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Sodium in PDB 4d1j: The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin

Enzymatic activity of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin

All present enzymatic activity of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin:
3.2.1.23;

Protein crystallography data

The structure of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin, PDB code: 4d1j was solved by J.Larsbrink, A.J.Thompson, M.Lundqvist, J.G.Gardner, G.J.Davies, H.Brumer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 116.11 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.257, 116.095, 116.113, 90.00, 90.05, 90.04
R / Rfree (%) 17.169 / 19.482

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Sodium atom in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin (pdb code 4d1j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 23 binding sites of Sodium where determined in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin, PDB code: 4d1j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 23 in 4d1j

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Sodium binding site 1 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:29.8
occ:1.00
 O A:HIS49 2.2 23.7 1.0
O A:HOH2333 2.3 33.2 1.0
O A:GLY367 2.6 25.8 1.0
O A:HOH2018 2.6 32.1 1.0
O A:SER417 3.0 46.7 1.0
OG A:SER417 3.1 34.0 0.5
C A:HIS49 3.4 24.8 1.0
C A:GLY367 3.5 23.2 1.0
O A:HOH2370 3.5 35.8 1.0
C A:SER417 3.6 33.9 1.0
CA A:GLY367 3.7 23.5 1.0
OG A:SER417 3.8 25.9 0.5
N A:HIS49 4.1 24.7 1.0
CB A:SER417 4.1 28.2 0.5
N A:TYR418 4.1 29.2 1.0
CB A:SER417 4.1 31.8 0.5
CA A:TYR418 4.2 30.1 1.0
CA A:HIS49 4.2 24.9 1.0
O A:HOH2315 4.3 20.6 1.0
N A:ALA50 4.4 25.6 1.0
O A:HOH2372 4.4 32.8 1.0
CA A:SER417 4.5 29.9 0.5
CA A:ALA50 4.5 25.6 1.0
CA A:SER417 4.5 31.7 0.5
O A:GLY368 4.6 20.7 1.0
CB A:TYR418 4.6 29.4 1.0
CG2 A:ILE369 4.6 25.6 1.0
N A:GLY368 4.7 21.2 1.0
CB A:HIS49 4.7 26.4 1.0
O A:HOH2332 4.7 30.8 1.0
O A:HOH2329 4.7 21.5 1.0
C A:GLY368 4.8 21.1 1.0
O A:HOH2019 4.8 24.1 1.0

Sodium binding site 2 out of 23 in 4d1j

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Sodium binding site 2 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:35.5
occ:1.00
 O A:HOH2396 2.3 38.6 1.0
OG A:SER518 2.4 31.6 1.0
O A:GLY466 2.4 25.7 1.0
O A:HOH2400 2.4 47.6 1.0
OD1 A:ASP464 2.4 34.2 1.0
O A:HOH2431 2.6 38.3 1.0
CG A:ASP464 3.2 34.9 1.0
CB A:SER518 3.2 32.9 1.0
OD2 A:ASP464 3.3 37.1 1.0
NA A:NA603 3.3 36.1 1.0
C A:GLY466 3.4 28.8 1.0
CA A:GLY466 3.9 29.9 1.0
N A:GLY466 4.0 26.5 1.0
OD1 A:ASP469 4.2 33.5 1.0
CB A:ASP464 4.5 31.6 1.0
CA A:SER518 4.6 34.2 1.0
N A:LEU467 4.6 29.2 1.0
O A:SER518 4.9 39.6 1.0
C A:SER518 4.9 36.8 1.0

Sodium binding site 3 out of 23 in 4d1j

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Sodium binding site 3 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:36.1
occ:1.00
 O A:HOH2432 2.2 46.1 1.0
O A:HOH2396 2.3 38.6 1.0
O A:HOH2431 2.3 38.3 1.0
OG A:SER518 2.4 31.6 1.0
O A:SER518 2.4 39.6 1.0
C A:SER518 3.2 36.8 1.0
NA A:NA602 3.3 35.5 1.0
CB A:SER518 3.4 32.9 1.0
CA A:SER518 3.6 34.2 1.0
OD2 A:ASP469 4.1 32.3 1.0
OD1 A:ASP469 4.2 33.5 1.0
O A:HOH2398 4.2 45.3 1.0
N A:GLN519 4.2 40.3 1.0
OD2 A:ASP464 4.5 37.1 1.0
CG A:ASP469 4.5 30.0 1.0
OD1 A:ASP464 4.6 34.2 1.0
CG A:ASP464 4.7 34.9 1.0
CA A:GLN519 4.7 45.4 1.0
O A:HOH2403 4.9 39.2 1.0

Sodium binding site 4 out of 23 in 4d1j

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Sodium binding site 4 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:44.1
occ:1.00
 O A:HOH2070 2.2 33.2 1.0
O A:HOH2491 2.3 45.3 1.0
O A:HOH2069 2.3 27.5 1.0
O A:HOH2492 2.4 56.4 1.0
O A:HOH2493 2.5 44.4 1.0
O A:HOH2116 3.6 35.3 1.0
O A:HOH2113 4.0 35.0 1.0
O A:HOH2063 4.3 31.9 1.0
O A:ALA87 4.5 21.1 1.0
OD1 A:ASN407 4.6 28.9 1.0
O A:GLY86 4.6 19.9 1.0
CB A:ASN88 4.7 20.5 1.0
O A:HOH2039 4.7 41.3 1.0
O A:HOH2071 4.8 25.6 1.0
CA A:ASN88 4.9 20.2 1.0
CG A:ASN407 4.9 24.0 1.0

Sodium binding site 5 out of 23 in 4d1j

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Sodium binding site 5 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:47.0
occ:1.00
 O B:HOH2392 2.2 43.4 1.0
OG B:SER518 2.5 41.0 1.0
O B:HOH2388 2.5 40.2 1.0
O B:SER518 2.8 44.6 1.0
NA B:NA602 2.8 42.4 1.0
C B:SER518 3.4 44.0 1.0
CB B:SER518 3.5 40.5 1.0
CA B:SER518 3.9 41.0 1.0
OD2 B:ASP464 4.2 43.1 1.0
OD1 B:ASP469 4.4 33.8 1.0
OD1 B:ASP464 4.4 35.9 1.0
N B:GLN519 4.4 46.3 1.0
CG B:ASP464 4.5 40.2 1.0
OD2 B:ASP469 4.5 33.4 1.0
O B:HOH2387 4.7 46.5 1.0
O B:GLY466 4.8 32.8 1.0
CG B:ASP469 4.9 35.0 1.0
CA B:GLN519 4.9 50.5 1.0

Sodium binding site 6 out of 23 in 4d1j

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Sodium binding site 6 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:42.4
occ:1.00
 O B:HOH2387 2.3 46.5 1.0
OG B:SER518 2.4 41.0 1.0
O B:GLY466 2.5 32.8 1.0
OD1 B:ASP464 2.5 35.9 1.0
O B:HOH2388 2.6 40.2 1.0
NA B:NA601 2.8 47.0 1.0
CG B:ASP464 3.2 40.2 1.0
OD2 B:ASP464 3.2 43.1 1.0
CB B:SER518 3.3 40.5 1.0
C B:GLY466 3.5 32.9 1.0
CA B:GLY466 4.0 33.4 1.0
N B:GLY466 4.1 34.7 1.0
O B:HOH2204 4.2 49.7 1.0
O B:HOH2392 4.2 43.4 1.0
OD1 B:ASP469 4.3 33.8 1.0
CA B:SER518 4.6 41.0 1.0
CB B:ASP464 4.6 35.9 1.0
O B:HOH2389 4.7 54.4 1.0
N B:LEU467 4.7 35.5 1.0
O B:SER518 4.8 44.6 1.0
C B:SER518 4.8 44.0 1.0

Sodium binding site 7 out of 23 in 4d1j

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Sodium binding site 7 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:33.5
occ:1.00
 O D:GLY466 2.2 26.0 1.0
OD1 D:ASP464 2.3 26.6 1.0
O D:HOH2428 2.4 32.1 1.0
OG D:SER518 2.5 29.8 1.0
O D:HOH2431 2.6 38.0 1.0
CG D:ASP464 3.2 30.2 1.0
C D:GLY466 3.2 23.3 1.0
OD2 D:ASP464 3.3 34.8 1.0
CB D:SER518 3.3 29.5 1.0
NA D:NA603 3.4 40.3 1.0
CA D:GLY466 3.5 25.7 1.0
N D:GLY466 3.7 24.6 1.0
OE1 D:GLN519 4.1 38.5 1.0
OD1 D:ASP469 4.4 25.0 1.0
N D:LEU467 4.4 26.1 1.0
CB D:ASP464 4.6 29.0 1.0
CA D:SER518 4.7 30.0 1.0
O D:HOH2434 4.9 33.2 1.0
CA D:LEU467 5.0 26.3 1.0
N D:LEU465 5.0 24.9 1.0
C D:LEU465 5.0 25.7 1.0

Sodium binding site 8 out of 23 in 4d1j

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Sodium binding site 8 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:41.5
occ:1.00
 O D:HOH2519 2.3 29.1 1.0
O D:HOH2533 2.4 38.4 1.0
O D:HOH2532 2.4 41.4 1.0
O D:HOH2520 2.5 28.9 1.0
O D:HOH2488 2.5 42.9 1.0
O D:HOH2534 2.6 44.6 1.0
O D:HOH2490 3.7 15.9 1.0
O D:PRO562 3.9 18.5 1.0
O D:HOH2266 4.0 48.8 1.0
O D:HOH2487 4.2 37.1 1.0
O D:HOH2499 4.2 26.8 1.0
O F:HOH2057 4.4 39.2 1.0
O D:HOH2518 4.5 34.1 1.0
O D:HOH2212 4.5 27.4 1.0
O F:HOH2068 4.6 33.9 1.0
CG D:PRO562 4.6 20.4 1.0
OE2 D:GLU533 4.8 17.9 1.0
C D:PRO562 5.0 18.0 1.0

Sodium binding site 9 out of 23 in 4d1j

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Sodium binding site 9 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na603

b:40.3
occ:1.00
 O D:HOH2434 2.3 33.2 1.0
O D:HOH2428 2.3 32.1 1.0
OG D:SER518 2.5 29.8 1.0
O D:SER518 2.5 33.8 1.0
O D:HOH2431 2.5 38.0 1.0
C D:SER518 3.3 32.8 1.0
O D:HOH2466 3.4 41.0 1.0
NA D:NA601 3.4 33.5 1.0
CB D:SER518 3.5 29.5 1.0
CA D:SER518 3.8 30.0 1.0
N D:GLN519 4.3 33.5 1.0
OD1 D:ASP469 4.4 25.0 1.0
OE1 D:GLN519 4.4 38.5 1.0
OD2 D:ASP464 4.4 34.8 1.0
OD2 D:ASP469 4.4 27.4 1.0
OD1 D:ASP464 4.6 26.6 1.0
CG D:ASP464 4.6 30.2 1.0
CA D:GLN519 4.7 36.6 1.0
CB D:GLN519 4.7 35.6 1.0
CG D:ASP469 4.9 23.8 1.0
O D:GLY466 4.9 26.0 1.0
O D:HOH2435 4.9 35.9 1.0

Sodium binding site 10 out of 23 in 4d1j

Go back to Sodium Binding Sites List in 4d1j
Sodium binding site 10 out of 23 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicas in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na604

b:31.0
occ:1.00
 O D:HOH2523 2.2 39.2 1.0
OG D:SER571 2.4 25.4 1.0
O D:HOH2522 2.4 27.6 1.0
O D:SER571 2.5 22.6 1.0
C D:SER571 3.3 23.3 1.0
CB D:SER571 3.5 25.1 1.0
N D:SER571 3.6 26.2 1.0
CA D:SER571 3.7 25.7 1.0
O D:HOH2524 4.0 40.0 1.0
O D:HOH2472 4.2 45.8 1.0
NZ D:LYS524 4.2 66.2 1.0
O D:HOH2456 4.3 22.4 1.0
N D:TYR572 4.3 27.2 1.0
O D:HOH2525 4.5 40.8 1.0
O D:HOH2268 4.7 42.0 1.0
C D:ALA570 4.8 26.4 1.0
CA D:TYR572 4.8 27.6 1.0
CD D:LYS524 4.9 53.5 1.0
CE D:LYS524 4.9 58.8 1.0

Reference:

J.Larsbrink, A.J.Thompson, M.Lundqvist, J.G.Gardner, G.J.Davies, H.Brumer. A Complex Gene Locus Enables Xyloglucan Utilization in the Model Saprophyte Cellvibrio Japonicus. Mol.Microbiol. V. 94 418 2014.
ISSN: ISSN 0950-382X
PubMed: 25171165
DOI: 10.1111/MMI.12776
Page generated: Mon Oct 7 14:49:52 2024

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