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Sodium in PDB 3vd3: E. Coli (Lacz) Beta-Galactosidase (N460D)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460D)

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460D), PDB code: 3vd3 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) 57.25 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.140, 151.650, 131.330, 90.00, 103.47, 90.00
R / Rfree (%) 20 / 28.2

Other elements in 3vd3:

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

Magnesium (Mg) 7 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (N460D) (pdb code 3vd3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460D), PDB code: 3vd3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 3vd3

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Sodium binding site 1 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:26.8
occ:1.00
O A:HOH4097 2.1 2.0 1.0
O A:HOH4099 2.3 13.6 1.0
OD1 A:ASN604 2.4 24.1 1.0
OD2 A:ASP201 2.4 29.2 1.0
O A:PHE601 2.6 27.1 1.0
CG A:ASP201 3.2 28.6 1.0
CG A:ASN604 3.4 23.4 1.0
OD1 A:ASP201 3.6 26.2 1.0
OH A:TYR100 3.7 13.8 1.0
O A:HOH4052 3.7 22.4 1.0
ND2 A:ASN604 3.7 25.4 1.0
O A:HOH4098 3.7 25.3 1.0
C A:PHE601 3.8 25.6 1.0
NE1 A:TRP568 3.8 29.1 1.0
CB A:ASP201 4.4 23.8 1.0
O A:ASP201 4.5 15.9 1.0
CA A:CYS602 4.5 22.5 1.0
N A:CYS602 4.5 22.5 1.0
NE2 A:HIS540 4.6 15.3 1.0
ND2 A:ASN102 4.6 39.7 1.0
CE2 A:TRP568 4.6 16.9 1.0
CB A:ASN604 4.7 20.0 1.0
CB A:PHE601 4.7 25.3 1.0
CZ2 A:TRP568 4.7 19.0 1.0
CA A:PHE601 4.8 24.6 1.0
CD1 A:TRP568 4.8 26.0 1.0
C A:CYS602 4.8 21.1 1.0
CZ A:TYR100 4.9 13.7 1.0

Sodium binding site 2 out of 12 in 3vd3

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Sodium binding site 2 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:15.8
occ:1.00
O A:PHE556 2.4 15.3 1.0
O A:TYR559 2.4 13.7 1.0
O A:LEU562 2.6 22.7 1.0
O A:PRO560 3.2 18.6 1.0
C A:TYR559 3.3 13.5 1.0
C A:PHE556 3.6 16.9 1.0
CA A:PRO560 3.6 14.1 1.0
C A:PRO560 3.6 15.3 1.0
C A:LEU562 3.7 20.0 1.0
N A:PRO560 3.9 14.1 1.0
CA A:ARG557 4.4 21.1 1.0
N A:LEU562 4.4 16.7 1.0
N A:ARG557 4.4 19.3 1.0
C A:ARG557 4.5 22.1 1.0
CA A:TYR559 4.5 12.7 1.0
CA A:LEU562 4.5 17.1 1.0
CA A:PHE556 4.6 15.0 1.0
N A:TYR559 4.6 13.9 1.0
O A:ARG557 4.6 25.6 1.0
N A:ARG561 4.7 14.3 1.0
N A:GLN563 4.7 16.8 1.0
CA A:GLN563 4.7 18.1 1.0
CB A:LEU562 4.8 14.3 1.0
CG A:GLN563 4.9 17.1 1.0

Sodium binding site 3 out of 12 in 3vd3

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Sodium binding site 3 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:35.9
occ:1.00
O A:THR970 2.4 33.0 1.0
O A:LEU967 2.9 26.1 1.0
O A:PRO932 3.0 28.6 1.0
O A:MET968 3.4 27.3 1.0
C A:THR970 3.6 32.8 1.0
CE1 A:PHE931 3.6 30.8 1.0
C A:MET968 3.7 29.7 1.0
CZ A:PHE931 3.9 31.7 1.0
CA A:MET968 3.9 29.3 1.0
C A:LEU967 4.0 24.8 1.0
C A:PRO932 4.0 28.7 1.0
CD A:PRO932 4.1 30.9 1.0
CD1 A:PHE931 4.2 35.4 1.0
N A:THR970 4.3 34.7 1.0
CB A:PRO932 4.4 29.3 1.0
N A:MET968 4.4 27.1 1.0
N A:SER971 4.5 33.2 1.0
CA A:THR970 4.5 34.7 1.0
N A:PRO932 4.5 28.9 1.0
CA A:SER971 4.5 33.8 1.0
C A:GLU969 4.5 35.6 1.0
N A:GLU969 4.5 32.2 1.0
CA A:PRO932 4.6 28.4 1.0
CG A:PRO932 4.6 31.2 1.0
CE2 A:PHE931 4.6 34.6 1.0
O A:GLU969 4.8 37.6 1.0
CG A:PHE931 4.9 32.7 1.0

Sodium binding site 4 out of 12 in 3vd3

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Sodium binding site 4 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:24.7
occ:1.00
O B:HOH4034 2.2 10.7 1.0
O B:HOH4086 2.3 20.8 1.0
O B:PHE601 2.4 25.9 1.0
OD1 B:ASN604 2.4 18.9 1.0
OD2 B:ASP201 2.4 37.0 1.0
CG B:ASP201 3.4 38.3 1.0
CG B:ASN604 3.4 20.7 1.0
OH B:TYR100 3.5 28.8 1.0
C B:PHE601 3.5 27.9 1.0
OD1 B:ASP201 3.7 36.8 1.0
ND2 B:ASN604 3.8 24.5 1.0
ND2 B:ASN102 4.1 39.5 1.0
NE1 B:TRP568 4.2 25.2 1.0
CB B:PHE601 4.3 29.9 1.0
N B:CYS602 4.4 27.6 1.0
NE2 B:HIS540 4.4 19.5 1.0
CA B:CYS602 4.4 25.0 1.0
CA B:PHE601 4.4 28.2 1.0
CB B:ASP201 4.6 34.7 1.0
CZ B:TYR100 4.7 26.7 1.0
CB B:ASN604 4.8 22.0 1.0
O B:HOH4001 4.8 33.0 1.0
CE2 B:TRP568 4.8 29.1 1.0
CZ2 B:TRP568 4.9 28.3 1.0
O B:ASP201 4.9 34.9 1.0
CG B:ASN102 5.0 38.3 1.0
C B:CYS602 5.0 24.1 1.0
CE1 B:HIS540 5.0 16.4 1.0
CD2 B:PHE601 5.0 36.4 1.0

Sodium binding site 5 out of 12 in 3vd3

Go back to Sodium Binding Sites List in 3vd3
Sodium binding site 5 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:18.2
occ:1.00
O B:PHE556 2.4 20.9 1.0
O B:HOH4082 2.4 10.8 1.0
O B:TYR559 2.4 20.9 1.0
O B:LEU562 2.4 14.4 1.0
C B:TYR559 3.3 19.1 1.0
O B:PRO560 3.3 17.5 1.0
CA B:PRO560 3.4 16.8 1.0
C B:LEU562 3.5 15.4 1.0
C B:PHE556 3.5 18.5 1.0
C B:PRO560 3.6 16.6 1.0
N B:PRO560 3.7 17.8 1.0
N B:LEU562 4.3 14.3 1.0
CA B:LEU562 4.3 15.1 1.0
N B:GLN563 4.4 17.0 1.0
CA B:PHE556 4.4 19.7 1.0
CA B:GLN563 4.4 18.6 1.0
CA B:TYR559 4.5 19.8 1.0
N B:ARG557 4.5 15.8 1.0
N B:TYR559 4.5 20.1 1.0
N B:ARG561 4.6 17.9 1.0
CA B:ARG557 4.6 16.1 1.0
CB B:LEU562 4.6 15.8 1.0
CG B:GLN563 4.7 14.5 1.0
C B:ARG557 4.7 14.8 1.0
CB B:PRO560 4.9 14.6 1.0
CB B:PHE556 5.0 18.8 1.0
O B:ARG557 5.0 16.0 1.0
CD1 B:LEU350 5.0 7.8 1.0

Sodium binding site 6 out of 12 in 3vd3

Go back to Sodium Binding Sites List in 3vd3
Sodium binding site 6 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:41.9
occ:1.00
O B:PRO932 2.6 35.3 1.0
O B:THR970 2.6 38.5 1.0
O B:HOH4050 2.7 25.9 1.0
O B:LEU967 2.9 21.7 1.0
O B:MET968 3.4 27.2 1.0
CZ B:PHE931 3.5 40.1 1.0
C B:THR970 3.7 37.9 1.0
CE1 B:PHE931 3.8 36.0 1.0
C B:MET968 3.8 30.0 1.0
C B:PRO932 3.8 31.6 1.0
CA B:MET968 3.8 28.5 1.0
C B:LEU967 3.9 23.4 1.0
CE2 B:PHE931 4.0 38.1 1.0
CD B:PRO932 4.2 31.3 1.0
N B:THR970 4.3 34.3 1.0
N B:PRO932 4.4 30.5 1.0
N B:MET968 4.4 25.2 1.0
CD1 B:PHE931 4.4 35.6 1.0
CB B:PRO932 4.4 31.1 1.0
CA B:PRO932 4.4 31.0 1.0
CA B:SER971 4.5 36.9 1.0
N B:SER971 4.5 37.6 1.0
CD2 B:PHE931 4.6 33.1 1.0
CA B:THR970 4.6 36.2 1.0
CG B:PRO932 4.7 32.0 1.0
N B:GLU969 4.8 32.5 1.0
CG B:PHE931 4.8 32.2 1.0
N B:SER933 4.9 31.1 1.0

Sodium binding site 7 out of 12 in 3vd3

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Sodium binding site 7 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:39.0
occ:1.00
O B:HOH4088 2.6 18.0 1.0
O B:GLU650 2.7 23.9 1.0
O B:HOH4087 2.8 32.9 1.0
O B:SER647 2.8 26.9 1.0
O B:LEU670 3.0 43.9 1.0
N B:GLU650 3.5 19.9 1.0
C B:GLU650 3.7 22.9 1.0
C B:ASP648 3.8 23.8 1.0
CA B:ASP648 3.9 25.1 1.0
C B:SER647 3.9 25.2 1.0
N B:ASN649 4.0 24.1 1.0
C B:LEU670 4.1 43.1 1.0
CA B:GLU650 4.1 21.4 1.0
N B:LEU670 4.2 42.1 1.0
O B:ASP648 4.2 22.8 1.0
N B:ASP648 4.4 25.0 1.0
CA B:ASN649 4.4 20.3 1.0
C B:ASN649 4.5 20.0 1.0
CA B:LEU670 4.6 43.2 1.0
CB B:GLU650 4.8 19.9 1.0
N B:LEU651 4.9 24.3 1.0
CB B:LEU670 5.0 43.9 1.0

Sodium binding site 8 out of 12 in 3vd3

Go back to Sodium Binding Sites List in 3vd3
Sodium binding site 8 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:30.4
occ:1.00
OD1 C:ASN604 2.4 35.6 1.0
OD2 C:ASP201 2.4 37.9 1.0
O C:PHE601 2.7 25.2 1.0
O C:HOH4084 2.8 28.3 1.0
CG C:ASN604 3.3 36.6 1.0
CG C:ASP201 3.3 35.2 1.0
ND2 C:ASN604 3.5 37.8 1.0
OD1 C:ASP201 3.7 35.6 1.0
OH C:TYR100 3.8 26.9 1.0
C C:PHE601 3.8 26.8 1.0
NE1 C:TRP568 4.2 22.6 1.0
NE2 C:HIS540 4.3 21.9 1.0
CE1 C:HIS540 4.5 21.6 1.0
CB C:PHE601 4.5 28.7 1.0
CB C:ASP201 4.5 33.2 1.0
CA C:PHE601 4.6 27.8 1.0
CB C:ASN604 4.7 36.5 1.0
N C:CYS602 4.7 27.7 1.0
CA C:CYS602 4.8 29.8 1.0
CD2 C:PHE601 4.9 27.3 1.0
O C:ASP201 4.9 31.7 1.0
O C:HOH4086 5.0 23.2 1.0
CE2 C:TRP568 5.0 20.7 1.0
CZ C:TYR100 5.0 29.2 1.0

Sodium binding site 9 out of 12 in 3vd3

Go back to Sodium Binding Sites List in 3vd3
Sodium binding site 9 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:23.3
occ:1.00
O C:LEU562 2.4 22.6 1.0
O C:HOH4085 2.7 21.3 1.0
O C:PHE556 2.8 17.7 1.0
O C:TYR559 3.2 17.5 1.0
C C:LEU562 3.5 20.5 1.0
O C:PRO560 3.5 22.2 1.0
CD1 C:LEU350 3.7 2.0 1.0
C C:PHE556 3.8 17.6 1.0
C C:PRO560 4.0 15.8 1.0
CA C:GLN563 4.0 19.2 1.0
CA C:PRO560 4.1 14.5 1.0
C C:TYR559 4.1 16.1 1.0
N C:GLN563 4.2 17.8 1.0
CG C:GLN563 4.4 21.6 1.0
CA C:PHE556 4.5 17.5 1.0
N C:PRO560 4.5 15.6 1.0
N C:LEU562 4.6 16.1 1.0
CA C:LEU562 4.6 18.6 1.0
CB C:PHE556 4.7 18.1 1.0
N C:ARG557 4.7 18.3 1.0
CB C:GLN563 4.7 19.6 1.0
CG C:LEU350 4.8 12.6 1.0
CA C:ARG557 4.9 22.5 1.0
N C:ARG561 4.9 15.3 1.0
CB C:LEU562 5.0 22.1 1.0
CB C:LEU350 5.0 14.8 1.0

Sodium binding site 10 out of 12 in 3vd3

Go back to Sodium Binding Sites List in 3vd3
Sodium binding site 10 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3105

b:38.5
occ:1.00
O C:ASN597 2.7 36.4 1.0
C C:ASN597 3.8 36.9 1.0
N C:ASN597 4.0 39.5 1.0
OE2 C:GLU797 4.1 43.0 1.0
OE1 C:GLU797 4.3 45.7 1.0
CB C:PRO596 4.3 42.2 1.0
CA C:ASN597 4.5 37.9 1.0
OD2 C:ASP598 4.6 42.2 1.0
CD C:GLU797 4.6 45.4 1.0
O C:HOH4009 4.7 4.5 1.0
C C:PRO596 4.7 41.2 1.0
N C:ASP598 4.8 36.8 1.0
CA C:PRO596 4.8 43.1 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: Tue Dec 15 06:28:29 2020

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