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Sodium in PDB 3vd4: E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg, PDB code: 3vd4 was solved by R.W.Wheatley, J.C.Kappelhoff, J.N.Hahn, M.L.Dugdale, M.J.Dutkoski, S.D.Tamman, M.E.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.90 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.762, 162.446, 203.360, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.2

Other elements in 3vd4:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Sodium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg (pdb code 3vd4). 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 (N460D) in Complex with Iptg, PDB code: 3vd4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 3vd4

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Sodium binding site 1 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:26.3
occ:1.00
 O A:HOH4255 2.3 29.3 1.0
OD1 A:ASN604 2.4 23.1 1.0
O6 A:IPT2001 2.4 20.9 0.9
O A:PHE601 2.4 26.8 1.0
OD2 A:ASP201 2.4 25.7 1.0
CG A:ASP201 3.2 23.6 1.0
CG A:ASN604 3.3 19.8 1.0
C6 A:IPT2001 3.4 20.4 0.9
C A:PHE601 3.5 26.1 1.0
OD1 A:ASP201 3.5 27.5 1.0
ND2 A:ASN604 3.6 22.3 1.0
OH A:TYR100 3.7 25.3 1.0
NE1 A:TRP568 4.0 19.5 1.0
O4 A:IPT2001 4.1 20.3 0.9
O A:HOH4050 4.1 23.3 1.0
CA A:CYS602 4.2 23.9 1.0
N A:CYS602 4.3 24.9 1.0
C4 A:IPT2001 4.4 23.7 0.9
C5 A:IPT2001 4.4 23.9 0.9
CB A:ASP201 4.5 20.5 1.0
O A:ASP201 4.5 17.9 1.0
CA A:PHE601 4.6 24.1 1.0
NE2 A:HIS540 4.6 14.6 1.0
C A:CYS602 4.6 21.8 1.0
CB A:PHE601 4.7 20.8 1.0
CB A:ASN604 4.7 19.9 1.0
CE2 A:TRP568 4.7 20.7 1.0
CZ2 A:TRP568 4.8 23.6 1.0
CZ A:TYR100 4.8 34.0 1.0
O A:CYS602 4.9 23.4 1.0

Sodium binding site 2 out of 14 in 3vd4

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Sodium binding site 2 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:17.8
occ:1.00
 O A:PHE556 2.4 16.6 1.0
O A:LEU562 2.4 14.4 1.0
O A:TYR559 2.4 17.8 1.0
O A:HOH4354 2.5 28.0 1.0
O A:HOH4500 2.6 27.4 1.0
O A:PRO560 3.2 11.8 1.0
C A:LEU562 3.4 12.6 1.0
C A:TYR559 3.4 13.3 1.0
C A:PHE556 3.5 14.7 1.0
C A:PRO560 3.7 14.6 1.0
O A:HOH4585 3.7 47.5 1.0
CA A:PRO560 3.8 13.7 1.0
O A:HOH4261 3.9 22.2 1.0
N A:PRO560 4.0 14.2 1.0
N A:LEU562 4.1 11.9 1.0
CA A:LEU562 4.2 12.1 1.0
CA A:PHE556 4.3 13.3 1.0
N A:GLN563 4.3 13.4 1.0
CA A:GLN563 4.3 13.0 1.0
CB A:LEU562 4.5 9.0 1.0
CA A:TYR559 4.5 11.9 1.0
N A:ARG557 4.6 14.5 1.0
N A:TYR559 4.6 11.5 1.0
N A:ARG561 4.6 10.4 1.0
CG A:GLN563 4.7 12.0 1.0
CA A:ARG557 4.7 15.3 1.0
CD1 A:LEU350 4.7 11.9 1.0
C A:ARG557 4.8 16.2 1.0
CB A:PHE556 4.9 12.5 1.0
O A:ARG557 4.9 14.9 1.0
C A:ARG561 4.9 11.3 1.0

Sodium binding site 3 out of 14 in 3vd4

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Sodium binding site 3 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:36.3
occ:1.00
 O A:HOH4549 2.6 39.5 1.0
O A:LEU967 2.6 24.3 1.0
O A:PRO932 2.6 16.2 1.0
O A:THR970 2.7 33.8 1.0
O A:HOH4193 2.9 22.9 1.0
O A:HOH4448 3.2 30.2 1.0
CZ A:PHE931 3.5 24.8 1.0
C A:PRO932 3.6 21.4 1.0
C A:LEU967 3.7 24.6 1.0
CE1 A:PHE931 3.7 26.0 1.0
C A:THR970 3.8 31.8 1.0
CE2 A:PHE931 3.9 22.5 1.0
O A:MET968 3.9 28.9 1.0
CA A:MET968 3.9 29.9 1.0
C A:MET968 4.0 30.5 1.0
CB A:PRO932 4.1 22.5 1.0
CD A:PRO932 4.1 22.3 1.0
CA A:PRO932 4.2 21.9 1.0
N A:PRO932 4.2 23.2 1.0
N A:MET968 4.3 27.1 1.0
CD1 A:PHE931 4.3 28.9 1.0
N A:THR970 4.4 29.9 1.0
CD2 A:PHE931 4.4 27.3 1.0
CG A:PRO932 4.5 21.6 1.0
CA A:SER971 4.5 29.9 1.0
N A:SER971 4.6 29.8 1.0
N A:SER933 4.6 19.2 1.0
CG A:PHE931 4.7 26.0 1.0
N A:GLU969 4.7 29.2 1.0
CA A:THR970 4.7 30.6 1.0
CA A:LEU967 4.9 25.8 1.0
C A:PHE931 5.0 25.1 1.0
CA A:SER933 5.0 19.9 1.0

Sodium binding site 4 out of 14 in 3vd4

Go back to Sodium Binding Sites List in 3vd4
Sodium binding site 4 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:16.9
occ:1.00
 O6 B:IPT2001 2.3 17.6 1.0
O B:HOH4279 2.3 20.6 1.0
O B:PHE601 2.4 17.3 1.0
OD1 B:ASN604 2.4 15.4 1.0
OD2 B:ASP201 2.4 16.5 1.0
C6 B:IPT2001 3.3 18.5 1.0
CG B:ASP201 3.3 18.8 1.0
CG B:ASN604 3.4 17.0 1.0
C B:PHE601 3.5 17.0 1.0
OD1 B:ASP201 3.6 18.4 1.0
OH B:TYR100 3.6 13.2 1.0
ND2 B:ASN604 3.7 11.2 1.0
NE1 B:TRP568 4.0 12.1 1.0
O4 B:IPT2001 4.0 15.6 1.0
CA B:CYS602 4.2 16.6 1.0
O B:HOH4061 4.3 19.2 1.0
N B:CYS602 4.3 16.0 1.0
C5 B:IPT2001 4.4 20.5 1.0
C4 B:IPT2001 4.4 24.4 1.0
CB B:ASP201 4.5 10.4 1.0
CA B:PHE601 4.5 16.6 1.0
CB B:PHE601 4.6 16.8 1.0
NE2 B:HIS540 4.6 10.7 1.0
O B:ASP201 4.6 13.4 1.0
C B:CYS602 4.7 16.2 1.0
CB B:ASN604 4.7 11.8 1.0
CZ B:TYR100 4.8 16.9 1.0
CE2 B:TRP568 4.8 13.7 1.0
CZ2 B:TRP568 4.8 13.5 1.0
O B:CYS602 5.0 15.5 1.0

Sodium binding site 5 out of 14 in 3vd4

Go back to Sodium Binding Sites List in 3vd4
Sodium binding site 5 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:20.0
occ:1.00
 O B:HOH4682 2.1 33.0 1.0
O B:PHE556 2.4 14.8 1.0
O B:TYR559 2.4 16.4 1.0
O B:LEU562 2.4 16.0 1.0
O B:HOH4396 2.6 25.3 1.0
O B:PRO560 3.2 14.5 1.0
C B:LEU562 3.4 13.9 1.0
C B:TYR559 3.4 14.0 1.0
C B:PHE556 3.5 12.4 1.0
C B:PRO560 3.6 14.6 1.0
CA B:PRO560 3.7 11.1 1.0
N B:PRO560 4.0 13.8 1.0
N B:LEU562 4.0 9.5 1.0
O B:HOH4286 4.1 20.4 1.0
CA B:LEU562 4.1 14.1 1.0
O B:HOH4702 4.2 31.3 1.0
CA B:PHE556 4.2 13.2 1.0
N B:GLN563 4.3 12.8 1.0
CA B:GLN563 4.3 12.8 1.0
CB B:LEU562 4.4 13.7 1.0
CA B:TYR559 4.5 15.3 1.0
N B:TYR559 4.5 14.6 1.0
N B:ARG561 4.5 11.3 1.0
N B:ARG557 4.6 10.5 1.0
CG B:GLN563 4.7 11.3 1.0
CA B:ARG557 4.8 14.8 1.0
CD1 B:LEU350 4.8 13.3 1.0
CB B:PHE556 4.8 9.9 1.0
C B:ARG557 4.9 13.6 1.0
O B:ARG557 4.9 11.4 1.0
C B:ARG561 4.9 13.5 1.0

Sodium binding site 6 out of 14 in 3vd4

Go back to Sodium Binding Sites List in 3vd4
Sodium binding site 6 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:37.8
occ:1.00
 O B:PRO932 2.6 19.0 1.0
O B:LEU967 2.6 20.8 1.0
O B:HOH4212 2.8 17.3 1.0
O B:THR970 2.9 24.3 1.0
O B:HOH4630 2.9 36.1 1.0
O B:HOH4896 3.3 34.4 1.0
CZ B:PHE931 3.5 22.0 1.0
C B:PRO932 3.6 18.2 1.0
CE1 B:PHE931 3.7 23.7 1.0
C B:LEU967 3.7 18.4 1.0
O B:MET968 3.8 23.0 1.0
CA B:MET968 3.8 21.5 1.0
C B:THR970 3.9 23.8 1.0
CE2 B:PHE931 3.9 15.7 1.0
C B:MET968 3.9 21.0 1.0
CB B:PRO932 4.2 20.4 1.0
CD B:PRO932 4.2 19.2 1.0
CA B:PRO932 4.2 18.9 1.0
N B:PRO932 4.2 18.1 1.0
N B:MET968 4.3 19.3 1.0
N B:THR970 4.3 21.5 1.0
CD1 B:PHE931 4.3 22.8 1.0
CD2 B:PHE931 4.5 18.5 1.0
N B:GLU969 4.7 18.8 1.0
N B:SER971 4.7 21.7 1.0
N B:SER933 4.7 16.4 1.0
CA B:SER971 4.7 23.6 1.0
CG B:PRO932 4.7 19.3 1.0
CG B:PHE931 4.7 17.6 1.0
CA B:THR970 4.7 22.2 1.0
CA B:LEU967 4.9 20.0 1.0
O B:HOH4649 5.0 37.2 1.0
C B:PHE931 5.0 18.4 1.0
CA B:SER933 5.0 16.6 1.0

Sodium binding site 7 out of 14 in 3vd4

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Sodium binding site 7 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:38.0
occ:1.00
 O B:GLU650 2.7 21.3 1.0
O B:SER647 2.7 25.3 1.0
O B:LEU670 2.8 23.2 1.0
O B:HOH4858 2.9 35.0 1.0
N B:GLU650 3.2 18.2 1.0
C B:GLU650 3.6 20.4 1.0
C B:ASP648 3.8 19.6 1.0
N B:ASN649 3.8 17.7 1.0
CA B:GLU650 3.8 19.7 1.0
C B:SER647 3.8 24.8 1.0
C B:LEU670 4.0 23.3 1.0
CA B:ASP648 4.0 23.7 1.0
N B:LEU670 4.2 28.0 1.0
O B:ASP648 4.2 22.2 1.0
C B:ASN649 4.2 17.6 1.0
CB B:GLU650 4.2 17.1 1.0
CA B:ASN649 4.3 17.7 1.0
N B:ASP648 4.4 24.1 1.0
CA B:LEU670 4.5 26.5 1.0
OG B:SER647 4.6 18.9 1.0
CB B:LEU670 4.7 25.4 1.0
N B:LEU651 4.8 20.8 1.0
OE1 B:GLU650 4.9 21.7 1.0

Sodium binding site 8 out of 14 in 3vd4

Go back to Sodium Binding Sites List in 3vd4
Sodium binding site 8 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:16.1
occ:1.00
 O C:HOH4284 2.2 26.7 1.0
O C:PHE601 2.4 15.8 1.0
OD1 C:ASN604 2.4 16.4 1.0
O6 C:IPT2001 2.4 23.1 1.0
OD2 C:ASP201 2.4 20.4 1.0
CG C:ASP201 3.2 21.7 1.0
CG C:ASN604 3.3 14.6 1.0
C6 C:IPT2001 3.4 20.6 1.0
C C:PHE601 3.5 13.7 1.0
OH C:TYR100 3.5 16.8 1.0
OD1 C:ASP201 3.6 18.7 1.0
ND2 C:ASN604 3.6 11.0 1.0
O4 C:IPT2001 4.0 16.0 1.0
NE1 C:TRP568 4.0 11.4 1.0
CA C:CYS602 4.2 16.7 1.0
O C:HOH4066 4.3 14.9 1.0
N C:CYS602 4.3 14.3 1.0
C4 C:IPT2001 4.4 21.1 1.0
C5 C:IPT2001 4.4 24.3 1.0
CB C:ASP201 4.4 11.9 1.0
O C:ASP201 4.5 14.6 1.0
CA C:PHE601 4.6 13.0 1.0
CB C:PHE601 4.6 11.3 1.0
C C:CYS602 4.6 15.8 1.0
CZ C:TYR100 4.7 15.9 1.0
CB C:ASN604 4.7 14.0 1.0
NE2 C:HIS540 4.7 8.8 1.0
CE2 C:TRP568 4.8 14.2 1.0
CZ2 C:TRP568 4.8 14.4 1.0

Sodium binding site 9 out of 14 in 3vd4

Go back to Sodium Binding Sites List in 3vd4
Sodium binding site 9 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:18.3
occ:1.00
 O C:HOH4581 2.4 35.1 1.0
O C:PHE556 2.4 16.2 1.0
O C:LEU562 2.4 13.3 1.0
O C:TYR559 2.4 15.5 1.0
O C:HOH4402 2.7 24.4 1.0
O C:PRO560 3.3 15.0 1.0
C C:LEU562 3.4 13.1 1.0
C C:TYR559 3.4 12.5 1.0
C C:PHE556 3.5 14.7 1.0
C C:PRO560 3.6 14.1 1.0
CA C:PRO560 3.7 11.8 1.0
N C:PRO560 4.0 13.4 1.0
N C:LEU562 4.1 8.6 1.0
O C:HOH4290 4.1 21.8 1.0
CA C:PHE556 4.2 15.6 1.0
CA C:LEU562 4.2 11.0 1.0
N C:GLN563 4.2 10.9 1.0
CA C:GLN563 4.3 10.8 1.0
CB C:LEU562 4.5 11.2 1.0
CA C:TYR559 4.5 13.0 1.0
N C:TYR559 4.5 12.8 1.0
N C:ARG561 4.6 11.4 1.0
N C:ARG557 4.6 13.5 1.0
CD1 C:LEU350 4.6 13.6 1.0
CG C:GLN563 4.7 13.4 1.0
CA C:ARG557 4.8 15.4 1.0
CB C:PHE556 4.8 10.4 1.0
C C:ARG557 4.8 15.9 1.0
O C:ARG557 4.8 16.5 1.0
C C:ARG561 4.9 12.7 1.0
O C:ALA555 5.0 14.0 1.0

Sodium binding site 10 out of 14 in 3vd4

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Sodium binding site 10 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460D) 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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3103

b:35.5
occ:1.00
 O C:HOH4644 2.5 36.7 1.0
O C:LEU967 2.6 22.3 1.0
O C:PRO932 2.6 18.1 1.0
O C:THR970 2.7 25.1 1.0
O C:HOH4216 3.0 15.0 1.0
O C:HOH4519 3.4 27.4 1.0
CZ C:PHE931 3.5 19.5 1.0
C C:PRO932 3.6 17.5 1.0
CE1 C:PHE931 3.7 21.3 1.0
C C:LEU967 3.7 17.7 1.0
C C:THR970 3.7 26.2 1.0
O C:MET968 3.8 23.8 1.0
CA C:MET968 3.9 23.6 1.0
CE2 C:PHE931 3.9 18.0 1.0
C C:MET968 3.9 23.1 1.0
CB C:PRO932 4.0 18.1 1.0
CD C:PRO932 4.1 16.8 1.0
CA C:PRO932 4.2 17.6 1.0
N C:PRO932 4.2 21.2 1.0
N C:THR970 4.3 20.7 1.0
N C:MET968 4.3 19.5 1.0
CD1 C:PHE931 4.3 24.3 1.0
CD2 C:PHE931 4.5 22.0 1.0
CG C:PRO932 4.5 17.5 1.0
N C:SER971 4.6 23.8 1.0
CA C:SER971 4.6 25.3 1.0
CA C:THR970 4.6 21.9 1.0
N C:SER933 4.6 16.9 1.0
CG C:PHE931 4.7 20.4 1.0
N C:GLU969 4.7 20.0 1.0
C C:PHE931 4.9 19.7 1.0
CA C:LEU967 4.9 17.1 1.0
CA C:SER933 5.0 16.0 1.0

Reference:

R.W.Wheatley, J.C.Kappelhoff, J.N.Hahn, M.L.Dugdale, M.J.Dutkoski, S.D.Tamman, M.E.Fraser, R.E.Huber. Substitution For ASN460 Cripples {Beta}-Galactosidase (Escherichia Coli) By Increasing Substrate Affinity and Decreasing Transition State Stability. Arch.Biochem.Biophys. V. 521 51 2012.
ISSN: ISSN 0003-9861
PubMed: 22446164
DOI: 10.1016/J.ABB.2012.03.014
Page generated: Mon Oct 7 13:41:09 2024

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