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Sodium in PDB 5a1a: 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor

Enzymatic activity of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor

All present enzymatic activity of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor:
3.2.1.23;

Other elements in 5a1a:

The structure of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor (pdb code 5a1a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor, PDB code: 5a1a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5a1a

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Sodium binding site 1 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4001

b:30.0
occ:1.00
 OD2 A:ASP201 2.2 11.7 1.0
O5 A:PTQ2001 2.3 20.0 1.0
C6 A:PTQ2001 2.4 20.0 1.0
OD1 A:ASN604 2.4 14.4 1.0
O A:HOH5013 2.6 30.0 1.0
O A:PHE601 2.7 12.1 1.0
CG A:ASN604 3.3 18.8 1.0
CG A:ASP201 3.4 17.0 1.0
C5 A:PTQ2001 3.6 20.0 1.0
ND2 A:ASN604 3.7 13.2 1.0
NE2 A:HIS540 3.8 11.7 1.0
C4 A:PTQ2001 3.8 20.0 1.0
C A:PHE601 3.8 17.8 1.0
NE1 A:TRP568 3.8 12.1 1.0
O4 A:PTQ2001 3.9 20.0 1.0
OD1 A:ASP201 3.9 16.2 1.0
OH A:TYR100 3.9 17.1 1.0
CE1 A:HIS540 4.2 12.7 1.0
CB A:PHE601 4.5 12.4 1.0
CB A:ASP201 4.5 12.1 1.0
CE2 A:TRP568 4.6 12.4 1.0
O A:HOH5012 4.6 30.0 1.0
CB A:ASN604 4.6 10.2 1.0
CZ2 A:TRP568 4.6 16.5 1.0
CA A:PHE601 4.7 16.4 1.0
O1 A:PTQ2001 4.7 20.0 1.0
N A:CYS602 4.7 12.4 1.0
CA A:CYS602 4.8 14.3 1.0
CD1 A:TRP568 4.8 10.8 1.0

Sodium binding site 2 out of 8 in 5a1a

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Sodium binding site 2 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4002

b:30.0
occ:1.00
 O A:TYR559 2.4 12.4 1.0
O A:PHE556 2.4 12.1 1.0
O A:HOH5082 2.6 30.0 1.0
O A:LEU562 2.7 10.0 1.0
O A:PRO560 3.3 12.7 1.0
C A:TYR559 3.3 12.3 1.0
O A:HOH5081 3.6 30.0 1.0
CA A:PRO560 3.6 9.6 1.0
C A:LEU562 3.6 12.6 1.0
C A:PRO560 3.7 10.7 1.0
C A:PHE556 3.7 14.0 1.0
O A:HOH5083 3.7 30.0 1.0
N A:PRO560 3.8 13.2 1.0
N A:LEU562 4.3 9.0 1.0
CA A:LEU562 4.4 10.4 1.0
N A:GLN563 4.5 8.6 1.0
CD1 A:LEU350 4.5 9.8 1.0
CA A:TYR559 4.6 8.6 1.0
CA A:GLN563 4.6 8.8 1.0
N A:ARG557 4.6 9.0 1.0
CA A:ARG557 4.6 4.7 1.0
CA A:PHE556 4.6 10.8 1.0
N A:TYR559 4.6 9.9 1.0
CB A:LEU562 4.6 9.0 1.0
C A:ARG557 4.7 11.7 1.0
N A:ARG561 4.7 9.7 1.0
O A:ARG557 4.7 12.1 1.0
CG A:GLN563 4.9 10.0 1.0

Sodium binding site 3 out of 8 in 5a1a

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Sodium binding site 3 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4001

b:30.0
occ:1.00
 OD2 B:ASP201 2.2 11.7 1.0
O5 B:PTQ2001 2.3 20.0 1.0
C6 B:PTQ2001 2.4 20.0 1.0
OD1 B:ASN604 2.4 14.4 1.0
O B:HOH5013 2.6 30.0 1.0
O B:PHE601 2.7 12.1 1.0
CG B:ASN604 3.3 18.8 1.0
CG B:ASP201 3.4 17.0 1.0
C5 B:PTQ2001 3.6 20.0 1.0
ND2 B:ASN604 3.7 13.2 1.0
NE2 B:HIS540 3.8 11.7 1.0
C4 B:PTQ2001 3.8 20.0 1.0
C B:PHE601 3.8 17.8 1.0
NE1 B:TRP568 3.8 12.1 1.0
O4 B:PTQ2001 3.9 20.0 1.0
OD1 B:ASP201 3.9 16.2 1.0
OH B:TYR100 3.9 17.1 1.0
CE1 B:HIS540 4.2 12.7 1.0
CB B:PHE601 4.5 12.4 1.0
CB B:ASP201 4.5 12.1 1.0
CE2 B:TRP568 4.6 12.4 1.0
O B:HOH5012 4.6 30.0 1.0
CB B:ASN604 4.6 10.2 1.0
CZ2 B:TRP568 4.6 16.5 1.0
CA B:PHE601 4.7 16.4 1.0
O1 B:PTQ2001 4.7 20.0 1.0
N B:CYS602 4.7 12.4 1.0
CA B:CYS602 4.8 14.3 1.0
CD1 B:TRP568 4.8 10.8 1.0

Sodium binding site 4 out of 8 in 5a1a

Go back to Sodium Binding Sites List in 5a1a
Sodium binding site 4 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4002

b:30.0
occ:1.00
 O B:TYR559 2.4 12.4 1.0
O B:PHE556 2.4 12.1 1.0
O B:HOH5082 2.6 30.0 1.0
O B:LEU562 2.7 10.0 1.0
O B:PRO560 3.3 12.7 1.0
C B:TYR559 3.3 12.3 1.0
O B:HOH5081 3.6 30.0 1.0
CA B:PRO560 3.6 9.6 1.0
C B:LEU562 3.6 12.6 1.0
C B:PRO560 3.7 10.7 1.0
C B:PHE556 3.7 14.0 1.0
O B:HOH5083 3.7 30.0 1.0
N B:PRO560 3.8 13.2 1.0
N B:LEU562 4.3 9.0 1.0
CA B:LEU562 4.4 10.4 1.0
N B:GLN563 4.5 8.6 1.0
CD1 B:LEU350 4.5 9.8 1.0
CA B:TYR559 4.6 8.6 1.0
CA B:GLN563 4.6 8.8 1.0
N B:ARG557 4.6 9.0 1.0
CA B:ARG557 4.6 4.7 1.0
CA B:PHE556 4.6 10.8 1.0
N B:TYR559 4.6 9.9 1.0
CB B:LEU562 4.6 9.0 1.0
C B:ARG557 4.7 11.7 1.0
N B:ARG561 4.7 9.7 1.0
O B:ARG557 4.7 12.1 1.0
CG B:GLN563 4.9 10.0 1.0

Sodium binding site 5 out of 8 in 5a1a

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Sodium binding site 5 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na4001

b:30.0
occ:1.00
 OD2 C:ASP201 2.2 11.7 1.0
O5 C:PTQ2001 2.3 20.0 1.0
C6 C:PTQ2001 2.4 20.0 1.0
OD1 C:ASN604 2.4 14.4 1.0
O C:HOH5013 2.6 30.0 1.0
O C:PHE601 2.7 12.1 1.0
CG C:ASN604 3.3 18.8 1.0
CG C:ASP201 3.4 17.0 1.0
C5 C:PTQ2001 3.6 20.0 1.0
ND2 C:ASN604 3.7 13.2 1.0
NE2 C:HIS540 3.8 11.7 1.0
C4 C:PTQ2001 3.8 20.0 1.0
C C:PHE601 3.8 17.8 1.0
NE1 C:TRP568 3.8 12.1 1.0
O4 C:PTQ2001 3.9 20.0 1.0
OD1 C:ASP201 3.9 16.2 1.0
OH C:TYR100 3.9 17.1 1.0
CE1 C:HIS540 4.2 12.7 1.0
CB C:PHE601 4.5 12.4 1.0
CB C:ASP201 4.5 12.1 1.0
CE2 C:TRP568 4.6 12.4 1.0
O C:HOH5012 4.6 30.0 1.0
CB C:ASN604 4.6 10.2 1.0
CZ2 C:TRP568 4.6 16.5 1.0
CA C:PHE601 4.7 16.4 1.0
O1 C:PTQ2001 4.7 20.0 1.0
N C:CYS602 4.7 12.4 1.0
CA C:CYS602 4.8 14.3 1.0
CD1 C:TRP568 4.8 10.8 1.0

Sodium binding site 6 out of 8 in 5a1a

Go back to Sodium Binding Sites List in 5a1a
Sodium binding site 6 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na4002

b:30.0
occ:1.00
 O C:TYR559 2.4 12.4 1.0
O C:PHE556 2.4 12.1 1.0
O C:HOH5082 2.6 30.0 1.0
O C:LEU562 2.7 10.0 1.0
O C:PRO560 3.3 12.7 1.0
C C:TYR559 3.3 12.3 1.0
O C:HOH5081 3.6 30.0 1.0
CA C:PRO560 3.6 9.6 1.0
C C:LEU562 3.6 12.6 1.0
C C:PRO560 3.7 10.7 1.0
C C:PHE556 3.7 14.0 1.0
O C:HOH5083 3.7 30.0 1.0
N C:PRO560 3.8 13.2 1.0
N C:LEU562 4.3 9.0 1.0
CA C:LEU562 4.4 10.4 1.0
N C:GLN563 4.5 8.6 1.0
CD1 C:LEU350 4.5 9.8 1.0
CA C:TYR559 4.6 8.6 1.0
CA C:GLN563 4.6 8.8 1.0
N C:ARG557 4.6 9.0 1.0
CA C:ARG557 4.6 4.7 1.0
CA C:PHE556 4.6 10.8 1.0
N C:TYR559 4.6 9.9 1.0
CB C:LEU562 4.6 9.0 1.0
C C:ARG557 4.7 11.7 1.0
N C:ARG561 4.7 9.7 1.0
O C:ARG557 4.7 12.1 1.0
CG C:GLN563 4.9 10.0 1.0

Sodium binding site 7 out of 8 in 5a1a

Go back to Sodium Binding Sites List in 5a1a
Sodium binding site 7 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4001

b:30.0
occ:1.00
 OD2 D:ASP201 2.2 11.7 1.0
O5 D:PTQ2001 2.3 20.0 1.0
C6 D:PTQ2001 2.4 20.0 1.0
OD1 D:ASN604 2.4 14.4 1.0
O D:HOH5013 2.6 30.0 1.0
O D:PHE601 2.7 12.1 1.0
CG D:ASN604 3.3 18.8 1.0
CG D:ASP201 3.4 17.0 1.0
C5 D:PTQ2001 3.6 20.0 1.0
ND2 D:ASN604 3.7 13.2 1.0
NE2 D:HIS540 3.8 11.7 1.0
C4 D:PTQ2001 3.8 20.0 1.0
C D:PHE601 3.8 17.8 1.0
NE1 D:TRP568 3.8 12.1 1.0
O4 D:PTQ2001 3.9 20.0 1.0
OD1 D:ASP201 3.9 16.2 1.0
OH D:TYR100 3.9 17.1 1.0
CE1 D:HIS540 4.2 12.7 1.0
CB D:PHE601 4.5 12.4 1.0
CB D:ASP201 4.5 12.1 1.0
CE2 D:TRP568 4.6 12.4 1.0
O D:HOH5012 4.6 30.0 1.0
CB D:ASN604 4.6 10.2 1.0
CZ2 D:TRP568 4.6 16.5 1.0
CA D:PHE601 4.7 16.4 1.0
O1 D:PTQ2001 4.7 20.0 1.0
N D:CYS602 4.7 12.4 1.0
CA D:CYS602 4.8 14.3 1.0
CD1 D:TRP568 4.8 10.8 1.0

Sodium binding site 8 out of 8 in 5a1a

Go back to Sodium Binding Sites List in 5a1a
Sodium binding site 8 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4002

b:30.0
occ:1.00
 O D:TYR559 2.4 12.4 1.0
O D:PHE556 2.4 12.1 1.0
O D:HOH5082 2.6 30.0 1.0
O D:LEU562 2.7 10.0 1.0
O D:PRO560 3.3 12.7 1.0
C D:TYR559 3.3 12.3 1.0
O D:HOH5081 3.6 30.0 1.0
CA D:PRO560 3.6 9.6 1.0
C D:LEU562 3.6 12.6 1.0
C D:PRO560 3.7 10.7 1.0
C D:PHE556 3.7 14.0 1.0
O D:HOH5083 3.7 30.0 1.0
N D:PRO560 3.8 13.2 1.0
N D:LEU562 4.3 9.0 1.0
CA D:LEU562 4.4 10.4 1.0
N D:GLN563 4.5 8.6 1.0
CD1 D:LEU350 4.5 9.8 1.0
CA D:TYR559 4.6 8.6 1.0
CA D:GLN563 4.6 8.8 1.0
N D:ARG557 4.6 9.0 1.0
CA D:ARG557 4.6 4.7 1.0
CA D:PHE556 4.6 10.8 1.0
N D:TYR559 4.6 9.9 1.0
CB D:LEU562 4.6 9.0 1.0
C D:ARG557 4.7 11.7 1.0
N D:ARG561 4.7 9.7 1.0
O D:ARG557 4.7 12.1 1.0
CG D:GLN563 4.9 10.0 1.0

Reference:

A.Bartesaghi, A.Merk, S.Banerjee, D.Matthies, X.Wu, J.Milne, S.Subramaniam. 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor Science 2015.
ISSN: ESSN 1095-9203
PubMed: 25953817
DOI: 10.1126/SCIENCE.AAB1576
Page generated: Sun Aug 17 22:51:00 2025

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