Atomistry » Sodium » PDB 3v45-3vi2 » 3vda
Atomistry »
  Sodium »
    PDB 3v45-3vi2 »
      3vda »

Sodium in PDB 3vda: E. Coli (Lacz) Beta-Galactosidase (N460T)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T), PDB code: 3vda 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) 46.05 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 152.596, 164.691, 203.245, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23.7

Other elements in 3vda:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (N460T) (pdb code 3vda). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460T), PDB code: 3vda:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 1 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:42.0
occ:1.00
 O A:HOH4311 2.3 43.7 1.0
O A:PHE601 2.4 40.6 1.0
OD1 A:ASN604 2.4 41.0 1.0
OD2 A:ASP201 2.4 49.2 1.0
CG A:ASP201 3.2 44.1 1.0
O A:HOH4286 3.3 44.1 1.0
CG A:ASN604 3.4 37.8 1.0
C A:PHE601 3.6 40.1 1.0
OD1 A:ASP201 3.6 47.3 1.0
ND2 A:ASN604 3.7 25.8 1.0
OH A:TYR100 3.8 49.3 1.0
O A:HOH4397 4.0 48.6 1.0
NE1 A:TRP568 4.1 37.8 1.0
CA A:CYS602 4.3 36.4 1.0
N A:CYS602 4.4 39.4 1.0
CB A:ASP201 4.4 38.5 1.0
CA A:PHE601 4.6 39.2 1.0
O A:HOH4084 4.6 37.1 1.0
CB A:PHE601 4.6 40.4 1.0
NE2 A:HIS540 4.7 34.7 1.0
CZ2 A:TRP568 4.7 34.4 1.0
O A:ASP201 4.7 39.5 1.0
CE2 A:TRP568 4.8 35.9 1.0
CB A:ASN604 4.8 37.0 1.0
C A:CYS602 4.9 35.8 1.0
ND2 A:ASN102 4.9 43.8 1.0

Sodium binding site 2 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 2 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:36.3
occ:1.00
 O A:PHE556 2.4 34.4 1.0
O A:TYR559 2.4 30.9 1.0
O A:LEU562 2.4 32.9 1.0
O A:HOH4041 2.4 44.7 1.0
O A:HOH4312 2.8 58.9 1.0
O A:PRO560 3.2 29.6 1.0
C A:TYR559 3.4 30.9 1.0
C A:LEU562 3.5 30.7 1.0
C A:PHE556 3.6 32.4 1.0
C A:PRO560 3.6 28.2 1.0
CA A:PRO560 3.6 28.6 1.0
N A:PRO560 3.9 30.0 1.0
N A:LEU562 4.1 28.7 1.0
CA A:LEU562 4.3 28.9 1.0
CA A:PHE556 4.3 30.1 1.0
N A:GLN563 4.5 31.4 1.0
CA A:TYR559 4.5 31.9 1.0
N A:ARG561 4.5 25.0 1.0
N A:TYR559 4.6 32.5 1.0
CA A:GLN563 4.6 31.6 1.0
CB A:LEU562 4.6 28.6 1.0
N A:ARG557 4.6 31.4 1.0
O A:ARG557 4.6 35.2 1.0
CA A:ARG557 4.7 32.2 1.0
C A:ARG557 4.7 33.7 1.0
CG A:GLN563 4.9 29.3 1.0
CD1 A:LEU350 4.9 29.9 1.0
C A:ARG561 5.0 27.4 1.0

Sodium binding site 3 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 3 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:41.4
occ:1.00
 O A:HOH4014 2.2 39.7 1.0
O A:PRO932 2.4 41.0 1.0
O A:LEU967 2.6 42.7 1.0
O A:HOH4065 2.7 50.9 1.0
O A:THR970 2.8 49.0 1.0
C A:PRO932 3.4 41.0 1.0
CZ A:PHE931 3.7 44.6 1.0
C A:LEU967 3.7 45.5 1.0
CA A:MET968 3.9 48.3 1.0
CE2 A:PHE931 3.9 46.1 1.0
O A:MET968 4.0 52.4 1.0
C A:MET968 4.0 50.0 1.0
C A:THR970 4.0 48.3 1.0
CE1 A:PHE931 4.1 46.1 1.0
CA A:PRO932 4.1 40.6 1.0
CB A:PRO932 4.1 41.0 1.0
CD A:PRO932 4.1 42.4 1.0
N A:PRO932 4.1 41.0 1.0
N A:MET968 4.3 45.4 1.0
CD2 A:PHE931 4.4 46.5 1.0
N A:SER933 4.5 40.8 1.0
N A:THR970 4.5 47.5 1.0
CD1 A:PHE931 4.6 49.7 1.0
CG A:PRO932 4.6 41.6 1.0
N A:GLU969 4.7 51.1 1.0
CG A:PHE931 4.8 46.9 1.0
CA A:SER933 4.9 39.1 1.0
CA A:THR970 4.9 46.3 1.0
CA A:LEU967 4.9 43.2 1.0
CA A:SER971 4.9 48.9 1.0
N A:SER971 4.9 47.1 1.0
C A:PHE931 5.0 43.0 1.0

Sodium binding site 4 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 4 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:44.5
occ:1.00
 OD2 B:ASP201 2.4 46.5 1.0
OD1 B:ASN604 2.4 44.0 1.0
O B:HOH4274 2.5 49.3 1.0
O B:HOH4372 2.7 61.6 1.0
O B:PHE601 2.7 39.9 1.0
CG B:ASP201 3.3 39.8 1.0
CG B:ASN604 3.5 41.8 1.0
OD1 B:ASP201 3.7 42.1 1.0
OH B:TYR100 3.8 43.9 1.0
C B:PHE601 3.8 40.4 1.0
ND2 B:ASN604 4.0 40.0 1.0
NE1 B:TRP568 4.1 31.0 1.0
CA B:CYS602 4.4 40.0 1.0
CB B:ASP201 4.5 35.6 1.0
N B:CYS602 4.5 40.1 1.0
O B:ASP201 4.6 37.0 1.0
CZ2 B:TRP568 4.7 32.7 1.0
NE2 B:HIS540 4.7 38.8 1.0
CE2 B:TRP568 4.8 28.8 1.0
CB B:ASN604 4.8 39.9 1.0
CA B:PHE601 4.9 41.5 1.0
CB B:PHE601 4.9 41.3 1.0
C B:CYS602 4.9 39.7 1.0

Sodium binding site 5 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 5 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:31.9
occ:1.00
 O B:PHE556 2.4 30.7 1.0
O B:TYR559 2.4 34.7 1.0
O B:LEU562 2.4 32.8 1.0
O B:HOH4079 2.6 27.9 1.0
O B:HOH4275 3.1 55.5 1.0
C B:TYR559 3.5 35.1 1.0
C B:LEU562 3.5 34.6 1.0
C B:PHE556 3.5 29.9 1.0
O B:PRO560 3.6 37.9 1.0
CA B:PRO560 3.9 36.5 1.0
C B:PRO560 3.9 35.3 1.0
O B:HOH4175 3.9 43.8 1.0
N B:PRO560 4.1 35.5 1.0
CA B:PHE556 4.3 29.3 1.0
N B:LEU562 4.3 31.8 1.0
CA B:LEU562 4.4 32.2 1.0
N B:GLN563 4.4 33.5 1.0
CA B:GLN563 4.4 34.5 1.0
CD1 B:LEU350 4.4 23.1 1.0
N B:ARG557 4.5 30.7 1.0
CA B:TYR559 4.6 32.7 1.0
O B:ARG557 4.6 29.8 1.0
N B:TYR559 4.6 33.0 1.0
CB B:LEU562 4.7 28.3 1.0
CA B:ARG557 4.7 31.3 1.0
C B:ARG557 4.7 30.1 1.0
N B:ARG561 4.8 34.7 1.0
CG B:GLN563 4.8 32.5 1.0
CB B:PHE556 4.8 28.7 1.0

