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

Sodium in PDB 6tbh: 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: 6tbh 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) 81.86 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.103, 115.386, 115.723, 90.21, 89.99, 89.85
R / Rfree (%) 13.1 / 18.2

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 6tbh). 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: 6tbh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na603

b:32.8
occ:1.00
 O A:GLY466 2.3 28.4 1.0
O A:HOH760 2.4 38.6 1.0
OD1 A:ASP464 2.5 26.9 1.0
O A:HOH1057 2.5 46.9 1.0
OG A:SER518 2.5 33.3 1.0
OE1 A:GLN519 2.7 47.8 1.0
CG A:ASP464 3.2 29.4 1.0
CB A:SER518 3.3 39.1 1.0
C A:GLY466 3.4 25.7 1.0
OD2 A:ASP464 3.4 32.9 1.0
NA A:NA604 3.5 39.5 1.0
CD A:GLN519 3.7 59.7 1.0
CA A:GLY466 3.7 25.0 1.0
N A:GLY466 3.9 25.9 1.0
NE2 A:GLN519 3.9 46.6 1.0
OD1 A:ASP469 4.4 29.1 1.0
N A:LEU467 4.6 27.9 1.0
CB A:ASP464 4.6 25.0 1.0
CA A:SER518 4.7 32.7 1.0
O A:HOH914 4.7 46.5 1.0

Sodium binding site 2 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na604

b:39.5
occ:1.00
 O A:HOH1041 2.2 46.5 1.0
O A:HOH914 2.3 46.5 1.0
O A:SER518 2.5 39.3 1.0
OG A:SER518 2.5 33.3 1.0
O A:HOH760 2.6 38.6 1.0
OE1 A:GLN519 2.7 47.8 1.0
C A:SER518 3.3 38.1 1.0
NA A:NA603 3.5 32.8 1.0
CB A:SER518 3.5 39.1 1.0
CA A:SER518 3.7 32.7 1.0
CD A:GLN519 3.7 59.7 1.0
N A:GLN519 4.2 36.5 1.0
CG A:GLN519 4.3 63.9 1.0
OD2 A:ASP469 4.3 31.9 1.0
OD1 A:ASP469 4.4 29.1 1.0
OD2 A:ASP464 4.6 32.9 1.0
CA A:GLN519 4.7 41.3 1.0
OD1 A:ASP464 4.7 26.9 1.0
CG A:ASP464 4.7 29.4 1.0
CG A:ASP469 4.8 25.7 1.0
NE2 A:GLN519 4.8 46.6 1.0

Sodium binding site 3 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na605

b:28.2
occ:1.00
 OE2 A:GLU533 2.5 22.4 1.0
O A:HOH856 2.5 23.2 1.0
O A:HOH880 2.6 39.1 1.0
OE1 A:GLU544 2.6 23.4 1.0
O A:HOH1083 2.7 42.4 1.0
O A:HOH815 3.2 33.7 1.0
CD A:GLU533 3.4 21.8 1.0
CD A:GLU544 3.6 24.4 1.0
CG A:GLU533 3.6 18.3 1.0
O A:HOH944 3.8 25.4 1.0
OE2 A:GLU544 3.9 26.9 1.0
O A:HOH1034 4.0 33.3 1.0
O A:PRO562 4.3 20.8 1.0
O A:GLY534 4.5 21.9 1.0
OE1 A:GLU533 4.5 19.6 1.0
ND1 A:HIS563 4.6 18.8 1.0
O A:HOH1056 4.7 26.6 1.0
CA A:HIS563 4.7 19.2 1.0
O A:HOH1119 4.8 29.6 1.0
O A:HOH1101 4.8 31.7 1.0
N A:LEU564 4.9 18.9 1.0
N A:GLY534 5.0 21.4 1.0
CG A:GLU544 5.0 24.2 1.0

Sodium binding site 4 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na606

b:35.8
occ:1.00
 O A:HIS49 2.4 26.6 1.0
O A:GLY367 2.6 21.8 1.0
OG A:SER417 2.9 33.6 1.0
O A:HOH975 3.0 32.7 1.0
O A:HOH945 3.2 29.4 1.0
C A:GLY367 3.4 19.7 1.0
CA A:GLY367 3.6 23.5 1.0
C A:HIS49 3.6 23.8 1.0
CB A:SER417 3.9 25.7 1.0
C A:SER417 3.9 33.5 1.0
N A:TYR418 4.0 24.6 1.0
O A:SER417 4.0 39.0 1.0
CA A:TYR418 4.2 23.7 1.0
N A:HIS49 4.3 24.8 1.0
O A:HOH1027 4.5 40.5 1.0
CA A:HIS49 4.5 25.8 1.0
CA A:SER417 4.5 26.0 1.0
O A:HOH948 4.5 26.5 1.0
O A:HOH953 4.5 21.6 1.0
N A:ALA50 4.6 23.1 1.0
CG2 A:ILE369 4.6 24.1 1.0
CA A:ALA50 4.6 26.1 1.0
CB A:TYR418 4.7 21.9 1.0
O A:GLY368 4.7 21.5 1.0
N A:GLY368 4.7 22.0 1.0
O A:HOH845 4.8 26.5 1.0
C A:GLY368 4.8 20.0 1.0
CB A:HIS49 4.9 23.9 1.0
O A:HOH980 4.9 29.4 1.0

Sodium binding site 5 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na602

b:35.5
occ:1.00
 O B:HOH1024 2.4 41.4 1.0
O B:GLY466 2.4 28.2 1.0
OG B:SER518 2.5 32.6 1.0
O B:HOH1089 2.5 39.1 1.0
O B:HOH1114 2.6 46.0 1.0
OD1 B:ASP464 2.6 26.9 1.0
CB B:SER518 3.3 37.6 1.0
O B:HOH702 3.3 29.7 1.0
CG B:ASP464 3.3 28.9 1.0
C B:GLY466 3.4 23.3 1.0
OD2 B:ASP464 3.4 37.4 1.0
CA B:GLY466 3.8 25.8 1.0
N B:GLY466 4.1 24.5 1.0
OD1 B:ASP469 4.4 31.4 1.0
O B:HOH1005 4.5 44.5 1.0
CA B:SER518 4.6 28.2 1.0
N B:LEU467 4.6 24.2 1.0
CB B:ASP464 4.7 25.0 1.0
O B:SER518 4.9 40.7 1.0
C B:SER518 4.9 35.1 1.0

Sodium binding site 6 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na603

b:29.6
occ:1.00
 O B:HOH1123 2.4 42.4 1.0
OE1 B:GLU544 2.5 26.8 1.0
OE2 B:GLU533 2.6 21.6 1.0
O B:HOH829 2.6 23.3 1.0
O B:HOH923 2.8 38.6 1.0
O B:HOH752 3.2 35.4 1.0
CD B:GLU533 3.4 18.0 1.0
CD B:GLU544 3.5 23.7 1.0
CG B:GLU533 3.6 18.6 1.0
O B:HOH1007 3.7 24.2 1.0
OE2 B:GLU544 3.8 30.5 1.0
O B:HOH1084 4.2 34.8 1.0
O B:GLY534 4.4 21.5 1.0
O B:PRO562 4.4 23.3 1.0
OE1 B:GLU533 4.6 20.5 1.0
ND1 B:HIS563 4.7 19.1 1.0
O B:HOH1101 4.7 27.0 1.0
O B:HOH1157 4.7 29.1 1.0
CA B:HIS563 4.7 18.4 1.0
O B:HOH1164 4.7 27.5 1.0
CG B:GLU544 4.8 22.1 1.0
N B:LEU564 5.0 20.6 1.0
N B:GLY534 5.0 21.9 1.0

Sodium binding site 7 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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
C:Na602

b:37.1
occ:1.00
 O C:GLY466 2.3 28.0 1.0
OG C:SER518 2.5 37.4 1.0
OD1 C:ASP464 2.5 33.8 1.0
O C:HOH971 2.5 43.4 1.0
O C:HOH1051 2.9 45.1 1.0
CG C:ASP464 3.3 31.1 1.0
C C:GLY466 3.3 25.4 1.0
CB C:SER518 3.4 31.8 1.0
NA C:NA605 3.4 42.9 1.0
OD2 C:ASP464 3.4 41.1 1.0
CA C:GLY466 3.6 23.8 1.0
N C:GLY466 3.9 24.5 1.0
O C:HOH1044 4.5 43.6 1.0
OD1 C:ASP469 4.5 28.7 1.0
N C:LEU467 4.5 28.7 1.0
CB C:ASP464 4.6 27.6 1.0
CA C:SER518 4.7 31.0 1.0
C C:SER518 5.0 40.6 1.0

