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Sodium in PDB 6tbi: 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: 6tbi 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) 116.10 / 1.46
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.120, 115.910, 116.103, 90.20, 89.96, 90.08
R / Rfree (%) 12.6 / 17.2

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Sodium atom in the Structure of A Beta Galactosidase with Inhibitor (pdb code 6tbi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 38 binding sites of Sodium where determined in the Structure of A Beta Galactosidase with Inhibitor, PDB code: 6tbi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 38 in 6tbi

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Sodium binding site 1 out of 38 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:32.1
occ:1.00
 O A:HOH1090 2.2 46.4 1.0
O A:GLY466 2.3 29.5 1.0
OG A:SER518 2.4 32.4 1.0
OD1 A:ASP464 2.5 27.2 1.0
O A:HOH883 2.5 34.8 1.0
OE1 A:GLN519 2.5 40.6 1.0
CG A:ASP464 3.2 34.9 1.0
CB A:SER518 3.3 31.4 1.0
C A:GLY466 3.3 26.8 1.0
NA A:NA604 3.4 36.7 1.0
OD2 A:ASP464 3.4 34.7 1.0
CD A:GLN519 3.5 53.5 1.0
CA A:GLY466 3.7 27.0 1.0
NE2 A:GLN519 3.9 48.9 1.0
N A:GLY466 3.9 27.2 1.0
OD1 A:ASP469 4.3 26.1 1.0
N A:LEU467 4.6 28.3 1.0
CA A:SER518 4.6 29.9 1.0
CB A:ASP464 4.6 30.5 1.0
O A:HOH813 4.7 37.2 1.0
C A:SER518 4.9 35.2 1.0
CG A:GLN519 4.9 50.6 1.0
O A:SER518 5.0 35.5 1.0

Sodium binding site 2 out of 38 in 6tbi

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Sodium binding site 2 out of 38 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:Na603

b:25.2
occ:1.00
 OE1 A:GLU544 2.5 26.4 1.0
OE2 A:GLU533 2.5 20.0 1.0
O A:HOH884 2.6 21.9 1.0
O A:HOH803 2.6 33.4 1.0
O A:HOH744 3.1 38.2 1.0
O A:HOH1166 3.3 50.2 1.0
CD A:GLU533 3.4 20.5 1.0
CD A:GLU544 3.5 23.9 1.0
CG A:GLU533 3.6 20.9 1.0
OE2 A:GLU544 3.8 28.5 1.0
O A:HOH1021 3.8 23.3 1.0
O A:HOH1075 4.0 34.4 1.0
O B:HOH810 4.2 52.6 1.0
O A:PRO562 4.4 19.8 1.0
O A:GLY534 4.5 21.8 1.0
OE1 A:GLU533 4.5 19.1 1.0
ND1 A:HIS563 4.7 19.6 1.0
O A:HOH1184 4.7 30.2 1.0
O A:HOH1097 4.7 28.3 1.0
CA A:HIS563 4.7 19.0 1.0
O A:HOH1158 4.9 28.4 1.0
CG A:GLU544 4.9 22.9 1.0
N A:LEU564 5.0 18.2 1.0
N A:GLY534 5.0 19.6 1.0
O A:HOH901 5.0 33.5 1.0

Sodium binding site 3 out of 38 in 6tbi

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Sodium binding site 3 out of 38 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:Na604

b:36.7
occ:1.00
 O A:HOH1088 2.1 52.3 1.0
O A:HOH813 2.3 37.2 1.0
O A:SER518 2.4 35.5 1.0
O A:HOH883 2.4 34.8 1.0
OG A:SER518 2.5 32.4 1.0
OE1 A:GLN519 2.6 40.6 1.0
C A:SER518 3.1 35.2 1.0
NA A:NA601 3.4 32.1 1.0
CB A:SER518 3.5 31.4 1.0
CD A:GLN519 3.6 53.5 1.0
CA A:SER518 3.7 29.9 1.0
CG A:GLN519 4.1 50.6 1.0
N A:GLN519 4.1 34.8 1.0
OD2 A:ASP469 4.3 31.2 1.0
OD1 A:ASP469 4.4 26.1 1.0
CA A:GLN519 4.6 37.1 1.0
NE2 A:GLN519 4.7 48.9 1.0
OD1 A:ASP464 4.7 27.2 1.0
OD2 A:ASP464 4.7 34.7 1.0
CG A:ASP469 4.7 27.2 1.0
CG A:ASP464 4.8 34.9 1.0
CB A:GLN519 4.9 43.0 1.0
O A:HOH1090 4.9 46.4 1.0
O A:GLY466 5.0 29.5 1.0
O A:HOH725 5.0 43.7 1.0

Sodium binding site 4 out of 38 in 6tbi

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Sodium binding site 4 out of 38 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:Na605

b:31.3
occ:1.00
 O A:HOH1012 2.1 28.2 0.5
O A:SER417 2.2 30.5 0.5
O A:HIS49 2.5 24.0 1.0
O A:GLY367 2.6 22.1 1.0
OG A:SER417 2.8 25.1 0.5
O A:HOH979 2.8 28.6 1.0
C A:SER417 3.3 31.1 0.5
O A:HOH870 3.4 30.9 1.0
C A:GLY367 3.4 21.6 1.0
CA A:GLY367 3.6 22.6 1.0
C A:HIS49 3.6 22.9 1.0
CB A:SER417 3.7 23.4 0.5
OG A:SER417 3.8 27.1 0.5
C A:SER417 3.9 25.4 0.5
N A:TYR418 4.0 24.1 1.0
O A:SER417 4.1 25.1 0.5
CB A:SER417 4.1 28.1 0.5
CA A:TYR418 4.2 27.0 1.0
N A:HIS49 4.2 26.5 1.0
O A:HOH1010 4.3 38.5 1.0
CA A:SER417 4.3 27.2 0.5
CA A:HIS49 4.4 24.0 1.0
CA A:SER417 4.5 25.5 0.5
O A:HOH961 4.5 24.6 1.0
N A:ALA50 4.6 21.9 1.0
O A:HOH907 4.6 21.7 1.0
N A:GLY368 4.6 19.8 1.0
O A:GLY368 4.6 21.5 1.0
CG2 A:ILE369 4.7 26.8 1.0
CA A:ALA50 4.7 24.1 1.0
CB A:TYR418 4.7 25.9 1.0
CB A:HIS49 4.7 22.8 1.0
O A:HOH952 4.7 26.6 1.0
C A:GLY368 4.8 19.8 1.0
O A:HOH774 4.9 27.9 1.0

Sodium binding site 5 out of 38 in 6tbi

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Sodium binding site 5 out of 38 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:32.6
occ:1.00
 O B:GLY466 2.3 26.1 1.0
OG B:SER518 2.4 32.4 1.0
O B:HOH1012 2.5 37.5 1.0
OD1 B:ASP464 2.5 28.5 1.0
O B:HOH1033 2.5 43.8 1.0
O B:HOH1168 2.5 45.6 1.0
CB B:SER518 3.3 30.8 1.0
CG B:ASP464 3.3 29.2 1.0
C B:GLY466 3.3 28.3 1.0
NA B:NA606 3.3 35.1 1.0
OD2 B:ASP464 3.5 33.1 1.0
CA B:GLY466 3.7 27.5 1.0
N B:GLY466 3.9 26.1 1.0
O B:HOH1170 4.0 51.5 1.0
OD1 B:ASP469 4.4 25.8 1.0
N B:LEU467 4.5 27.3 1.0
CA B:SER518 4.6 31.1 1.0
CB B:ASP464 4.6 24.5 1.0
O B:HOH949 4.7 36.0 1.0
O B:SER518 4.8 31.4 1.0
C B:SER518 4.9 35.0 1.0

Sodium binding site 6 out of 38 in 6tbi

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Sodium binding site 6 out of 38 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:Na604

b:25.9
occ:1.00
 O B:HOH933 2.5 22.3 1.0
OE1 B:GLU544 2.5 25.0 1.0
OE2 B:GLU533 2.6 19.9 1.0
O B:HOH802 2.6 37.4 1.0
O B:HOH775 2.9 37.8 1.0
CD B:GLU533 3.4 21.1 1.0
CD B:GLU544 3.5 22.6 1.0
CG B:GLU533 3.7 18.9 1.0
O B:HOH1015 3.8 22.4 1.0
OE2 B:GLU544 3.8 26.2 1.0
O B:HOH1145 4.1 34.6 1.0
O H:HOH728 4.3 53.9 1.0
O B:PRO562 4.3 22.9 1.0
O B:GLY534 4.5 19.9 1.0
O B:HOH1167 4.6 27.8 1.0
OE1 B:GLU533 4.6 19.1 1.0
ND1 B:HIS563 4.6 19.2 1.0
O B:HOH1256 4.7 27.3 1.0
CA B:HIS563 4.7 18.7 1.0
O B:HOH1272 4.7 27.9 1.0
O B:HOH826 4.9 31.4 1.0
CG B:GLU544 4.9 23.3 1.0
N B:LEU564 5.0 16.9 1.0

Sodium binding site 7 out of 38 in 6tbi

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Sodium binding site 7 out of 38 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:Na605

b:42.5
occ:1.00
 O B:HOH1062 2.2 25.8 0.5
O B:HOH1157 2.2 35.6 0.5
O B:HOH1151 2.3 52.8 1.0
O B:HOH910 2.5 24.8 1.0
O B:THR488 2.7 23.5 0.5
O B:THR488 2.8 27.4 0.5
O B:HOH1028 2.9 36.1 1.0
O B:HOH723 3.6 51.8 1.0
C B:THR488 3.6 23.3 0.5
C B:THR488 3.7 28.1 0.5
NZ B:LYS510 4.0 28.6 1.0
N B:THR488 4.1 20.8 0.5
N B:THR488 4.2 25.3 0.5
CD B:PRO489 4.2 24.4 1.0
N B:PRO489 4.2 26.2 1.0
O B:HOH1069 4.3 26.1 1.0
CA B:THR488 4.5 23.2 0.5
CA B:THR488 4.6 28.8 0.5
OG1 B:THR488 4.7 34.1 0.5
O B:PRO489 4.7 21.5 1.0
CB B:ASN487 4.8 20.2 1.0
O B:HOH1171 4.8 38.8 1.0
CG2 B:THR488 4.9 48.0 0.5
CD B:LYS510 4.9 21.4 1.0
CE B:LYS510 5.0 27.1 1.0

Sodium binding site 8 out of 38 in 6tbi

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Sodium binding site 8 out of 38 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
B:Na606

b:35.1
occ:1.00
 O B:HOH1160 2.2 42.1 1.0
O B:HOH949 2.3 36.0 1.0
O B:HOH1012 2.3 37.5 1.0
O B:SER518 2.4 31.4 1.0
OG B:SER518 2.4 32.4 1.0
O B:HOH1033 2.6 43.8 1.0
C B:SER518 3.2 35.0 1.0
NA B:NA601 3.3 32.6 1.0
CB B:SER518 3.5 30.8 1.0
CA B:SER518 3.7 31.1 1.0
N B:GLN519 4.2 35.4 1.0
OD2 B:ASP469 4.3 34.7 1.0
OD1 B:ASP469 4.4 25.8 1.0
CA B:GLN519 4.6 35.9 1.0
OD1 B:ASP464 4.7 28.5 1.0
O B:HOH1170 4.7 51.5 1.0
OD2 B:ASP464 4.8 33.1 1.0
CG B:ASP469 4.8 24.8 1.0
CG B:ASP464 4.8 29.2 1.0
CB B:GLN519 4.9 45.7 1.0
O B:HOH777 5.0 36.8 1.0
O B:GLY466 5.0 26.1 1.0

Sodium binding site 9 out of 38 in 6tbi

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Sodium binding site 9 out of 38 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:Na601

b:43.4
occ:1.00
 O C:HOH967 2.2 46.5 1.0
O C:HOH1088 2.2 48.6 1.0
OG C:SER518 2.4 38.1 1.0
O C:HOH910 2.5 48.4 1.0
O C:SER518 2.5 42.9 1.0
C C:SER518 3.3 38.5 1.0
NA C:NA602 3.3 35.9 1.0
CB C:SER518 3.5 35.8 1.0
CA C:SER518 3.8 36.7 1.0
N C:GLN519 4.3 43.6 1.0
OD2 C:ASP469 4.4 31.6 1.0
OD1 C:ASP469 4.4 30.1 1.0
OD1 C:ASP464 4.6 30.3 1.0
OD2 C:ASP464 4.7 41.4 1.0
CG C:ASP464 4.7 35.6 1.0
CA C:GLN519 4.8 50.6 1.0
CG C:ASP469 4.9 26.9 1.0
O C:GLY466 4.9 30.4 1.0

Sodium binding site 10 out of 38 in 6tbi

Go back to Sodium Binding Sites List in 6tbi
Sodium binding site 10 out of 38 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:Na602

b:35.9
occ:1.00
 O C:HOH1157 2.2 37.2 0.5
O C:GLY466 2.3 30.4 1.0
O C:HOH1088 2.4 48.6 1.0
OG C:SER518 2.5 38.1 1.0
O C:HOH910 2.5 48.4 1.0
OD1 C:ASP464 2.5 30.3 1.0
CG C:ASP464 3.3 35.6 1.0
NA C:NA601 3.3 43.4 1.0
CB C:SER518 3.3 35.8 1.0
C C:GLY466 3.4 29.2 1.0
OD2 C:ASP464 3.5 41.4 1.0
CA C:GLY466 3.7 25.3 1.0
N C:GLY466 4.0 26.2 1.0
OD1 C:ASP469 4.4 30.1 1.0
N C:LEU467 4.6 26.8 1.0
O C:HOH967 4.6 46.5 1.0
CA C:SER518 4.6 36.7 1.0
CB C:ASP464 4.6 30.7 1.0
C C:SER518 4.9 38.5 1.0

Reference:

W.Offen, G.Davies. Structure of A Beta Galactosidase with Inhibitor To Be Published.
Page generated: Mon Aug 18 07:20:43 2025

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