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Sodium in PDB 3t2p: E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg, PDB code: 3t2p was solved by L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.67 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 150.869, 166.171, 200.786, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 24.2

Other elements in 3t2p:

The structure of E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg 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 (S796D) in Complex with Iptg (pdb code 3t2p). 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 (S796D) in Complex with Iptg, PDB code: 3t2p:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 3t2p

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Sodium binding site 1 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:67.4
occ:1.00
 O A:HOH4340 2.4 64.7 1.0
OD1 A:ASN604 2.4 53.8 1.0
O A:PHE601 2.4 66.2 1.0
O6 A:IPT2001 2.5 55.0 0.9
OD2 A:ASP201 2.7 57.9 1.0
CG A:ASN604 3.3 53.6 1.0
CG A:ASP201 3.5 54.4 1.0
C6 A:IPT2001 3.5 59.0 0.9
C A:PHE601 3.6 68.0 1.0
ND2 A:ASN604 3.6 48.3 1.0
NE1 A:TRP568 3.6 45.8 1.0
OD1 A:ASP201 3.7 54.0 1.0
OH A:TYR100 3.9 65.2 1.0
O A:HOH4025 3.9 58.5 1.0
CA A:CYS602 4.0 63.6 1.0
CZ2 A:TRP568 4.2 47.5 1.0
N A:CYS602 4.2 65.4 1.0
O4 A:IPT2001 4.3 55.7 0.9
CE2 A:TRP568 4.3 48.3 1.0
C A:CYS602 4.4 62.4 1.0
O A:ASP201 4.6 48.2 1.0
C5 A:IPT2001 4.6 59.4 0.9
C4 A:IPT2001 4.6 59.0 0.9
CB A:ASP201 4.6 51.6 1.0
CB A:ASN604 4.7 52.1 1.0
CA A:PHE601 4.7 69.3 1.0
NE2 A:HIS540 4.8 53.0 1.0
O A:CYS602 4.8 61.8 1.0
CD1 A:TRP568 4.8 42.5 1.0
CB A:PHE601 4.9 70.6 1.0
N A:MET603 4.9 61.1 1.0
CZ A:TYR100 5.0 64.7 1.0

Sodium binding site 2 out of 10 in 3t2p

Go back to Sodium Binding Sites List in 3t2p
Sodium binding site 2 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:37.2
occ:1.00
 O A:LEU562 2.4 36.3 1.0
O A:PHE556 2.4 35.2 1.0
O A:TYR559 2.4 34.2 1.0
O A:HOH4155 2.5 40.5 1.0
O A:HOH4216 2.9 38.9 1.0
O A:PRO560 3.1 31.8 1.0
C A:LEU562 3.3 33.8 1.0
C A:TYR559 3.5 30.9 1.0
C A:PRO560 3.5 30.2 1.0
C A:PHE556 3.6 35.0 1.0
O A:HOH4128 3.7 33.6 1.0
CA A:PRO560 3.7 30.8 1.0
N A:PRO560 4.0 31.2 1.0
N A:LEU562 4.0 31.5 1.0
N A:GLN563 4.1 32.0 1.0
CA A:GLN563 4.2 33.8 1.0
CA A:LEU562 4.2 32.9 1.0
CA A:PHE556 4.3 30.8 1.0
N A:ARG561 4.5 28.9 1.0
CB A:LEU562 4.5 32.4 1.0
CG A:GLN563 4.5 33.7 1.0
N A:ARG557 4.6 34.2 1.0
CA A:TYR559 4.7 28.5 1.0
CD1 A:LEU350 4.7 22.3 1.0
CA A:ARG557 4.8 33.1 1.0
N A:TYR559 4.8 27.8 1.0
C A:ARG561 4.8 32.6 1.0
CB A:PHE556 4.9 29.4 1.0
CB A:GLN563 5.0 31.5 1.0
C A:ARG557 5.0 33.4 1.0

Sodium binding site 3 out of 10 in 3t2p

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Sodium binding site 3 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:72.6
occ:1.00
 O A:HOH4179 2.7 55.2 1.0
O A:THR970 2.8 69.4 1.0
O A:LEU967 3.1 59.0 1.0
O A:HOH4099 3.2 45.1 1.0
O A:PRO932 3.5 54.3 1.0
O A:MET968 3.5 65.1 1.0
CZ A:PHE931 3.5 73.7 1.0
C A:MET968 3.7 64.1 1.0
CE2 A:PHE931 3.7 69.5 1.0
C A:THR970 3.7 69.8 1.0
CA A:MET968 3.8 62.0 1.0
CE1 A:PHE931 4.0 78.1 1.0
C A:LEU967 4.1 56.8 1.0
N A:THR970 4.1 67.4 1.0
CD2 A:PHE931 4.4 68.9 1.0
N A:GLU969 4.4 66.9 1.0
N A:MET968 4.5 59.2 1.0
N A:SER971 4.5 70.6 1.0
CA A:SER971 4.5 70.9 1.0
CD A:PRO932 4.5 53.1 1.0
C A:PRO932 4.5 53.6 1.0
CA A:THR970 4.6 68.2 1.0
CD1 A:PHE931 4.7 72.7 1.0
C A:GLU969 4.8 68.3 1.0
CG A:PHE931 4.9 65.4 1.0
N A:PRO932 4.9 55.8 1.0
CB A:MET968 5.0 61.9 1.0

Sodium binding site 4 out of 10 in 3t2p

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Sodium binding site 4 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:60.7
occ:1.00
 O B:HOH4263 2.4 67.9 1.0
OD1 B:ASN604 2.4 60.8 1.0
O B:PHE601 2.4 63.0 1.0
OD2 B:ASP201 2.4 50.5 1.0
O6 B:IPT2001 2.4 59.3 1.0
CG B:ASP201 3.2 47.0 1.0
CG B:ASN604 3.4 59.7 1.0
C B:PHE601 3.5 62.3 1.0
C6 B:IPT2001 3.6 69.7 1.0
OD1 B:ASP201 3.6 48.6 1.0
OH B:TYR100 3.7 54.6 1.0
NE1 B:TRP568 3.8 48.1 1.0
ND2 B:ASN604 3.9 50.1 1.0
CA B:CYS602 4.0 58.1 1.0
O4 B:IPT2001 4.0 71.3 1.0
N B:CYS602 4.2 58.6 1.0
CZ2 B:TRP568 4.3 48.3 1.0
O B:ASP201 4.4 46.3 1.0
CE2 B:TRP568 4.4 45.5 1.0
C4 B:IPT2001 4.4 72.2 1.0
C B:CYS602 4.5 56.7 1.0
CB B:ASP201 4.5 45.1 1.0
C5 B:IPT2001 4.6 69.9 1.0
CA B:PHE601 4.7 63.7 1.0
CB B:ASN604 4.7 62.0 1.0
CZ B:TYR100 4.8 58.2 1.0
CB B:PHE601 4.8 62.6 1.0
O B:CYS602 4.8 53.1 1.0
NE2 B:HIS540 4.8 44.1 1.0
CD1 B:TRP568 4.9 47.4 1.0
N B:MET603 5.0 56.7 1.0

Sodium binding site 5 out of 10 in 3t2p

Go back to Sodium Binding Sites List in 3t2p
Sodium binding site 5 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:44.8
occ:1.00
 O B:PHE556 2.4 43.0 1.0
O B:LEU562 2.6 35.1 1.0
O B:TYR559 2.6 39.7 1.0
O B:HOH4125 2.8 43.0 1.0
O B:PRO560 3.4 38.9 1.0
C B:PHE556 3.5 38.3 1.0
C B:TYR559 3.7 37.9 1.0
C B:LEU562 3.7 34.8 1.0
O B:HOH4110 3.8 34.8 1.0
CA B:PRO560 3.8 36.8 1.0
C B:PRO560 3.9 38.0 1.0
N B:PRO560 4.2 36.6 1.0
CA B:PHE556 4.4 37.3 1.0
CA B:GLN563 4.4 32.5 1.0
CD1 B:LEU350 4.5 33.5 1.0
N B:GLN563 4.5 33.1 1.0
N B:ARG557 4.5 37.6 1.0
N B:LEU562 4.6 34.6 1.0
CA B:ARG557 4.6 38.8 1.0
CA B:LEU562 4.6 34.5 1.0
CG B:GLN563 4.6 33.1 1.0
C B:ARG557 4.7 38.4 1.0
O B:ARG557 4.7 40.3 1.0
N B:TYR559 4.8 39.4 1.0
CA B:TYR559 4.8 36.9 1.0
CB B:PHE556 4.9 37.2 1.0
CB B:LEU562 4.9 32.4 1.0
N B:ARG561 5.0 38.1 1.0

