Atomistry » Sodium » PDB 4zm0-5ac7 » 5a1a
Atomistry »
  Sodium »
    PDB 4zm0-5ac7 »
      5a1a »

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

Go back to Sodium Binding Sites List in 5a1a
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

Go back to Sodium Binding Sites List in 5a1a
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

Go back to Sodium Binding Sites List in 5a1a
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

Go back to Sodium Binding Sites List in 5a1a
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: Mon Oct 7 19:48:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy