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Sodium in PDB 5jaw: 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: 5jaw 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) 81.99 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.168, 115.660, 115.935, 90.15, 90.11, 90.11
R / Rfree (%) 19.7 / 21.4

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Sodium atom in the Structure of A Beta Galactosidase with Inhibitor (pdb code 5jaw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 25 binding sites of Sodium where determined in the Structure of A Beta Galactosidase with Inhibitor, PDB code: 5jaw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 25 in 5jaw

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Sodium binding site 1 out of 25 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:Na602

b:21.4
occ:1.00
 O A:GLY466 2.3 18.4 1.0
OG A:SER518 2.5 21.3 1.0
O A:HOH855 2.5 27.0 1.0
OE1 A:GLN519 2.5 29.2 1.0
OD1 A:ASP464 2.6 22.2 1.0
NA A:NA604 3.1 26.3 1.0
C A:GLY466 3.3 14.3 1.0
CB A:SER518 3.3 21.6 1.0
CG A:ASP464 3.4 24.7 1.0
OD2 A:ASP464 3.5 27.3 1.0
CD A:GLN519 3.7 30.8 1.0
CA A:GLY466 3.7 16.9 1.0
N A:GLY466 3.9 18.2 1.0
NE2 A:GLN519 4.2 26.6 1.0
OD1 A:ASP469 4.4 26.9 1.0
N A:LEU467 4.5 16.7 1.0
O A:SER518 4.7 23.1 1.0
CA A:SER518 4.7 20.2 1.0
O A:HOH796 4.7 24.2 1.0
CB A:ASP464 4.7 21.7 1.0
C A:SER518 4.9 22.4 1.0
CG A:GLN519 4.9 32.9 1.0
CA A:LEU467 5.0 16.8 1.0

Sodium binding site 2 out of 25 in 5jaw

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Sodium binding site 2 out of 25 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:25.6
occ:1.00
 O A:HIS49 2.4 23.4 1.0
O A:GLY367 2.6 19.7 1.0
O A:HOH900 2.8 26.4 1.0
OG A:SER417 3.1 19.6 0.5
O A:HOH797 3.1 24.5 1.0
C A:GLY367 3.5 19.8 1.0
C A:HIS49 3.6 22.4 1.0
CA A:GLY367 3.7 20.8 1.0
CB A:SER417 3.8 22.0 0.5
C A:SER417 3.8 27.5 0.5
O A:SER417 3.8 28.2 0.5
CB A:SER417 3.9 26.9 0.5
OG A:SER417 4.0 27.1 0.5
C A:SER417 4.0 25.6 0.5
N A:TYR418 4.0 24.2 1.0
N A:HIS49 4.2 23.8 1.0
O A:SER417 4.2 24.4 0.5
CA A:TYR418 4.2 24.6 1.0
CA A:HIS49 4.4 22.9 1.0
O A:HOH825 4.4 30.0 1.0
O A:HOH845 4.4 18.3 1.0
CA A:SER417 4.5 27.1 0.5
N A:ALA50 4.5 21.4 1.0
CA A:SER417 4.5 24.2 0.5
O A:GLY368 4.5 18.0 1.0
CA A:ALA50 4.6 20.4 1.0
O A:HOH784 4.6 18.2 1.0
N A:GLY368 4.7 17.9 1.0
CG2 A:ILE369 4.7 20.0 1.0
CB A:TYR418 4.7 21.9 1.0
CB A:HIS49 4.8 24.4 1.0
C A:GLY368 4.8 18.3 1.0
O A:HOH748 4.8 24.9 1.0
O A:HOH837 4.9 25.1 1.0

Sodium binding site 3 out of 25 in 5jaw

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Sodium binding site 3 out of 25 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:26.3
occ:1.00
 O A:HOH855 2.3 27.0 1.0
O A:SER518 2.4 23.1 1.0
O A:HOH796 2.4 24.2 1.0
OG A:SER518 2.5 21.3 1.0
OE1 A:GLN519 2.7 29.2 1.0
NA A:NA602 3.1 21.4 1.0
C A:SER518 3.3 22.4 1.0
CB A:SER518 3.5 21.6 1.0
CD A:GLN519 3.5 30.8 1.0
CA A:SER518 3.8 20.2 1.0
CG A:GLN519 3.9 32.9 1.0
N A:GLN519 4.3 22.8 1.0
OD1 A:ASP469 4.4 26.9 1.0
OD2 A:ASP469 4.5 24.5 1.0
OD2 A:ASP464 4.5 27.3 1.0
OD1 A:ASP464 4.6 22.2 1.0
NE2 A:GLN519 4.7 26.6 1.0
CG A:ASP464 4.7 24.7 1.0
CA A:GLN519 4.7 24.5 1.0
O A:GLY466 4.8 18.4 1.0
CB A:GLN519 4.9 28.4 1.0
CG A:ASP469 4.9 21.2 1.0

Sodium binding site 4 out of 25 in 5jaw

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Sodium binding site 4 out of 25 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
B:Na602

b:45.0
occ:1.00
 O B:LYS157 2.7 28.0 1.0
O B:GLU158 3.2 35.2 1.0
O B:TYR215 3.3 29.0 1.0
C B:GLU158 3.7 33.4 1.0
C B:LYS157 3.8 27.8 1.0
CB B:TYR215 3.8 27.4 1.0
N B:GLY160 3.9 32.3 1.0
CA B:GLU158 3.9 32.3 1.0
CG1 B:VAL156 4.0 24.0 1.0
CA B:GLY160 4.0 29.8 1.0
C B:TYR215 4.0 27.2 1.0
N B:GLU158 4.3 30.4 1.0
N B:ASP159 4.6 35.4 1.0
CA B:TYR215 4.7 25.8 1.0
O B:VAL156 4.8 21.8 1.0
C B:ASP159 4.8 34.6 1.0
N B:SER216 4.8 25.6 1.0
CB B:VAL156 4.8 23.2 1.0
C B:VAL156 4.9 20.9 1.0
CG B:TYR215 5.0 26.2 1.0
N B:LYS157 5.0 22.3 1.0

Sodium binding site 5 out of 25 in 5jaw

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Sodium binding site 5 out of 25 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:Na603

b:34.8
occ:1.00
 O B:HOH1303 2.1 37.8 1.0
O B:SER518 2.4 33.9 1.0
OG B:SER518 2.6 31.4 1.0
OE1 B:GLN519 2.8 39.8 1.0
C B:SER518 3.3 30.2 1.0
NA B:NA604 3.6 32.4 1.0
CB B:SER518 3.6 30.9 1.0
O B:HOH1103 3.7 42.0 1.0
CD B:GLN519 3.7 40.5 1.0
CA B:SER518 3.8 31.5 1.0
CG B:GLN519 4.2 40.4 1.0
N B:GLN519 4.2 35.4 1.0
OD2 B:ASP469 4.4 33.3 1.0
OD1 B:ASP469 4.5 28.0 1.0
CA B:GLN519 4.6 36.6 1.0
OD1 B:ASP464 4.7 32.5 1.0
NE2 B:GLN519 4.9 43.3 1.0
CG B:ASP469 4.9 28.5 1.0
OD2 B:ASP464 4.9 35.0 1.0
CG B:ASP464 4.9 34.6 1.0

Sodium binding site 6 out of 25 in 5jaw

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Sodium binding site 6 out of 25 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:32.4
occ:1.00
 OD1 B:ASP464 2.4 32.5 1.0
O B:GLY466 2.4 26.9 1.0
OG B:SER518 2.7 31.4 1.0
OE1 B:GLN519 2.8 39.8 1.0
CG B:ASP464 3.3 34.6 1.0
C B:GLY466 3.4 23.7 1.0
CB B:SER518 3.5 30.9 1.0
OD2 B:ASP464 3.5 35.0 1.0
NA B:NA603 3.6 34.8 1.0
CA B:GLY466 3.8 26.9 1.0
CD B:GLN519 3.8 40.5 1.0
N B:GLY466 3.9 27.9 1.0
NE2 B:GLN519 4.1 43.3 1.0
OD1 B:ASP469 4.5 28.0 1.0
N B:LEU467 4.6 25.6 1.0
CB B:ASP464 4.6 29.3 1.0
CA B:SER518 4.8 31.5 1.0
O B:HOH1303 5.0 37.8 1.0

Sodium binding site 7 out of 25 in 5jaw

Go back to Sodium Binding Sites List in 5jaw
Sodium binding site 7 out of 25 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:22.0
occ:1.00
 O C:GLY466 2.2 21.3 1.0
OD1 C:ASP464 2.5 23.3 1.0
O C:HOH935 2.6 25.0 1.0
OE1 C:GLN519 2.6 29.8 1.0
OG C:SER518 2.6 21.6 1.0
C C:GLY466 3.2 15.3 1.0
NA C:NA603 3.3 24.2 1.0
CG C:ASP464 3.3 24.5 1.0
CB C:SER518 3.4 21.3 1.0
OD2 C:ASP464 3.5 27.7 1.0
CA C:GLY466 3.6 19.4 1.0
CD C:GLN519 3.7 32.9 1.0
N C:GLY466 3.8 18.1 1.0
NZ D:LYS524 4.0 33.6 1.0
NE2 C:GLN519 4.2 27.2 1.0
N C:LEU467 4.4 16.9 1.0
OD1 C:ASP469 4.5 22.0 1.0
CB C:ASP464 4.7 20.5 1.0
CE D:LYS524 4.7 30.6 1.0
CA C:SER518 4.7 18.7 1.0
O C:HOH904 4.7 26.8 1.0
O C:HOH842 4.7 23.7 1.0
O C:SER518 4.8 23.7 1.0
CA C:LEU467 4.9 18.6 1.0
CG C:GLN519 4.9 30.1 1.0
C C:SER518 4.9 20.3 1.0

Sodium binding site 8 out of 25 in 5jaw

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Sodium binding site 8 out of 25 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:24.2
occ:1.00
 O C:HOH935 2.1 25.0 1.0
O C:HOH842 2.3 23.7 1.0
OG C:SER518 2.4 21.6 1.0
O C:SER518 2.4 23.7 1.0
OE1 C:GLN519 3.1 29.8 1.0
C C:SER518 3.3 20.3 1.0
NA C:NA602 3.3 22.0 1.0
CB C:SER518 3.4 21.3 1.0
O C:HOH904 3.5 26.8 1.0
CD C:GLN519 3.7 32.9 1.0
CA C:SER518 3.7 18.7 1.0
CG C:GLN519 3.9 30.1 1.0
O C:HOH730 3.9 36.5 1.0
O C:HOH942 4.2 32.0 1.0
N C:GLN519 4.4 23.5 1.0
OD1 C:ASP469 4.4 22.0 1.0
OD1 C:ASP464 4.4 23.3 1.0
OD2 C:ASP469 4.5 22.3 1.0
OD2 C:ASP464 4.6 27.7 1.0
CG C:ASP464 4.6 24.5 1.0
NE2 C:GLN519 4.7 27.2 1.0
CA C:GLN519 4.8 23.9 1.0
CG C:ASP469 4.8 18.1 1.0
O C:GLY466 4.8 21.3 1.0
CB C:GLN519 4.9 24.9 1.0

Sodium binding site 9 out of 25 in 5jaw

Go back to Sodium Binding Sites List in 5jaw
Sodium binding site 9 out of 25 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:23.0
occ:1.00
 OE2 C:GLU533 2.5 20.6 1.0
O C:HOH823 2.6 21.4 1.0
OE1 C:GLU544 2.7 22.6 1.0
O C:HOH714 3.1 33.1 1.0
CD C:GLU533 3.5 21.4 1.0
CD C:GLU544 3.6 24.7 1.0
CG C:GLU533 3.8 19.8 1.0
O C:HOH905 3.8 22.1 1.0
OE2 C:GLU544 3.8 28.9 1.0
O C:PRO562 4.2 18.6 1.0
OE1 C:GLU533 4.6 20.3 1.0
O C:GLY534 4.6 20.8 1.0
O C:HOH945 4.6 22.9 1.0
ND1 C:HIS563 4.7 20.8 1.0
CA C:HIS563 4.7 18.2 1.0
O C:HOH962 4.7 21.7 1.0
O C:HOH959 4.8 25.7 1.0
N C:LEU564 4.9 17.0 1.0
CG C:GLU544 5.0 23.2 1.0

Sodium binding site 10 out of 25 in 5jaw

Go back to Sodium Binding Sites List in 5jaw
Sodium binding site 10 out of 25 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:25.3
occ:1.00
 O C:HOH818 2.4 20.8 1.0
O C:HOH800 2.4 29.5 1.0
O C:SER571 2.5 16.4 1.0
OG C:SER571 2.6 21.7 1.0
C C:SER571 3.3 19.1 1.0
N C:SER571 3.7 19.5 1.0
CB C:SER571 3.7 20.7 1.0
CA C:SER571 3.7 20.6 1.0
O C:HOH949 4.0 30.9 1.0
O C:HOH865 4.1 29.2 1.0
NZ C:LYS524 4.3 29.2 1.0
N C:TYR572 4.3 18.9 1.0
O C:HOH746 4.4 19.7 1.0
OD2 D:ASP501 4.6 28.3 1.0
CD C:LYS524 4.8 25.9 1.0
CA C:TYR572 4.8 19.9 1.0
C C:ALA570 4.8 18.9 1.0
CE C:LYS524 4.9 26.5 1.0
O C:HOH858 5.0 28.9 1.0

Reference:

S.P.Schroder, J.W.Van De Sande, W.W.Kallemeijn, C.L.Kuo, M.Artola, E.J.Van Rooden, J.Jiang, T.J.M.Beenakker, B.I.Florea, W.A.Offen, G.J.Davies, A.J.Minnaard, J.M.F.G.Aerts, J.D.C.Codee, G.A.Van Der Marel, H.S.Overkleeft. Towards Broad Spectrum Activity-Based Glycosidase Probes: Synthesis and Evaluation of Deoxygenated Cyclophellitol Aziridines. Chem. Commun. (Camb.) V. 53 12528 2017.
ISSN: ESSN 1364-548X
PubMed: 29116266
DOI: 10.1039/C7CC07730K
Page generated: Mon Oct 7 21:51:32 2024

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