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Sodium in PDB 8ri6: Beta-Galactosidase (Lacz) Purified From E. Coli.

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

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

Other elements in 8ri6:

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

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Beta-Galactosidase (Lacz) Purified From E. Coli. (pdb code 8ri6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Beta-Galactosidase (Lacz) Purified From E. Coli., PDB code: 8ri6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8ri6

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Sodium binding site 1 out of 8 in the Beta-Galactosidase (Lacz) Purified From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Beta-Galactosidase (Lacz) Purified From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2003

b:16.0
occ:1.00
 OD2 A:ASP202 2.4 12.0 1.0
O A:HOH2246 2.4 13.9 1.0
O A:PHE602 2.5 15.4 1.0
OD1 A:ASN605 2.5 10.8 1.0
CG A:ASP202 3.5 12.0 1.0
CG A:ASN605 3.5 10.8 1.0
C A:PHE602 3.7 15.4 1.0
OH A:TYR101 3.7 12.8 1.0
ND2 A:ASN605 3.8 10.8 1.0
OD1 A:ASP202 3.9 12.0 1.0
NE1 A:TRP569 4.3 8.4 1.0
CB A:PHE602 4.3 15.4 1.0
NE2 A:HIS541 4.4 10.0 1.0
CA A:PHE602 4.5 15.4 1.0
N A:CYS603 4.6 13.1 1.0
CD1 A:PHE602 4.6 15.4 1.0
CA A:CYS603 4.6 13.1 1.0
O A:HOH2158 4.6 13.0 1.0
CB A:ASP202 4.7 12.0 1.0
CE1 A:HIS541 4.8 10.0 1.0
CB A:ASN605 4.9 10.8 1.0
CZ A:TYR101 4.9 12.8 1.0
CG A:PHE602 5.0 15.4 1.0

Sodium binding site 2 out of 8 in 8ri6

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Sodium binding site 2 out of 8 in the Beta-Galactosidase (Lacz) Purified From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Beta-Galactosidase (Lacz) Purified From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2004

b:11.7
occ:1.00
 O A:LEU563 2.3 5.9 1.0
O A:TYR560 2.4 7.4 1.0
O A:PHE557 2.5 12.9 1.0
C A:LEU563 3.3 5.9 1.0
O A:PRO561 3.4 6.8 1.0
C A:TYR560 3.5 7.4 1.0
C A:PHE557 3.7 12.9 1.0
C A:PRO561 3.8 6.8 1.0
CA A:PRO561 3.8 6.8 1.0
O A:HOH2120 3.9 11.9 1.0
O A:HOH2151 3.9 11.0 1.0
N A:LEU563 4.1 5.9 1.0
N A:PRO561 4.1 6.8 1.0
CA A:LEU563 4.2 5.9 1.0
N A:GLN564 4.2 5.9 1.0
CA A:GLN564 4.3 5.9 1.0
CA A:PHE557 4.4 12.9 1.0
CB A:LEU563 4.5 5.9 1.0
CA A:TYR560 4.6 7.4 1.0
N A:TYR560 4.6 7.4 1.0
N A:ARG562 4.6 6.7 1.0
N A:ARG558 4.7 7.8 1.0
CD1 A:LEU351 4.8 5.6 1.0
CA A:ARG558 4.8 7.8 1.0
C A:ARG558 4.9 7.8 1.0
CG A:GLN564 4.9 5.9 1.0
C A:ARG562 5.0 6.7 1.0
O A:ARG558 5.0 7.8 1.0

Sodium binding site 3 out of 8 in 8ri6

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Sodium binding site 3 out of 8 in the Beta-Galactosidase (Lacz) Purified From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Beta-Galactosidase (Lacz) Purified From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2003

b:15.2
occ:1.00
 OD2 B:ASP202 2.4 11.7 1.0
O B:HOH2248 2.4 14.0 1.0
O B:PHE602 2.5 15.3 1.0
OD1 B:ASN605 2.5 10.7 1.0
CG B:ASP202 3.5 11.7 1.0
CG B:ASN605 3.5 10.7 1.0
C B:PHE602 3.7 15.3 1.0
OH B:TYR101 3.7 12.8 1.0
ND2 B:ASN605 3.8 10.7 1.0
OD1 B:ASP202 3.9 11.7 1.0
NE1 B:TRP569 4.3 8.3 1.0
CB B:PHE602 4.3 15.3 1.0
NE2 B:HIS541 4.4 9.8 1.0
CA B:PHE602 4.5 15.3 1.0
N B:CYS603 4.6 12.9 1.0
CD1 B:PHE602 4.6 15.3 1.0
O B:HOH2157 4.6 12.7 1.0
CA B:CYS603 4.6 12.9 1.0
CB B:ASP202 4.7 11.7 1.0
CE1 B:HIS541 4.8 9.8 1.0
CB B:ASN605 4.9 10.7 1.0
CZ B:TYR101 4.9 12.8 1.0
CG B:PHE602 5.0 15.3 1.0

Sodium binding site 4 out of 8 in 8ri6

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Sodium binding site 4 out of 8 in the Beta-Galactosidase (Lacz) Purified From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Beta-Galactosidase (Lacz) Purified From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2004

b:9.6
occ:1.00
 O B:LEU563 2.3 4.9 1.0
O B:TYR560 2.4 6.8 1.0
O B:PHE557 2.5 2.5 1.0
C B:LEU563 3.3 4.9 1.0
O B:PRO561 3.4 6.4 1.0
C B:TYR560 3.5 6.8 1.0
C B:PHE557 3.7 2.5 1.0
C B:PRO561 3.8 6.4 1.0
CA B:PRO561 3.8 6.4 1.0
O B:HOH2117 3.9 11.8 1.0
O B:HOH2149 3.9 11.4 1.0
N B:LEU563 4.1 4.9 1.0
N B:PRO561 4.1 6.4 1.0
CA B:LEU563 4.2 4.9 1.0
N B:GLN564 4.2 5.4 1.0
CA B:GLN564 4.3 5.4 1.0
CA B:PHE557 4.4 2.5 1.0
CB B:LEU563 4.5 4.9 1.0
CA B:TYR560 4.6 6.8 1.0
N B:TYR560 4.6 6.8 1.0
N B:ARG562 4.6 6.1 1.0
N B:ARG558 4.7 6.7 1.0
CD1 B:LEU351 4.8 6.7 1.0
CA B:ARG558 4.8 6.7 1.0
C B:ARG558 4.9 6.7 1.0
CG B:GLN564 4.9 5.4 1.0
C B:ARG562 5.0 6.1 1.0
O B:ARG558 5.0 6.7 1.0

Sodium binding site 5 out of 8 in 8ri6

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Sodium binding site 5 out of 8 in the Beta-Galactosidase (Lacz) Purified From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Beta-Galactosidase (Lacz) Purified From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2003

b:15.6
occ:1.00
 OD2 C:ASP202 2.4 11.8 1.0
O C:HOH2248 2.4 13.9 1.0
O C:PHE602 2.5 15.2 1.0
OD1 C:ASN605 2.5 10.6 1.0
CG C:ASP202 3.5 11.8 1.0
CG C:ASN605 3.5 10.6 1.0
C C:PHE602 3.7 15.2 1.0
OH C:TYR101 3.7 12.5 1.0
ND2 C:ASN605 3.8 10.6 1.0
OD1 C:ASP202 3.9 11.8 1.0
NE1 C:TRP569 4.3 8.3 1.0
CB C:PHE602 4.3 15.2 1.0
NE2 C:HIS541 4.4 10.0 1.0
CA C:PHE602 4.5 15.2 1.0
N C:CYS603 4.6 12.9 1.0
CD1 C:PHE602 4.6 15.2 1.0
CA C:CYS603 4.6 12.9 1.0
O C:HOH2153 4.6 13.0 1.0
CB C:ASP202 4.7 11.8 1.0
CE1 C:HIS541 4.8 10.0 1.0
CB C:ASN605 4.9 10.6 1.0
CZ C:TYR101 4.9 12.5 1.0
CG C:PHE602 5.0 15.2 1.0

Sodium binding site 6 out of 8 in 8ri6

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Sodium binding site 6 out of 8 in the Beta-Galactosidase (Lacz) Purified From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Beta-Galactosidase (Lacz) Purified From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2004

b:11.1
occ:1.00
 O C:LEU563 2.3 5.5 1.0
O C:TYR560 2.4 7.4 1.0
O C:PHE557 2.5 12.9 1.0
C C:LEU563 3.3 5.5 1.0
O C:PRO561 3.4 6.9 1.0
C C:TYR560 3.5 7.4 1.0
C C:PHE557 3.7 12.9 1.0
C C:PRO561 3.8 6.9 1.0
CA C:PRO561 3.8 6.9 1.0
O C:HOH2118 3.9 12.5 1.0
O C:HOH2149 3.9 11.1 1.0
N C:LEU563 4.1 5.5 1.0
N C:PRO561 4.1 6.9 1.0
CA C:LEU563 4.2 5.5 1.0
N C:GLN564 4.2 5.4 1.0
CA C:GLN564 4.3 5.4 1.0
CA C:PHE557 4.4 12.9 1.0
CB C:LEU563 4.5 5.5 1.0
CA C:TYR560 4.6 7.4 1.0
N C:TYR560 4.6 7.4 1.0
N C:ARG562 4.6 6.3 1.0
N C:ARG558 4.7 7.8 1.0
CD1 C:LEU351 4.8 5.8 1.0
CA C:ARG558 4.8 7.8 1.0
C C:ARG558 4.9 7.8 1.0
CG C:GLN564 4.9 5.4 1.0
C C:ARG562 5.0 6.3 1.0
O C:ARG558 5.0 7.8 1.0

Sodium binding site 7 out of 8 in 8ri6

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Sodium binding site 7 out of 8 in the Beta-Galactosidase (Lacz) Purified From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Beta-Galactosidase (Lacz) Purified From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1103

b:14.6
occ:1.00
 OD2 D:ASP202 2.4 12.2 1.0
O D:HOH1357 2.4 14.3 1.0
O D:PHE602 2.5 15.3 1.0
OD1 D:ASN605 2.5 10.6 1.0
CG D:ASP202 3.5 12.2 1.0
CG D:ASN605 3.5 10.6 1.0
C D:PHE602 3.7 15.3 1.0
OH D:TYR101 3.7 13.1 1.0
ND2 D:ASN605 3.8 10.6 1.0
OD1 D:ASP202 3.9 12.2 1.0
NE1 D:TRP569 4.3 8.4 1.0
CB D:PHE602 4.3 15.3 1.0
NE2 D:HIS541 4.4 9.8 1.0
CA D:PHE602 4.5 15.3 1.0
N D:CYS603 4.6 13.0 1.0
CD1 D:PHE602 4.6 15.3 1.0
CA D:CYS603 4.6 13.0 1.0
O D:HOH1257 4.6 12.7 1.0
CB D:ASP202 4.7 12.2 1.0
CE1 D:HIS541 4.8 9.8 1.0
CB D:ASN605 4.9 10.6 1.0
CZ D:TYR101 4.9 13.1 1.0
CG D:PHE602 5.0 15.3 1.0

Sodium binding site 8 out of 8 in 8ri6

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Sodium binding site 8 out of 8 in the Beta-Galactosidase (Lacz) Purified From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Beta-Galactosidase (Lacz) Purified From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1104

b:11.3
occ:1.00
 O D:LEU563 2.3 5.6 1.0
O D:TYR560 2.4 7.4 1.0
O D:PHE557 2.5 12.9 1.0
C D:LEU563 3.3 5.6 1.0
O D:PRO561 3.4 6.8 1.0
C D:TYR560 3.5 7.4 1.0
C D:PHE557 3.7 12.9 1.0
C D:PRO561 3.7 6.8 1.0
CA D:PRO561 3.8 6.8 1.0
O D:HOH1222 3.8 12.1 1.0
O D:HOH1251 3.9 11.4 1.0
N D:LEU563 4.0 5.6 1.0
N D:PRO561 4.1 6.8 1.0
CA D:LEU563 4.2 5.6 1.0
N D:GLN564 4.2 5.7 1.0
CA D:GLN564 4.3 5.7 1.0
CA D:PHE557 4.4 12.9 1.0
CB D:LEU563 4.5 5.6 1.0
N D:ARG562 4.6 6.3 1.0
CA D:TYR560 4.6 7.4 1.0
N D:TYR560 4.7 7.4 1.0
N D:ARG558 4.7 8.1 1.0
CA D:ARG558 4.8 8.1 1.0
CD1 D:LEU351 4.8 7.0 1.0
CG D:GLN564 4.9 5.7 1.0
C D:ARG562 4.9 6.3 1.0
C D:ARG558 4.9 8.1 1.0
O D:ARG558 5.0 8.1 1.0

Reference:

N.J.Hardenbrook, Y.Sheng, N.Sanguankiattichai, P.Zhang, G.Preston, R.Van Der Hoorn. Identification of A Novel Inhibitor For Beta-Galactosidase From Pseudomonas Syringae. To Be Published.
Page generated: Sat Feb 8 23:42:08 2025

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