Sodium binding site 6 out of 10 in 3t2p

Go back to Sodium Binding Sites List in 3t2p
Sodium binding site 6 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:58.9
occ:1.00
 O C:HOH4310 2.3 59.7 1.0
OD1 C:ASN604 2.4 56.2 1.0
O C:PHE601 2.4 60.7 1.0
OD2 C:ASP201 2.4 53.7 1.0
O6 C:IPT2001 2.7 52.5 1.0
CG C:ASP201 3.2 51.2 1.0
CG C:ASN604 3.4 57.1 1.0
C C:PHE601 3.5 62.9 1.0
OD1 C:ASP201 3.5 57.3 1.0
OH C:TYR100 3.5 60.8 1.0
C6 C:IPT2001 3.6 54.4 1.0
ND2 C:ASN604 3.9 55.5 1.0
CA C:CYS602 4.0 60.5 1.0
O4 C:IPT2001 4.1 61.0 1.0
NE1 C:TRP568 4.1 49.2 1.0
N C:CYS602 4.1 60.1 1.0
C C:CYS602 4.5 59.9 1.0
CB C:ASP201 4.5 49.2 1.0
O C:ASP201 4.5 53.4 1.0
C4 C:IPT2001 4.5 66.5 1.0
CZ2 C:TRP568 4.5 50.6 1.0
CA C:PHE601 4.6 64.8 1.0
C5 C:IPT2001 4.6 62.1 1.0
CZ C:TYR100 4.6 58.2 1.0
CB C:PHE601 4.6 64.7 1.0
CE2 C:TRP568 4.7 48.4 1.0
CB C:ASN604 4.7 59.9 1.0
N C:MET603 4.9 58.4 1.0
NE2 C:HIS540 4.9 43.4 1.0
O C:CYS602 4.9 57.7 1.0
CE1 C:TYR100 5.0 57.0 1.0

Sodium binding site 7 out of 10 in 3t2p

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Sodium binding site 7 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:42.1
occ:1.00
 O C:HOH4192 2.4 52.7 1.0
O C:PHE556 2.4 40.3 1.0
O C:LEU562 2.4 37.0 1.0
O C:HOH4159 2.5 43.5 1.0
O C:TYR559 2.6 37.6 1.0
O C:PRO560 3.2 33.9 1.0
C C:LEU562 3.5 36.4 1.0
C C:PHE556 3.5 38.4 1.0
C C:TYR559 3.6 36.4 1.0
C C:PRO560 3.7 33.8 1.0
O C:HOH4132 3.8 37.8 1.0
CA C:PRO560 3.8 34.0 1.0
N C:PRO560 4.1 35.9 1.0
CA C:GLN563 4.2 34.8 1.0
N C:GLN563 4.3 35.4 1.0
CA C:PHE556 4.3 35.0 1.0
N C:LEU562 4.4 32.8 1.0
CD1 C:LEU350 4.4 26.9 1.0
CA C:LEU562 4.4 32.8 1.0
N C:ARG557 4.5 38.0 1.0
CG C:GLN563 4.5 32.9 1.0
CA C:ARG557 4.6 37.5 1.0
CA C:TYR559 4.7 34.9 1.0
N C:TYR559 4.8 36.6 1.0
N C:ARG561 4.8 33.7 1.0
C C:ARG557 4.8 39.9 1.0
CB C:LEU562 4.8 29.1 1.0
O C:ARG557 4.8 40.5 1.0
CB C:PHE556 4.9 36.0 1.0

Sodium binding site 8 out of 10 in 3t2p

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Sodium binding site 8 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3104

b:57.7
occ:1.00
 O C:LEU670 2.8 49.3 1.0
O C:SER647 2.8 49.3 1.0
O C:HOH4321 2.8 41.5 1.0
O C:GLU650 2.9 49.3 1.0
N C:GLU650 3.5 45.5 1.0
C C:ASP648 3.8 50.9 1.0
C C:GLU650 3.8 47.6 1.0
C C:SER647 3.9 46.9 1.0
CA C:ASP648 3.9 50.0 1.0
C C:LEU670 3.9 49.8 1.0
N C:ASN649 4.0 49.5 1.0
CA C:GLU650 4.2 44.6 1.0
N C:LEU670 4.2 54.7 1.0
O C:ASP648 4.2 53.0 1.0
N C:ASP648 4.3 48.0 1.0
CB C:GLU650 4.5 42.0 1.0
C C:ASN649 4.5 45.4 1.0
CA C:ASN649 4.5 46.9 1.0
O C:HOH4322 4.6 45.7 1.0
CA C:LEU670 4.6 51.7 1.0
OG C:SER647 4.9 40.3 1.0
CB C:PRO669 4.9 60.0 1.0
CB C:LEU670 4.9 52.9 1.0
C C:PRO669 5.0 56.0 1.0

Sodium binding site 9 out of 10 in 3t2p

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Sodium binding site 9 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3101

b:58.3
occ:1.00
 O D:HOH4372 2.2 51.9 1.0
OD1 D:ASN604 2.4 48.2 1.0
O D:PHE601 2.4 60.2 1.0
OD2 D:ASP201 2.4 53.9 1.0
O6 D:IPT2001 2.5 59.1 1.0
CG D:ASP201 3.2 48.2 1.0
CG D:ASN604 3.4 47.2 1.0
C6 D:IPT2001 3.5 56.5 1.0
OD1 D:ASP201 3.5 49.4 1.0
C D:PHE601 3.6 60.7 1.0
NE1 D:TRP568 3.7 49.7 1.0
OH D:TYR100 3.7 69.4 1.0
ND2 D:ASN604 3.8 47.2 1.0
CA D:CYS602 4.0 61.8 1.0
O D:HOH4158 4.1 49.4 1.0
O4 D:IPT2001 4.2 53.9 1.0
N D:CYS602 4.2 60.0 1.0
CZ2 D:TRP568 4.3 47.9 1.0
CE2 D:TRP568 4.3 48.2 1.0
O D:ASP201 4.4 45.3 1.0
C D:CYS602 4.5 62.1 1.0
CB D:ASP201 4.5 45.7 1.0
C4 D:IPT2001 4.6 57.9 1.0
C5 D:IPT2001 4.6 57.6 1.0
CA D:PHE601 4.7 62.5 1.0
CB D:ASN604 4.7 50.7 1.0
CD1 D:TRP568 4.8 46.8 1.0
CB D:PHE601 4.8 64.1 1.0
CZ D:TYR100 4.8 67.7 1.0
NE2 D:HIS540 4.8 47.9 1.0
O D:CYS602 4.9 63.6 1.0

Sodium binding site 10 out of 10 in 3t2p

Go back to Sodium Binding Sites List in 3t2p
Sodium binding site 10 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3102

b:38.1
occ:1.00
 O D:PHE556 2.4 37.1 1.0
O D:LEU562 2.4 37.9 1.0
O D:TYR559 2.4 36.5 1.0
O D:HOH4016 2.5 52.1 1.0
O D:HOH4194 3.0 38.9 1.0
O D:PRO560 3.2 38.9 1.0
C D:TYR559 3.4 35.5 1.0
C D:LEU562 3.5 35.9 1.0
C D:PHE556 3.6 33.9 1.0
C D:PRO560 3.6 37.2 1.0
CA D:PRO560 3.7 35.6 1.0
O D:HOH4162 3.8 33.8 1.0
N D:PRO560 3.9 34.4 1.0
N D:LEU562 4.2 33.6 1.0
CA D:LEU562 4.3 34.3 1.0
N D:GLN563 4.3 34.7 1.0
CA D:PHE556 4.3 31.3 1.0
CA D:GLN563 4.4 33.0 1.0
CD1 D:LEU350 4.5 30.2 1.0
N D:ARG557 4.5 33.5 1.0
N D:ARG561 4.6 35.5 1.0
CA D:TYR559 4.6 34.4 1.0
CB D:LEU562 4.6 30.5 1.0
CA D:ARG557 4.6 35.3 1.0
N D:TYR559 4.7 33.5 1.0
CG D:GLN563 4.7 27.3 1.0
C D:ARG557 4.8 37.9 1.0
O D:ARG557 4.8 40.6 1.0
CB D:PHE556 4.9 31.4 1.0

Reference:

L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.E.Fraser, R.E.Huber. Ser-796 of Beta-Galactosidase (E. Coli) Plays A Key Role in Maintaining An Optimum Balance Between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Arch.Biochem.Biophys. V. 517 111 2012.
ISSN: ISSN 0003-9861
PubMed: 22155115
DOI: 10.1016/J.ABB.2011.11.017
Page generated: Mon Oct 7 13:07:29 2024

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