Sodium binding site 6 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 6 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:44.1
occ:1.00
 O C:HOH4368 2.4 62.2 1.0
O C:PHE601 2.4 42.2 1.0
OD1 C:ASN604 2.4 46.8 1.0
OD2 C:ASP201 2.6 44.8 1.0
O C:HOH4279 2.7 41.6 1.0
CG C:ASN604 3.3 42.7 1.0
O C:HOH4241 3.5 47.8 1.0
ND2 C:ASN604 3.6 42.1 1.0
C C:PHE601 3.6 39.5 1.0
CG C:ASP201 3.7 42.4 1.0
OH C:TYR100 3.9 42.0 1.0
OD1 C:ASP201 4.1 44.5 1.0
NE2 C:HIS540 4.3 43.2 1.0
NE1 C:TRP568 4.3 38.2 1.0
CB C:PHE601 4.4 38.1 1.0
CA C:PHE601 4.4 39.5 1.0
CE1 C:HIS540 4.5 41.5 1.0
CD1 C:PHE601 4.5 38.7 1.0
N C:CYS602 4.5 39.1 1.0
CA C:CYS602 4.6 39.2 1.0
CB C:ASN604 4.7 41.5 1.0
ND2 C:ASN102 4.7 48.2 1.0
CB C:ASP201 4.9 39.9 1.0

Sodium binding site 7 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 7 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:33.7
occ:1.00
 O C:HOH4280 2.3 40.6 1.0
O C:PHE556 2.4 32.5 1.0
O C:TYR559 2.4 32.6 1.0
O C:LEU562 2.4 32.8 1.0
O C:HOH4275 2.6 49.1 1.0
O C:PRO560 3.2 34.2 1.0
C C:TYR559 3.4 32.7 1.0
C C:LEU562 3.4 31.1 1.0
C C:PHE556 3.5 31.8 1.0
C C:PRO560 3.6 31.8 1.0
CA C:PRO560 3.7 32.2 1.0
N C:PRO560 3.9 32.5 1.0
O C:HOH4305 4.1 40.4 1.0
N C:LEU562 4.1 30.2 1.0
CA C:LEU562 4.2 29.5 1.0
CA C:PHE556 4.2 29.4 1.0
N C:GLN563 4.3 30.4 1.0
CA C:GLN563 4.3 30.7 1.0
CB C:LEU562 4.5 27.7 1.0
N C:ARG561 4.5 31.0 1.0
CA C:TYR559 4.5 31.3 1.0
N C:ARG557 4.6 31.1 1.0
N C:TYR559 4.6 32.0 1.0
CD1 C:LEU350 4.7 29.1 1.0
CG C:GLN563 4.7 27.0 1.0
O C:ARG557 4.7 32.6 1.0
CA C:ARG557 4.7 32.6 1.0
C C:ARG557 4.8 32.4 1.0
CB C:PHE556 4.9 28.7 1.0
C C:ARG561 4.9 33.2 1.0
O C:HOH4336 4.9 44.5 1.0
O C:ALA555 5.0 33.0 1.0

Sodium binding site 8 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 8 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3101

b:43.5
occ:1.00
 O D:PHE601 2.4 43.4 1.0
O D:HOH4049 2.4 42.3 1.0
OD2 D:ASP201 2.4 45.9 1.0
OD1 D:ASN604 2.4 45.8 1.0
O D:HOH4212 2.5 47.7 1.0
CG D:ASP201 3.2 45.1 1.0
CG D:ASN604 3.4 40.2 1.0
OD1 D:ASP201 3.5 51.0 1.0
C D:PHE601 3.6 44.7 1.0
O D:HOH4301 3.6 52.5 1.0
OH D:TYR100 3.8 45.1 1.0
ND2 D:ASN604 3.8 42.3 1.0
NE1 D:TRP568 4.2 38.0 1.0
CB D:ASP201 4.3 41.2 1.0
CA D:CYS602 4.3 40.9 1.0
N D:CYS602 4.4 42.5 1.0
O D:HOH4080 4.4 43.0 1.0
CA D:PHE601 4.6 44.5 1.0
CB D:PHE601 4.7 44.9 1.0
CB D:ASN604 4.8 40.0 1.0
NE2 D:HIS540 4.8 37.8 1.0
CZ2 D:TRP568 4.8 40.3 1.0
C D:CYS602 4.8 40.5 1.0
CE2 D:TRP568 4.8 35.9 1.0
CZ D:TYR100 5.0 50.0 1.0
O D:ASP201 5.0 38.7 1.0

