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Sodium in PDB 6cvm: Atomic Resolution Cryo-Em Structure of Beta-Galactosidase

Enzymatic activity of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase

All present enzymatic activity of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase:
3.2.1.23;

Other elements in 6cvm:

The structure of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 8 in 6cvm

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Sodium binding site 1 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2004

b:67.6
occ:1.00
 OD2 A:ASP201 2.5 68.8 1.0
O A:PHE601 2.5 70.0 1.0
OD1 A:ASN604 2.5 62.4 1.0
O A:HOH2633 2.5 65.7 1.0
O3 A:PTQ2001 3.0 70.6 1.0
CG A:ASP201 3.3 68.8 1.0
OH A:TYR100 3.5 68.3 1.0
CG A:ASN604 3.6 62.4 1.0
C A:PHE601 3.6 70.0 1.0
C3 A:PTQ2001 3.6 70.6 1.0
OD1 A:ASP201 3.7 68.8 1.0
NE1 A:TRP568 3.8 56.4 1.0
ND2 A:ASN604 4.1 62.4 1.0
O A:HOH2400 4.3 64.6 1.0
CB A:ASP201 4.3 68.8 1.0
C4 A:PTQ2001 4.3 70.6 1.0
CA A:CYS602 4.4 68.0 1.0
CZ2 A:TRP568 4.4 56.4 1.0
N A:CYS602 4.5 68.0 1.0
CE2 A:TRP568 4.5 56.4 1.0
CB A:PHE601 4.5 70.0 1.0
O A:ASP201 4.6 68.8 1.0
CA A:PHE601 4.6 70.0 1.0
NE2 A:HIS540 4.7 60.9 1.0
CZ A:TYR100 4.7 68.3 1.0
C A:CYS602 4.8 68.0 1.0
CB A:ASN604 4.8 62.4 1.0
C2 A:PTQ2001 4.9 70.6 1.0
CD1 A:TRP568 4.9 56.4 1.0
O2 A:PTQ2001 4.9 70.6 1.0
O A:CYS602 5.0 68.0 1.0

Sodium binding site 2 out of 8 in 6cvm

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Sodium binding site 2 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2005

b:61.3
occ:1.00
 O A:TYR559 2.5 57.9 1.0
O A:PHE556 2.5 49.1 1.0
O A:LEU562 2.5 51.5 1.0
O A:HOH2643 2.7 59.4 1.0
O A:HOH2432 3.1 59.1 1.0
O A:PRO560 3.5 57.6 1.0
C A:TYR559 3.6 57.9 1.0
C A:LEU562 3.6 51.5 1.0
O A:HOH2315 3.7 63.1 1.0
C A:PHE556 3.7 49.1 1.0
CA A:PRO560 3.7 57.6 1.0
C A:PRO560 3.8 57.6 1.0
N A:PRO560 4.1 57.6 1.0
CD1 A:LEU350 4.3 51.1 1.0
CA A:GLN563 4.3 53.1 1.0
N A:LEU562 4.4 51.5 1.0
N A:GLN563 4.4 53.1 1.0
O A:HOH3034 4.5 62.7 1.0
CA A:LEU562 4.5 51.5 1.0
CA A:PHE556 4.5 49.1 1.0
N A:TYR559 4.7 57.9 1.0
N A:ARG557 4.7 55.2 1.0
CA A:ARG557 4.7 55.2 1.0
CA A:TYR559 4.7 57.9 1.0
N A:ARG561 4.8 54.6 1.0
CG A:GLN563 4.8 53.1 1.0
CB A:LEU562 4.8 51.5 1.0
C A:ARG557 4.9 55.2 1.0
O A:ARG557 4.9 55.2 1.0

Sodium binding site 3 out of 8 in 6cvm

Go back to Sodium Binding Sites List in 6cvm
Sodium binding site 3 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2004

b:67.6
occ:1.00
 OD2 B:ASP201 2.5 68.8 1.0
O B:PHE601 2.5 70.0 1.0
OD1 B:ASN604 2.5 62.4 1.0
O B:HOH2633 2.5 65.5 1.0
O3 B:PTQ2001 3.0 70.5 1.0
CG B:ASP201 3.3 68.8 1.0
OH B:TYR100 3.5 68.3 1.0
CG B:ASN604 3.6 62.4 1.0
C B:PHE601 3.6 70.0 1.0
C3 B:PTQ2001 3.6 70.5 1.0
OD1 B:ASP201 3.7 68.8 1.0
NE1 B:TRP568 3.8 56.5 1.0
ND2 B:ASN604 4.1 62.4 1.0
O B:HOH2400 4.3 64.5 1.0
CB B:ASP201 4.3 68.8 1.0
C4 B:PTQ2001 4.3 70.5 1.0
CA B:CYS602 4.4 68.1 1.0
CZ2 B:TRP568 4.4 56.5 1.0
N B:CYS602 4.5 68.1 1.0
CE2 B:TRP568 4.5 56.5 1.0
CB B:PHE601 4.5 70.0 1.0
O B:ASP201 4.6 68.8 1.0
CA B:PHE601 4.6 70.0 1.0
NE2 B:HIS540 4.7 60.8 1.0
CZ B:TYR100 4.7 68.3 1.0
C B:CYS602 4.8 68.1 1.0
CB B:ASN604 4.8 62.4 1.0
C2 B:PTQ2001 4.9 70.5 1.0
CD1 B:TRP568 4.9 56.5 1.0
O2 B:PTQ2001 4.9 70.5 1.0
O B:CYS602 5.0 68.1 1.0

Sodium binding site 4 out of 8 in 6cvm

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Sodium binding site 4 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2005

b:61.1
occ:1.00
 O B:TYR559 2.5 57.8 1.0
O B:PHE556 2.5 49.0 1.0
O B:LEU562 2.5 51.4 1.0
O B:HOH2643 2.7 59.5 1.0
O B:HOH2432 3.1 59.0 1.0
O B:PRO560 3.5 57.6 1.0
C B:TYR559 3.6 57.8 1.0
C B:LEU562 3.6 51.4 1.0
O B:HOH2315 3.7 63.0 1.0
C B:PHE556 3.7 49.0 1.0
CA B:PRO560 3.7 57.6 1.0
C B:PRO560 3.8 57.6 1.0
N B:PRO560 4.1 57.6 1.0
CD1 B:LEU350 4.3 51.2 1.0
CA B:GLN563 4.3 53.1 1.0
N B:LEU562 4.4 51.4 1.0
N B:GLN563 4.4 53.1 1.0
O B:HOH3035 4.5 62.7 1.0
CA B:LEU562 4.5 51.4 1.0
CA B:PHE556 4.5 49.0 1.0
N B:TYR559 4.7 57.8 1.0
N B:ARG557 4.7 55.1 1.0
CA B:ARG557 4.7 55.1 1.0
CA B:TYR559 4.7 57.8 1.0
N B:ARG561 4.8 54.6 1.0
CG B:GLN563 4.8 53.1 1.0
CB B:LEU562 4.8 51.4 1.0
C B:ARG557 4.9 55.1 1.0
O B:ARG557 4.9 55.1 1.0

Sodium binding site 5 out of 8 in 6cvm

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Sodium binding site 5 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2004

b:67.6
occ:1.00
 OD2 C:ASP201 2.5 68.8 1.0
O C:PHE601 2.5 70.0 1.0
OD1 C:ASN604 2.5 62.5 1.0
O C:HOH2634 2.5 65.5 1.0
O3 C:PTQ2001 3.0 70.6 1.0
CG C:ASP201 3.3 68.8 1.0
OH C:TYR100 3.5 68.3 1.0
CG C:ASN604 3.6 62.5 1.0
C C:PHE601 3.6 70.0 1.0
C3 C:PTQ2001 3.7 70.6 1.0
OD1 C:ASP201 3.7 68.8 1.0
NE1 C:TRP568 3.8 56.5 1.0
ND2 C:ASN604 4.1 62.5 1.0
O C:HOH2401 4.3 64.5 1.0
CB C:ASP201 4.3 68.8 1.0
C4 C:PTQ2001 4.3 70.6 1.0
CA C:CYS602 4.4 68.0 1.0
CZ2 C:TRP568 4.4 56.5 1.0
N C:CYS602 4.5 68.0 1.0
CE2 C:TRP568 4.5 56.5 1.0
CB C:PHE601 4.5 70.0 1.0
O C:ASP201 4.6 68.8 1.0
CA C:PHE601 4.6 70.0 1.0
NE2 C:HIS540 4.7 60.9 1.0
CZ C:TYR100 4.7 68.3 1.0
C C:CYS602 4.8 68.0 1.0
CB C:ASN604 4.8 62.5 1.0
C2 C:PTQ2001 4.9 70.6 1.0
CD1 C:TRP568 4.9 56.5 1.0
O2 C:PTQ2001 4.9 70.6 1.0
O C:CYS602 5.0 68.0 1.0

Sodium binding site 6 out of 8 in 6cvm

Go back to Sodium Binding Sites List in 6cvm
Sodium binding site 6 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2005

b:61.3
occ:1.00
 O C:TYR559 2.5 57.9 1.0
O C:PHE556 2.5 49.1 1.0
O C:LEU562 2.5 51.5 1.0
O C:HOH2644 2.7 59.3 1.0
O C:HOH2433 3.1 58.9 1.0
O C:PRO560 3.5 57.5 1.0
C C:TYR559 3.6 57.9 1.0
C C:LEU562 3.6 51.5 1.0
O C:HOH2315 3.7 63.0 1.0
C C:PHE556 3.7 49.1 1.0
CA C:PRO560 3.7 57.5 1.0
C C:PRO560 3.8 57.5 1.0
N C:PRO560 4.1 57.5 1.0
CD1 C:LEU350 4.3 51.1 1.0
CA C:GLN563 4.3 53.0 1.0
N C:LEU562 4.4 51.5 1.0
N C:GLN563 4.4 53.0 1.0
O C:HOH3037 4.5 62.6 1.0
CA C:LEU562 4.5 51.5 1.0
CA C:PHE556 4.5 49.1 1.0
N C:TYR559 4.7 57.9 1.0
N C:ARG557 4.7 55.2 1.0
CA C:ARG557 4.7 55.2 1.0
CA C:TYR559 4.7 57.9 1.0
N C:ARG561 4.8 54.6 1.0
CG C:GLN563 4.8 53.0 1.0
CB C:LEU562 4.8 51.5 1.0
C C:ARG557 4.9 55.2 1.0
O C:ARG557 4.9 55.2 1.0

Sodium binding site 7 out of 8 in 6cvm

Go back to Sodium Binding Sites List in 6cvm
Sodium binding site 7 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2004

b:67.6
occ:1.00
 OD2 D:ASP201 2.5 68.8 1.0
O D:PHE601 2.5 70.0 1.0
OD1 D:ASN604 2.5 62.4 1.0
O D:HOH2633 2.5 65.6 1.0
O3 D:PTQ2001 3.0 70.5 1.0
CG D:ASP201 3.3 68.8 1.0
OH D:TYR100 3.5 68.2 1.0
CG D:ASN604 3.6 62.4 1.0
C D:PHE601 3.6 70.0 1.0
C3 D:PTQ2001 3.7 70.5 1.0
OD1 D:ASP201 3.7 68.8 1.0
NE1 D:TRP568 3.8 56.5 1.0
ND2 D:ASN604 4.1 62.4 1.0
O D:HOH2401 4.3 64.6 1.0
CB D:ASP201 4.3 68.8 1.0
C4 D:PTQ2001 4.3 70.5 1.0
CA D:CYS602 4.4 67.9 1.0
CZ2 D:TRP568 4.4 56.5 1.0
N D:CYS602 4.5 67.9 1.0
CE2 D:TRP568 4.5 56.5 1.0
CB D:PHE601 4.5 70.0 1.0
O D:ASP201 4.6 68.8 1.0
CA D:PHE601 4.6 70.0 1.0
NE2 D:HIS540 4.7 60.9 1.0
CZ D:TYR100 4.7 68.2 1.0
C D:CYS602 4.8 67.9 1.0
CB D:ASN604 4.8 62.4 1.0
C2 D:PTQ2001 4.9 70.5 1.0
CD1 D:TRP568 4.9 56.5 1.0
O2 D:PTQ2001 4.9 70.5 1.0
O D:CYS602 5.0 67.9 1.0

Sodium binding site 8 out of 8 in 6cvm

Go back to Sodium Binding Sites List in 6cvm
Sodium binding site 8 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2005

b:61.1
occ:1.00
 O D:TYR559 2.5 57.8 1.0
O D:PHE556 2.5 49.0 1.0
O D:LEU562 2.5 51.4 1.0
O D:HOH2644 2.7 59.2 1.0
O D:HOH2433 3.1 58.9 1.0
O D:PRO560 3.5 57.5 1.0
C D:TYR559 3.6 57.8 1.0
C D:LEU562 3.6 51.4 1.0
O D:HOH2316 3.7 62.9 1.0
C D:PHE556 3.7 49.0 1.0
CA D:PRO560 3.7 57.5 1.0
C D:PRO560 3.8 57.5 1.0
N D:PRO560 4.1 57.5 1.0
CD1 D:LEU350 4.3 51.2 1.0
CA D:GLN563 4.3 53.1 1.0
N D:LEU562 4.4 51.4 1.0
N D:GLN563 4.4 53.1 1.0
O D:HOH3036 4.5 62.7 1.0
CA D:LEU562 4.5 51.4 1.0
CA D:PHE556 4.5 49.0 1.0
N D:TYR559 4.7 57.8 1.0
N D:ARG557 4.7 55.2 1.0
CA D:ARG557 4.7 55.2 1.0
CA D:TYR559 4.7 57.8 1.0
N D:ARG561 4.8 54.6 1.0
CG D:GLN563 4.8 53.1 1.0
CB D:LEU562 4.8 51.4 1.0
C D:ARG557 4.9 55.2 1.0
O D:ARG557 4.9 55.2 1.0

Reference:

A.Bartesaghi, C.Aguerrebere, V.Falconieri, S.Banerjee, L.A.Earl, X.Zhu, N.Grigorieff, J.L.S.Milne, G.Sapiro, X.Wu, S.Subramaniam. Atomic Resolution Cryo-Em Structure of Beta-Galactosidase. Structure V. 26 848 2018.
ISSN: ISSN 1878-4186
PubMed: 29754826
DOI: 10.1016/J.STR.2018.04.004
Page generated: Tue Oct 8 06:48:29 2024

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