Atomistry » Sodium » PDB 1ghy-1hn1 » 1hn1
Atomistry »
  Sodium »
    PDB 1ghy-1hn1 »
      1hn1 »

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

Go back to Sodium Binding Sites List in 1hn1
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

Go back to Sodium Binding Sites List in 1hn1
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

Go back to Sodium Binding Sites List in 1hn1
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

Go back to Sodium Binding Sites List in 1hn1
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

Go back to Sodium Binding Sites List in 1hn1
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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy