.8 1.0 CG C:GLN563 4.6 9.1 1.0 CA C:ARG557 4.7 11.0 1.0 O C:ARG557 4.7 11.5 1.0 CB C:PHE556 4.8 6.5 1.0 C C:ARG557 4.8 11.3 1.0 C C:ARG561 5.0 7.5 1.0

Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3102 b:44.9 occ:1.00 O C:HOH4538 2.5 51.4 1.0 O C:THR970 2.7 34.8 1.0 O C:LEU967 2.7 27.8 1.0 O C:PRO932 2.9 24.3 1.0 O C:HOH4434 2.9 25.8 1.0 O C:HOH4182 3.3 20.8 1.0 O C:MET968 3.6 30.3 1.0 C C:THR970 3.8 34.1 1.0 CZ C:PHE931 3.9 42.8 1.0 CE2 C:PHE931 3.9 41.3 1.0 C C:LEU967 3.9 27.3 1.0 C C:PRO932 3.9 23.8 1.0 C C:MET968 3.9 31.3 1.0 CD C:PRO932 4.1 27.2 1.0 CA C:MET968 4.2 30.7 1.0 CB C:PRO932 4.2 26.2 1.0 N C:PRO932 4.3 27.5 1.0 N C:THR970 4.3 33.9 1.0 CE1 C:PHE931 4.3 41.7 1.0 CD2 C:PHE931 4.3 40.2 1.0 CA C:PRO932 4.4 26.0 1.0 N C:MET968 4.5 28.6 1.0 CG C:PRO932 4.5 26.4 1.0 CA C:THR970 4.6 34.0 1.0 N C:SER971 4.7 34.3 1.0 N C:GLU969 4.7 32.2 1.0 CA C:SER971 4.7 33.9 1.0 CD1 C:PHE931 4.7 40.2 1.0 CG C:PHE931 4.7 36.0 1.0 C C:PHE931 4.9 28.5 1.0

S.Lo, M.L.Dugdale, N.Jeerh, T.Ku, N.J.Roth, R.E.Huber. Studies of Glu-416 Variants of Beta-Galactosidase (E. Coli) Show That the Active Site Mg(2+) Is Not Important For Structure and Indicate That the Main Role of Mg (2+) Is to Mediate Optimization of Active Site Chemistry Protein J. V. 29 26 2010.
ISSN: ISSN 1572-3887
PubMed: 19936901
DOI: 10.1007/S10930-009-9216-X