Sodium binding site 8 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na603

b:26.8
occ:1.00
 OE2 C:GLU533 2.5 20.7 1.0
O C:HOH1114 2.6 30.1 0.5
OE1 C:GLU544 2.6 22.7 1.0
O C:HOH903 2.6 22.3 1.0
O C:HOH832 2.9 37.2 1.0
O C:HOH758 3.2 31.3 1.0
CD C:GLU533 3.4 18.4 1.0
CD C:GLU544 3.5 22.0 1.0
O C:HOH1100 3.5 47.1 1.0
CG C:GLU533 3.7 16.4 1.0
OE2 C:GLU544 3.7 25.9 1.0
O C:HOH960 3.8 22.2 1.0
O C:HOH1052 4.0 30.4 1.0
O C:PRO562 4.4 19.7 1.0
O C:GLY534 4.5 18.7 1.0
OE1 C:GLU533 4.6 20.2 1.0
ND1 C:HIS563 4.7 19.7 1.0
O C:HOH1078 4.7 26.2 1.0
O C:HOH1142 4.7 27.3 1.0
O C:HOH1130 4.7 28.1 1.0
CA C:HIS563 4.7 18.1 1.0
CG C:GLU544 4.8 20.3 1.0
N C:LEU564 5.0 19.1 1.0
N C:GLY534 5.0 17.0 1.0

Sodium binding site 9 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na604

b:31.6
occ:1.00
 O C:HIS49 2.4 23.3 1.0
O C:GLY367 2.6 19.1 1.0
O C:SER417 2.7 33.5 0.2
OG C:SER417 2.8 30.7 0.8
O C:HOH1010 3.0 27.9 1.0
O C:HOH841 3.2 26.7 1.0
C C:SER417 3.4 29.3 0.2
C C:GLY367 3.4 18.5 1.0
CB C:SER417 3.6 25.9 0.8
CA C:GLY367 3.6 18.6 1.0
C C:HIS49 3.7 18.9 1.0
OG C:SER417 3.8 23.4 0.2
CB C:SER417 4.0 25.7 0.2
C C:SER417 4.0 28.1 0.8
N C:TYR418 4.0 22.6 1.0
CA C:TYR418 4.3 23.7 1.0
O C:SER417 4.3 29.6 0.8
O C:HOH1024 4.3 36.9 1.0
CA C:SER417 4.3 24.1 0.2
N C:HIS49 4.4 22.0 1.0
CA C:SER417 4.4 22.2 0.8
O C:HOH952 4.5 19.4 1.0
CA C:HIS49 4.5 22.2 1.0
O C:HOH970 4.6 23.7 1.0
N C:ALA50 4.6 20.3 1.0
O C:GLY368 4.6 19.2 1.0
N C:GLY368 4.6 18.0 1.0
CB C:TYR418 4.6 24.3 1.0
CA C:ALA50 4.6 22.1 1.0
CG2 C:ILE369 4.8 25.1 1.0
C C:GLY368 4.8 17.8 1.0
O C:HOH760 4.8 24.2 1.0
O C:HOH887 4.9 27.4 1.0
CB C:HIS49 4.9 24.1 1.0
O C:ALA414 5.0 20.9 1.0

Sodium binding site 10 out of 32 in 6tbh

Go back to Sodium Binding Sites List in 6tbh
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:Na605

b:42.9
occ:1.00
 O C:HOH1044 2.2 43.6 1.0
O C:HOH971 2.4 43.4 1.0
OG C:SER518 2.5 37.4 1.0
O C:SER518 2.5 46.6 1.0
O C:HOH1051 2.5 45.1 1.0
C C:SER518 3.1 40.6 1.0
NA C:NA602 3.4 37.1 1.0
CB C:SER518 3.5 31.8 1.0
CA C:SER518 3.7 31.0 1.0
N C:GLN519 4.1 45.9 1.0
OD2 C:ASP469 4.5 32.6 1.0
OD1 C:ASP469 4.6 28.7 1.0
CA C:GLN519 4.6 44.8 1.0
OD1 C:ASP464 4.7 33.8 1.0
OD2 C:ASP464 4.8 41.1 1.0
CG C:ASP464 4.9 31.1 1.0
O C:GLY466 4.9 28.0 1.0
CB C:GLN519 4.9 53.6 1.0
CG C:ASP469 5.0 24.3 1.0

Reference:

W.Offen, G.Davies. Structure of A Beta Galactosidase with Inhibitor To Be Published.
Page generated: Tue Oct 8 13:39:37 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy