Atomistry » Sodium » PDB 6syc-6tbn » 6tbk
Atomistry »
  Sodium »
    PDB 6syc-6tbn »
      6tbk »

Sodium in PDB 6tbk: Structure of A Beta Galactosidase with Inhibitor

Enzymatic activity of Structure of A Beta Galactosidase with Inhibitor

All present enzymatic activity of Structure of A Beta Galactosidase with Inhibitor:
3.2.1.23;

Protein crystallography data

The structure of Structure of A Beta Galactosidase with Inhibitor, PDB code: 6tbk was solved by W.Offen, G.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.20 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 98.952, 116.052, 115.576, 89.84, 90.07, 89.98
R / Rfree (%) 15.2 / 21.2

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Sodium atom in the Structure of A Beta Galactosidase with Inhibitor (pdb code 6tbk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 32 binding sites of Sodium where determined in the Structure of A Beta Galactosidase with Inhibitor, PDB code: 6tbk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 1 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:37.5
occ:1.00
 O A:HOH916 2.2 46.7 1.0
O A:GLY466 2.4 32.4 1.0
OD1 A:ASP464 2.5 29.0 1.0
OG A:SER518 2.5 40.6 1.0
O A:HOH751 2.5 40.0 1.0
OE1 A:GLN519 2.6 51.0 1.0
CB A:SER518 3.2 44.1 1.0
CG A:ASP464 3.2 35.8 1.0
NA A:NA602 3.3 40.2 1.0
C A:GLY466 3.4 27.1 1.0
OD2 A:ASP464 3.4 39.0 1.0
CD A:GLN519 3.5 63.3 1.0
NE2 A:GLN519 3.7 59.0 1.0
CA A:GLY466 3.8 30.0 1.0
N A:GLY466 3.9 27.3 1.0
OD1 A:ASP469 4.4 39.5 1.0
N A:LEU467 4.6 29.0 1.0
CA A:SER518 4.6 38.6 1.0
O A:HOH828 4.6 40.7 1.0
CB A:ASP464 4.6 29.7 1.0
C A:SER518 4.9 42.6 1.0
CG A:GLN519 5.0 60.7 1.0

Sodium binding site 2 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 2 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:40.2
occ:1.00
 O A:HOH828 2.2 40.7 1.0
O A:HOH751 2.6 40.0 1.0
O A:SER518 2.6 44.3 1.0
OE1 A:GLN519 2.6 51.0 1.0
OG A:SER518 2.7 40.6 1.0
C A:SER518 3.2 42.6 1.0
NA A:NA601 3.3 37.5 1.0
CB A:SER518 3.5 44.1 1.0
CD A:GLN519 3.6 63.3 1.0
CA A:SER518 3.7 38.6 1.0
CG A:GLN519 4.2 60.7 1.0
N A:GLN519 4.2 43.6 1.0
OD2 A:ASP469 4.4 31.2 1.0
OD1 A:ASP469 4.4 39.5 1.0
OD1 A:ASP464 4.4 29.0 1.0
NE2 A:GLN519 4.6 59.0 1.0
OD2 A:ASP464 4.6 39.0 1.0
CG A:ASP464 4.7 35.8 1.0
CA A:GLN519 4.7 51.0 1.0
CG A:ASP469 4.8 32.2 1.0
O A:HOH916 4.8 46.7 1.0

Sodium binding site 3 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 3 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:33.4
occ:1.00
 O A:HOH810 2.4 24.3 1.0
OE2 A:GLU533 2.5 28.0 1.0
OE1 A:GLU544 2.6 28.8 1.0
O A:HOH827 3.1 37.2 1.0
CD A:GLU533 3.4 33.6 1.0
CD A:GLU544 3.6 30.9 1.0
CG A:GLU533 3.7 22.5 1.0
OE2 A:GLU544 3.8 35.5 1.0
O A:HOH849 3.9 28.0 1.0
O A:HOH912 4.1 38.1 1.0
O A:PRO562 4.4 25.0 1.0
O A:GLY534 4.4 26.6 1.0
OE1 A:GLU533 4.5 25.9 1.0
CA A:HIS563 4.6 23.2 1.0
O A:HOH936 4.6 31.7 1.0
O A:HOH920 4.7 28.2 1.0
ND1 A:HIS563 4.7 24.2 1.0
O A:HOH929 4.9 33.9 1.0
N A:LEU564 4.9 19.5 1.0
O A:HOH753 4.9 33.0 1.0
N A:GLY534 5.0 22.0 1.0
CG A:GLU544 5.0 25.5 1.0
C A:GLY534 5.0 30.1 1.0

Sodium binding site 4 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 4 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:39.8
occ:1.00
 O A:HIS49 2.5 27.8 1.0
O A:GLY367 2.5 29.1 1.0
O A:HOH868 3.0 35.8 1.0
O A:HOH872 3.2 36.4 1.0
C A:GLY367 3.4 25.1 1.0
C A:HIS49 3.6 27.2 1.0
CA A:GLY367 3.7 24.5 1.0
OG A:SER417 3.7 50.4 1.0
CB A:SER417 3.8 38.2 1.0
C A:SER417 3.9 35.5 1.0
N A:TYR418 4.0 27.1 1.0
O A:SER417 4.0 41.3 1.0
CA A:TYR418 4.2 25.5 1.0
N A:HIS49 4.3 31.1 1.0
O A:HOH853 4.4 27.7 1.0
O A:GLY368 4.4 23.7 1.0
CA A:SER417 4.5 27.6 1.0
CA A:HIS49 4.5 27.7 1.0
O A:HOH858 4.5 24.3 1.0
N A:ALA50 4.6 27.3 1.0
CA A:ALA50 4.6 27.7 1.0
O A:HOH857 4.6 30.2 1.0
CG2 A:ILE369 4.6 29.4 1.0
N A:GLY368 4.6 23.1 1.0
C A:GLY368 4.6 24.8 1.0
CB A:TYR418 4.7 28.6 1.0
CB A:HIS49 4.8 31.2 1.0
O A:HOH846 4.8 33.3 1.0

Sodium binding site 5 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 5 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:38.3
occ:1.00
 O B:HOH963 2.2 38.5 1.0
O B:GLY466 2.3 31.4 1.0
OG B:SER518 2.4 36.5 1.0
OD1 B:ASP464 2.5 34.9 1.0
CG B:ASP464 3.3 36.7 1.0
CB B:SER518 3.3 49.6 1.0
O B:HOH703 3.3 32.4 1.0
C B:GLY466 3.4 33.7 1.0
OD2 B:ASP464 3.4 42.0 1.0
CA B:GLY466 3.8 29.1 1.0
N B:GLY466 4.0 34.1 1.0
OD1 B:ASP469 4.4 33.6 1.0
NE2 B:GLN519 4.5 48.4 0.5
N B:LEU467 4.6 30.8 1.0
CB B:ASP464 4.6 30.1 1.0
CA B:SER518 4.6 39.7 1.0
O B:HOH794 4.7 37.6 1.0
O B:SER518 5.0 41.0 1.0
C B:SER518 5.0 42.8 1.0

Sodium binding site 6 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 6 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:34.1
occ:1.00
 OE1 B:GLU544 2.4 29.2 1.0
OE2 B:GLU533 2.5 27.4 1.0
O B:HOH754 2.6 25.5 1.0
O B:HOH732 3.2 35.2 1.0
CD B:GLU533 3.4 22.5 1.0
CD B:GLU544 3.5 28.2 1.0
CG B:GLU533 3.6 21.5 1.0
O B:HOH882 3.7 29.5 1.0
OE2 B:GLU544 3.8 31.6 1.0
O H:HOH828 4.2 49.0 1.0
O B:GLY534 4.4 25.5 1.0
O B:PRO562 4.5 22.8 1.0
OE1 B:GLU533 4.5 25.1 1.0
ND1 B:HIS563 4.7 23.4 1.0
O B:HOH736 4.7 36.4 1.0
O B:HOH977 4.8 29.1 1.0
CA B:HIS563 4.8 20.8 1.0
O B:HOH998 4.8 32.2 1.0
CG B:GLU544 4.8 24.1 1.0
O B:HOH994 4.9 31.1 1.0

Sodium binding site 7 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 7 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:36.1
occ:1.00
 O B:HIS49 2.4 29.6 1.0
O B:GLY367 2.6 24.8 1.0
OG B:SER417 2.9 40.6 1.0
O B:HOH950 2.9 37.5 1.0
O B:HOH946 3.1 33.2 1.0
C B:GLY367 3.5 25.8 1.0
C B:HIS49 3.6 24.7 1.0
CA B:GLY367 3.7 24.5 1.0
CB B:SER417 3.8 28.4 1.0
C B:SER417 3.9 40.6 1.0
N B:TYR418 4.1 28.6 1.0
O B:SER417 4.1 49.4 1.0
N B:HIS49 4.3 25.9 1.0
CA B:TYR418 4.3 30.4 1.0
O B:HOH891 4.4 41.8 1.0
CA B:HIS49 4.4 26.5 1.0
CA B:SER417 4.5 24.1 1.0
O B:HOH896 4.5 26.1 1.0
N B:ALA50 4.5 23.6 1.0
O B:HOH838 4.6 23.0 1.0
O B:GLY368 4.6 23.6 1.0
CA B:ALA50 4.6 26.5 1.0
N B:GLY368 4.7 23.3 1.0
CG2 B:ILE369 4.7 29.8 1.0
C B:GLY368 4.8 21.9 1.0
CB B:HIS49 4.8 25.0 1.0
O B:HOH807 4.8 28.1 1.0
CB B:TYR418 4.8 30.2 1.0
O B:HOH812 5.0 38.7 1.0

Sodium binding site 8 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 8 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:33.9
occ:1.00
 O C:HOH855 2.4 25.2 1.0
OE2 C:GLU533 2.5 28.0 1.0
OE1 C:GLU544 2.6 28.3 1.0
O C:HOH706 2.6 39.2 1.0
O C:HOH812 3.2 37.0 1.0
CD C:GLU533 3.3 27.1 1.0
CD C:GLU544 3.5 30.0 1.0
CG C:GLU533 3.6 20.6 1.0
OE2 C:GLU544 3.8 32.0 1.0
O C:HOH897 3.8 29.0 1.0
O C:HOH905 4.0 46.4 1.0
O C:PRO562 4.3 26.7 1.0
O C:GLY534 4.4 23.6 1.0
OE1 C:GLU533 4.5 26.7 1.0
ND1 C:HIS563 4.6 25.8 1.0
O C:HOH950 4.7 26.0 1.0
CA C:HIS563 4.7 20.6 1.0
O C:HOH979 4.7 26.9 1.0
CG C:GLU544 4.9 28.3 1.0
N C:LEU564 4.9 22.8 1.0
N C:GLY534 4.9 24.7 1.0
O C:HOH973 5.0 34.4 1.0
CB C:GLU533 5.0 20.9 1.0

Sodium binding site 9 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 9 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:39.3
occ:1.00
 O C:HIS49 2.3 30.3 1.0
O C:GLY367 2.5 28.2 1.0
O C:HOH927 2.7 32.8 1.0
OG C:SER417 3.1 49.4 1.0
C C:GLY367 3.4 25.7 1.0
O C:HOH763 3.5 31.5 0.7
C C:HIS49 3.6 31.5 1.0
CA C:GLY367 3.6 24.4 1.0
O C:SER417 3.6 61.8 1.0
C C:SER417 3.8 42.1 1.0
CB C:SER417 4.0 38.2 1.0
N C:TYR418 4.1 29.7 1.0
CA C:TYR418 4.2 36.1 1.0
N C:HIS49 4.2 25.0 1.0
O C:HOH895 4.3 38.4 1.0
O C:HOH835 4.4 27.7 1.0
CA C:HIS49 4.4 28.3 1.0
CA C:SER417 4.5 28.9 1.0
N C:ALA50 4.5 26.1 1.0
O C:GLY368 4.6 24.0 1.0
N C:GLY368 4.6 22.6 1.0
O C:HOH851 4.6 22.8 1.0
CA C:ALA50 4.7 27.5 1.0
CB C:HIS49 4.7 26.9 1.0
CG2 C:ILE369 4.8 29.9 1.0
CB C:TYR418 4.8 29.4 1.0
C C:GLY368 4.8 24.4 1.0
O C:HOH839 4.9 32.7 1.0
O C:HOH747 4.9 29.9 1.0

Sodium binding site 10 out of 32 in 6tbk

Go back to Sodium Binding Sites List in 6tbk
Sodium binding site 10 out of 32 in the Structure of A Beta Galactosidase with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of A Beta Galactosidase with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:48.0
occ:1.00
 O C:GLY466 2.3 36.8 1.0
OD1 C:ASP464 2.5 37.4 1.0
OG C:SER518 2.5 44.0 1.0
O C:HOH941 2.6 42.1 1.0
NA C:NA604 3.1 50.6 1.0
CB C:SER518 3.2 47.9 1.0
CG C:ASP464 3.2 41.0 1.0
OD2 C:ASP464 3.3 48.9 1.0
C C:GLY466 3.4 31.9 1.0
CA C:GLY466 3.8 37.1 1.0
N C:GLY466 3.9 35.9 1.0
OD1 C:ASP469 4.3 44.6 1.0
CA C:SER518 4.6 42.2 1.0
N C:LEU467 4.6 36.5 1.0
O C:HOH776 4.6 36.5 0.5
CB C:ASP464 4.6 37.3 1.0
C C:SER518 4.9 52.3 1.0

Reference:

W.Offen, G.Davies. Structure of A Beta Galactosidase with Inhibitor To Be Published.
Page generated: Tue Oct 8 13:39:54 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy