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Sodium in PDB 3vd7: E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole, PDB code: 3vd7 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) 44.78 / 2.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.460, 152.370, 135.110, 90.00, 104.25, 90.00
R / Rfree (%) 18.8 / 25

Other elements in 3vd7:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole (pdb code 3vd7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole, PDB code: 3vd7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3vd7

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Sodium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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 (N460S) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:46.9
occ:1.00
 OD1 A:ASN604 2.4 38.8 1.0
O A:PHE601 2.4 44.2 1.0
O6 A:GTZ2001 2.4 56.3 1.0
OD2 A:ASP201 2.4 48.5 1.0
C6 A:GTZ2001 3.1 71.1 1.0
CG A:ASN604 3.4 39.1 1.0
CG A:ASP201 3.4 48.7 1.0
C A:PHE601 3.6 42.3 1.0
OH A:TYR100 3.7 48.3 1.0
ND2 A:ASN604 3.8 41.5 1.0
O4 A:GTZ2001 3.9 81.0 1.0
OD1 A:ASP201 4.0 50.6 1.0
NE1 A:TRP568 4.0 41.9 1.0
C4 A:GTZ2001 4.2 76.9 1.0
C5 A:GTZ2001 4.2 77.0 1.0
CA A:CYS602 4.3 42.3 1.0
N A:CYS602 4.4 41.8 1.0
CB A:ASP201 4.5 46.5 1.0
NE2 A:HIS540 4.5 33.0 1.0
CA A:PHE601 4.6 42.6 1.0
CB A:PHE601 4.7 42.2 1.0
CZ2 A:TRP568 4.7 42.1 1.0
CE2 A:TRP568 4.8 39.6 1.0
CB A:ASN604 4.8 37.2 1.0
C A:CYS602 4.8 39.7 1.0
CZ A:TYR100 4.9 47.0 1.0
CE1 A:HIS540 5.0 29.9 1.0
O A:ASP201 5.0 47.2 1.0

Sodium binding site 2 out of 8 in 3vd7

Go back to Sodium Binding Sites List in 3vd7
Sodium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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 (N460S) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2102

b:25.6
occ:1.00
 O A:HOH4064 2.3 37.2 1.0
O A:PHE556 2.4 24.4 1.0
O A:TYR559 2.4 24.3 1.0
O A:LEU562 2.6 25.9 1.0
O A:PRO560 3.3 23.3 1.0
C A:TYR559 3.4 22.9 1.0
C A:PHE556 3.6 21.7 1.0
CA A:PRO560 3.6 21.9 1.0
C A:PRO560 3.7 22.6 1.0
C A:LEU562 3.8 26.0 1.0
N A:PRO560 3.9 22.6 1.0
CA A:ARG557 4.4 24.2 1.0
N A:ARG557 4.4 23.0 1.0
O A:ARG557 4.4 30.6 1.0
C A:ARG557 4.5 26.2 1.0
CA A:PHE556 4.5 20.1 1.0
N A:LEU562 4.5 23.0 1.0
CA A:TYR559 4.6 22.8 1.0
N A:TYR559 4.7 23.8 1.0
CA A:LEU562 4.7 22.5 1.0
N A:GLN563 4.7 24.8 1.0
CA A:GLN563 4.8 25.0 1.0
N A:ARG561 4.8 22.6 1.0
CG A:GLN563 4.9 21.6 1.0
CD1 A:LEU350 4.9 20.6 1.0
CB A:LEU562 4.9 19.5 1.0

Sodium binding site 3 out of 8 in 3vd7

Go back to Sodium Binding Sites List in 3vd7
Sodium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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 (N460S) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:44.9
occ:1.00
 O B:HOH4093 2.3 40.5 1.0
O B:PHE601 2.4 43.3 1.0
OD1 B:ASN604 2.4 47.0 1.0
O6 B:GTZ2001 2.4 53.3 1.0
OD2 B:ASP201 2.4 48.7 1.0
C6 B:GTZ2001 2.9 65.0 1.0
CG B:ASN604 3.3 47.5 1.0
CG B:ASP201 3.5 45.7 1.0
C B:PHE601 3.5 45.7 1.0
ND2 B:ASN604 3.6 48.3 1.0
OH B:TYR100 3.8 41.7 1.0
NE1 B:TRP568 3.8 27.8 1.0
O4 B:GTZ2001 3.9 67.3 1.0
OD1 B:ASP201 4.0 47.9 1.0
C5 B:GTZ2001 4.1 70.0 1.0
C4 B:GTZ2001 4.1 69.3 1.0
CA B:CYS602 4.2 41.9 1.0
N B:CYS602 4.2 43.4 1.0
NE2 B:HIS540 4.5 31.0 1.0
CA B:PHE601 4.5 49.0 1.0
CB B:ASN604 4.5 45.7 1.0
CB B:PHE601 4.6 51.4 1.0
CE2 B:TRP568 4.6 28.6 1.0
CB B:ASP201 4.7 43.1 1.0
CZ2 B:TRP568 4.7 29.7 1.0
C B:CYS602 4.7 41.9 1.0
O B:ASP201 4.7 40.4 1.0
CD1 B:TRP568 4.8 25.6 1.0
CE1 B:HIS540 5.0 25.0 1.0

Sodium binding site 4 out of 8 in 3vd7

Go back to Sodium Binding Sites List in 3vd7
Sodium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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 (N460S) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:19.7
occ:1.00
 O B:PHE556 2.4 21.2 1.0
O B:TYR559 2.4 20.0 1.0
O B:LEU562 2.4 20.0 1.0
O B:HOH4016 2.8 20.9 1.0
O B:PRO560 3.1 19.7 1.0
C B:TYR559 3.4 22.8 1.0
C B:LEU562 3.5 21.3 1.0
C B:PHE556 3.6 19.5 1.0
C B:PRO560 3.6 18.1 1.0
CA B:PRO560 3.7 20.5 1.0
N B:PRO560 4.0 21.1 1.0
CA B:GLN563 4.3 18.8 1.0
N B:LEU562 4.3 19.8 1.0
N B:GLN563 4.4 20.0 1.0
CA B:PHE556 4.4 18.4 1.0
CA B:LEU562 4.4 22.0 1.0
CA B:TYR559 4.5 21.9 1.0
N B:ARG557 4.6 19.5 1.0
N B:TYR559 4.6 25.4 1.0
CA B:ARG557 4.6 19.8 1.0
N B:ARG561 4.7 17.3 1.0
O B:ARG557 4.7 23.9 1.0
C B:ARG557 4.7 20.1 1.0
CB B:LEU562 4.7 22.9 1.0
CG B:GLN563 4.7 16.0 1.0
CD1 B:LEU350 4.7 17.9 1.0
CB B:PHE556 5.0 18.3 1.0

Sodium binding site 5 out of 8 in 3vd7

Go back to Sodium Binding Sites List in 3vd7
Sodium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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 (N460S) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:49.4
occ:1.00
 OD1 C:ASN604 2.4 35.0 1.0
O C:PHE601 2.4 44.1 1.0
OD2 C:ASP201 2.4 39.0 1.0
O6 C:GTZ2001 2.4 51.7 1.0
O C:HOH4077 2.4 38.1 1.0
C6 C:GTZ2001 3.2 58.8 1.0
CG C:ASN604 3.4 34.3 1.0
CG C:ASP201 3.4 37.8 1.0
OH C:TYR100 3.6 45.9 1.0
C C:PHE601 3.6 43.6 1.0
ND2 C:ASN604 3.8 39.4 1.0
NE1 C:TRP568 3.9 27.6 1.0
O4 C:GTZ2001 3.9 60.9 1.0
OD1 C:ASP201 4.0 44.5 1.0
C4 C:GTZ2001 4.1 61.9 1.0
C5 C:GTZ2001 4.2 62.4 1.0
CA C:CYS602 4.2 42.5 1.0
N C:CYS602 4.3 42.2 1.0
CB C:ASP201 4.5 33.9 1.0
NE2 C:HIS540 4.6 26.0 1.0
O C:ASP201 4.6 32.1 1.0
CZ2 C:TRP568 4.6 35.1 1.0
CE2 C:TRP568 4.6 33.1 1.0
CB C:ASN604 4.7 32.2 1.0
CA C:PHE601 4.7 45.9 1.0
C C:CYS602 4.7 41.1 1.0
CB C:PHE601 4.7 47.7 1.0
CZ C:TYR100 4.8 43.6 1.0
O C:CYS602 4.9 41.2 1.0
CD1 C:TRP568 5.0 31.3 1.0

Sodium binding site 6 out of 8 in 3vd7

Go back to Sodium Binding Sites List in 3vd7
Sodium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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 (N460S) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:29.1
occ:1.00
 O C:HOH4078 2.1 40.2 1.0
O C:LEU562 2.4 25.1 1.0
O C:PHE556 2.4 22.9 1.0
O C:TYR559 2.4 25.3 1.0
C C:LEU562 3.3 22.8 1.0
C C:TYR559 3.4 22.3 1.0
O C:PRO560 3.5 26.6 1.0
C C:PHE556 3.5 18.7 1.0
C C:PRO560 3.7 25.3 1.0
CA C:PRO560 3.8 24.1 1.0
N C:PRO560 3.9 23.5 1.0
N C:LEU562 4.1 19.2 1.0
CA C:LEU562 4.1 19.7 1.0
N C:GLN563 4.2 22.7 1.0
O C:HOH4063 4.2 31.0 1.0
CA C:GLN563 4.2 22.7 1.0
CA C:PHE556 4.3 17.1 1.0
CB C:LEU562 4.4 16.8 1.0
CA C:TYR559 4.5 20.5 1.0
N C:ARG557 4.5 19.2 1.0
N C:TYR559 4.6 22.1 1.0
N C:ARG561 4.6 20.1 1.0
CG C:GLN563 4.7 16.3 1.0
CA C:ARG557 4.7 19.8 1.0
CD1 C:LEU350 4.7 26.2 1.0
C C:ARG557 4.7 19.2 1.0
O C:ARG557 4.8 21.1 1.0
CB C:PHE556 4.8 17.7 1.0
C C:ARG561 5.0 18.8 1.0

Sodium binding site 7 out of 8 in 3vd7

Go back to Sodium Binding Sites List in 3vd7
Sodium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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 (N460S) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3101

b:46.2
occ:1.00
 O D:HOH4123 2.2 30.4 1.0
OD1 D:ASN604 2.4 27.1 1.0
O6 D:GTZ2001 2.4 63.8 1.0
OD2 D:ASP201 2.4 49.1 1.0
O D:PHE601 2.5 37.1 1.0
C6 D:GTZ2001 3.1 80.2 1.0
CG D:ASP201 3.4 45.6 1.0
CG D:ASN604 3.4 32.0 1.0
O4 D:GTZ2001 3.4 80.4 1.0
C D:PHE601 3.7 39.3 1.0
NE1 D:TRP568 3.8 41.5 1.0
OH D:TYR100 3.9 55.2 1.0
ND2 D:ASN604 3.9 31.9 1.0
C4 D:GTZ2001 4.0 80.9 1.0
OD1 D:ASP201 4.0 49.6 1.0
C5 D:GTZ2001 4.1 83.3 1.0
CA D:CYS602 4.3 33.8 1.0
CZ2 D:TRP568 4.3 32.5 1.0
N D:CYS602 4.4 36.9 1.0
CE2 D:TRP568 4.4 35.8 1.0
CB D:ASP201 4.5 41.9 1.0
O D:ASP201 4.5 39.5 1.0
NE2 D:HIS540 4.5 22.4 1.0
CB D:PHE601 4.7 43.1 1.0
CA D:PHE601 4.7 42.7 1.0
CB D:ASN604 4.7 29.9 1.0
C D:CYS602 4.9 33.3 1.0
CD1 D:TRP568 4.9 35.9 1.0
CZ D:TYR100 5.0 44.6 1.0

Sodium binding site 8 out of 8 in 3vd7

Go back to Sodium Binding Sites List in 3vd7
Sodium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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 (N460S) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3102

b:21.7
occ:1.00
 O D:LEU562 2.4 16.7 1.0
O D:PHE556 2.4 22.9 1.0
O D:TYR559 2.4 23.2 1.0
O D:HOH4086 2.9 17.7 1.0
O D:HOH4114 3.0 41.1 1.0
C D:TYR559 3.4 22.5 1.0
O D:PRO560 3.5 24.8 1.0
C D:PHE556 3.5 21.5 1.0
C D:LEU562 3.5 16.9 1.0
CA D:PRO560 3.8 20.8 1.0
C D:PRO560 3.8 22.6 1.0
N D:PRO560 4.0 22.2 1.0
N D:LEU562 4.3 19.6 1.0
CA D:PHE556 4.4 20.4 1.0
CA D:LEU562 4.4 15.6 1.0
N D:GLN563 4.4 16.0 1.0
CA D:GLN563 4.4 15.7 1.0
N D:ARG557 4.5 21.4 1.0
CA D:TYR559 4.6 19.4 1.0
N D:TYR559 4.6 19.8 1.0
CA D:ARG557 4.6 17.3 1.0
CG D:GLN563 4.6 8.9 1.0
CB D:LEU562 4.7 10.8 1.0
N D:ARG561 4.7 19.9 1.0
C D:ARG557 4.7 17.4 1.0
CD1 D:LEU350 4.7 13.6 1.0
O D:ARG557 4.8 17.9 1.0
CB D:PHE556 4.9 23.8 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 13:41:11 2024

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