Sodium binding site 9 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 9 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3102

b:35.8
occ:1.00
 O D:PHE556 2.4 34.4 1.0
O D:TYR559 2.4 36.2 1.0
O D:LEU562 2.4 33.0 1.0
O D:HOH4124 2.6 39.1 1.0
O D:HOH4244 2.6 36.7 1.0
O D:PRO560 3.3 33.3 1.0
C D:LEU562 3.4 32.0 1.0
C D:TYR559 3.4 33.7 1.0
C D:PHE556 3.5 30.2 1.0
C D:PRO560 3.6 33.1 1.0
CA D:PRO560 3.7 31.1 1.0
N D:PRO560 4.0 32.7 1.0
N D:LEU562 4.1 30.6 1.0
CA D:LEU562 4.2 31.2 1.0
CA D:PHE556 4.2 29.8 1.0
N D:GLN563 4.3 33.0 1.0
CA D:GLN563 4.4 32.8 1.0
N D:ARG561 4.5 32.0 1.0
CB D:LEU562 4.5 28.6 1.0
CA D:TYR559 4.6 32.8 1.0
N D:ARG557 4.6 31.3 1.0
CG D:GLN563 4.6 31.1 1.0
N D:TYR559 4.7 32.4 1.0
CD1 D:LEU350 4.7 27.9 1.0
CA D:ARG557 4.7 32.5 1.0
C D:ARG561 4.9 30.7 1.0
C D:ARG557 4.9 34.0 1.0
CB D:PHE556 4.9 28.3 1.0
O D:ARG557 4.9 37.7 1.0

Sodium binding site 10 out of 10 in 3vda

Go back to Sodium Binding Sites List in 3vda
Sodium binding site 10 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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 (N460T) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3103

b:52.0
occ:1.00
 O D:LEU967 2.6 40.6 1.0
O D:HOH4217 2.6 52.5 1.0
O D:HOH4134 2.8 51.1 1.0
O D:THR970 2.8 49.5 1.0
O D:PRO932 2.8 41.2 1.0
CZ D:PHE931 3.5 35.1 1.0
O D:MET968 3.7 49.8 1.0
CE1 D:PHE931 3.7 33.1 1.0
C D:LEU967 3.7 43.0 1.0
CA D:MET968 3.8 47.5 1.0
C D:MET968 3.8 48.2 1.0
C D:THR970 3.9 50.5 1.0
C D:PRO932 3.9 42.1 1.0
CE2 D:PHE931 4.1 34.2 1.0
N D:MET968 4.2 44.2 1.0
CD D:PRO932 4.3 43.8 1.0
N D:THR970 4.4 51.4 1.0
CD1 D:PHE931 4.4 36.2 1.0
CB D:PRO932 4.5 43.5 1.0
N D:PRO932 4.5 43.0 1.0
CA D:PRO932 4.5 42.2 1.0
N D:GLU969 4.5 49.5 1.0
CD2 D:PHE931 4.7 35.1 1.0
CA D:SER971 4.7 46.8 1.0
N D:SER971 4.7 47.7 1.0
CA D:THR970 4.8 51.4 1.0
N D:SER933 4.9 40.5 1.0
CG D:PHE931 4.9 36.9 1.0
CG D:PRO932 4.9 44.1 1.0
CB D:MET968 5.0 48.3 1.0
C D:GLU969 5.0 50.5 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 13:43:04 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy