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Sodium in PDB 1hn1: E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)

Enzymatic activity of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)

All present enzymatic activity of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic):
3.1.2.23;

Protein crystallography data

The structure of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic), PDB code: 1hn1 was solved by D.H.Juers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 153.900, 171.400, 204.500, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1hn1:

The structure of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) (pdb code 1hn1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic), PDB code: 1hn1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1hn1

Go back to Sodium Binding Sites List in 1hn1
Sodium binding site 1 out of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:52.1
occ:1.00
 OD2 A:ASP201 2.7 63.2 1.0
O A:PHE601 2.7 37.7 1.0
OD1 A:ASN604 2.9 69.9 1.0
ND2 A:ASN604 2.9 7.9 1.0
CG A:ASN604 3.2 54.3 1.0
NE1 A:TRP568 3.9 27.2 1.0
CG A:ASP201 3.9 72.2 1.0
C A:PHE601 3.9 29.9 1.0
NE2 A:HIS540 4.1 50.0 1.0
OD1 A:ASP201 4.4 89.2 1.0
OH A:TYR100 4.4 34.8 1.0
CD1 A:TRP568 4.6 27.5 1.0
CB A:ASN604 4.6 41.0 1.0
CB A:PHE601 4.7 31.2 1.0
CA A:CYS602 4.7 30.2 1.0
CE2 A:TRP568 4.7 33.5 1.0
N A:CYS602 4.7 30.3 1.0
CA A:PHE601 4.7 24.2 1.0
CE1 A:HIS540 4.8 48.6 1.0
CD2 A:PHE601 4.8 47.5 1.0
O A:HOH4052 4.8 25.6 1.0
CZ2 A:TRP568 5.0 36.3 1.0
CB A:ASP201 5.0 35.0 1.0

Sodium binding site 2 out of 7 in 1hn1

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Sodium binding site 2 out of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:24.3
occ:1.00
 O A:PHE556 2.4 31.6 1.0
O A:LEU562 2.5 38.0 1.0
O A:TYR559 2.7 25.2 1.0
O A:PRO560 3.5 11.1 1.0
C A:LEU562 3.6 33.7 1.0
C A:PHE556 3.6 24.8 1.0
C A:TYR559 3.7 21.9 1.0
C A:PRO560 3.9 14.1 1.0
CA A:PRO560 4.0 15.7 1.0
N A:LEU562 4.2 29.0 1.0
N A:PRO560 4.3 25.2 1.0
CA A:LEU562 4.4 34.5 1.0
CD1 A:LEU350 4.4 11.5 1.0
N A:GLN563 4.4 18.2 1.0
CA A:PHE556 4.5 12.1 1.0
CA A:GLN563 4.5 15.2 1.0
N A:ARG557 4.5 15.8 1.0
CB A:LEU562 4.5 35.3 1.0
CA A:ARG557 4.6 22.6 1.0
CG A:GLN563 4.8 14.4 1.0
C A:ARG557 4.8 17.2 1.0
CA A:TYR559 4.8 9.9 1.0
N A:ARG561 4.9 19.1 1.0
N A:TYR559 5.0 11.9 1.0
O A:ARG557 5.0 17.1 1.0
CB A:PHE556 5.0 16.7 1.0

Sodium binding site 3 out of 7 in 1hn1

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Sodium binding site 3 out of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:32.3
occ:1.00
 O B:TYR559 2.5 23.8 1.0
O B:PHE556 2.6 26.6 1.0
O B:LEU562 2.8 13.0 1.0
C B:TYR559 3.4 28.9 1.0
O B:PRO560 3.5 27.6 1.0
C B:PHE556 3.7 26.2 1.0
CA B:PRO560 3.7 24.2 1.0
C B:LEU562 3.8 19.4 1.0
N B:PRO560 3.9 31.0 1.0
C B:PRO560 3.9 22.6 1.0
CA B:PHE556 4.5 18.2 1.0
O B:ARG557 4.5 31.1 1.0
N B:ARG557 4.6 17.2 1.0
CA B:TYR559 4.6 19.8 1.0
N B:LEU562 4.6 17.6 1.0
N B:GLN563 4.6 21.7 1.0
N B:TYR559 4.7 24.4 1.0
C B:ARG557 4.7 15.7 1.0
CA B:GLN563 4.7 20.5 1.0
CA B:LEU562 4.7 12.8 1.0
CD1 B:LEU350 4.7 25.2 1.0
CA B:ARG557 4.7 14.6 1.0
CB B:LEU562 4.8 10.6 1.0
CB B:PHE556 4.9 20.5 1.0

Sodium binding site 4 out of 7 in 1hn1

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Sodium binding site 4 out of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:45.8
occ:1.00
 O B:PRO932 2.3 39.6 1.0
O B:LEU967 2.6 29.9 1.0
O B:THR970 2.8 34.1 1.0
C B:PRO932 3.2 31.8 1.0
CG B:PRO932 3.4 35.4 1.0
CB B:PRO932 3.4 33.8 1.0
CZ B:PHE931 3.6 27.6 1.0
C B:LEU967 3.7 32.8 1.0
CE1 B:PHE931 3.7 29.8 1.0
O B:MET968 3.8 58.2 1.0
CA B:PRO932 3.8 29.9 1.0
C B:THR970 4.0 35.8 1.0
CE2 B:PHE931 4.0 38.9 1.0
N B:PRO932 4.0 28.5 1.0
CD B:PRO932 4.0 27.2 1.0
C B:MET968 4.1 42.3 1.0
CA B:MET968 4.1 21.2 1.0
CD1 B:PHE931 4.2 33.0 1.0
N B:SER933 4.3 25.9 1.0
N B:MET968 4.3 15.1 1.0
CD2 B:PHE931 4.5 43.8 1.0
CG B:PHE931 4.6 34.5 1.0
N B:THR970 4.6 34.1 1.0
C B:PHE931 4.7 32.4 1.0
CA B:SER933 4.7 28.2 1.0
CA B:LEU967 4.8 37.6 1.0
O B:PRO788 4.9 45.7 1.0
CA B:THR970 4.9 26.3 1.0
N B:SER971 4.9 38.0 1.0
CA B:SER971 4.9 33.6 1.0
N B:GLU969 5.0 38.9 1.0

Sodium binding site 5 out of 7 in 1hn1

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Sodium binding site 5 out of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:49.3
occ:1.00
 OD2 C:ASP201 2.2 62.9 1.0
O C:PHE601 2.6 33.6 1.0
OD1 C:ASN604 2.6 5.0 1.0
CG C:ASP201 3.1 36.9 1.0
OD1 C:ASP201 3.5 31.4 1.0
C C:PHE601 3.6 35.2 1.0
CG C:ASN604 3.7 70.9 1.0
OH C:TYR100 3.9 26.6 1.0
ND2 C:ASN604 4.1 43.8 1.0
NE1 C:TRP568 4.2 23.0 1.0
CB C:PHE601 4.2 38.0 1.0
CB C:ASP201 4.3 31.1 1.0
N C:CYS602 4.4 40.3 1.0
CA C:PHE601 4.5 34.6 1.0
CA C:CYS602 4.5 43.8 1.0
CZ2 C:TRP568 4.7 29.1 1.0
NE2 C:HIS540 4.7 20.3 1.0
CE2 C:TRP568 4.8 27.0 1.0
ND2 C:ASN102 4.8 22.1 1.0
O C:ASP201 4.8 23.8 1.0
CZ C:TYR100 5.0 31.5 1.0
CB C:ASN604 5.0 21.8 1.0
C C:CYS602 5.0 38.2 1.0

Sodium binding site 6 out of 7 in 1hn1

Go back to Sodium Binding Sites List in 1hn1
Sodium binding site 6 out of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:24.6
occ:1.00
 O C:PHE556 2.4 23.5 1.0
O C:LEU562 2.6 9.7 1.0
O C:TYR559 2.7 22.9 1.0
O C:PRO560 3.5 30.5 1.0
C C:TYR559 3.6 31.5 1.0
C C:PHE556 3.6 27.2 1.0
C C:LEU562 3.7 18.2 1.0
CD1 C:LEU350 3.8 30.8 1.0
CA C:PRO560 4.0 20.8 1.0
C C:PRO560 4.0 17.9 1.0
N C:PRO560 4.1 29.1 1.0
CA C:PHE556 4.4 22.4 1.0
N C:LEU562 4.4 11.6 1.0
N C:GLN563 4.5 21.3 1.0
CA C:LEU562 4.5 13.6 1.0
CA C:GLN563 4.6 14.1 1.0
N C:ARG557 4.7 19.8 1.0
CA C:ARG557 4.7 17.7 1.0
CA C:TYR559 4.7 25.5 1.0
O C:ARG557 4.8 43.2 1.0
C C:ARG557 4.8 27.6 1.0
N C:TYR559 4.8 30.8 1.0
CB C:PHE556 4.8 30.9 1.0
CB C:LEU562 4.8 24.3 1.0
CG C:GLN563 4.9 11.6 1.0

Sodium binding site 7 out of 7 in 1hn1

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Sodium binding site 7 out of 7 in the E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of E. Coli (Lac Z) Beta-Galactosidase (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3102

b:47.7
occ:1.00
 O D:PHE556 2.3 31.9 1.0
O D:LEU562 2.5 30.8 1.0
O D:TYR559 2.5 31.6 1.0
C D:PHE556 3.4 23.2 1.0
C D:TYR559 3.5 19.4 1.0
C D:LEU562 3.7 30.5 1.0
O D:PRO560 3.7 34.8 1.0
CA D:PRO560 3.9 17.9 1.0
C D:PRO560 4.0 37.2 1.0
N D:PRO560 4.1 15.7 1.0
CA D:PHE556 4.3 14.2 1.0
O D:ARG557 4.3 26.1 1.0
N D:ARG557 4.3 5.3 1.0
CD1 D:LEU350 4.4 8.9 1.0
N D:TYR559 4.4 10.4 1.0
C D:ARG557 4.5 20.1 1.0
CA D:ARG557 4.5 9.5 1.0
CA D:TYR559 4.5 8.8 1.0
CB D:LEU562 4.5 19.2 1.0
N D:LEU562 4.5 17.6 1.0
CA D:LEU562 4.5 19.1 1.0
N D:GLN563 4.6 20.6 1.0
CA D:GLN563 4.7 8.8 1.0
CB D:PHE556 4.8 17.7 1.0
O D:ALA555 4.9 24.8 1.0
N D:ARG561 4.9 33.3 1.0

Reference:

D.H.Juers, B.W.Matthews. Reversible Lattice Repacking Illustrates the Temperature Dependence of Macromolecular Interactions. J.Mol.Biol. V. 311 851 2001.
ISSN: ISSN 0022-2836
PubMed: 11518535
DOI: 10.1006/JMBI.2001.4891
Page generated: Sun Oct 6 18:46:07 2024

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