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Sodium in PDB 4d1i: The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus

Enzymatic activity of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus

All present enzymatic activity of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus:
3.2.1.23;

Protein crystallography data

The structure of The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus, PDB code: 4d1i 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) 116.03 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 98.911, 115.783, 116.036, 90.21, 90.25, 90.38
R / Rfree (%) 18.483 / 21.153

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus (pdb code 4d1i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus, PDB code: 4d1i:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in 4d1i

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Sodium binding site 1 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na600

b:37.5
occ:1.00
 O A:HOH2301 2.2 47.0 1.0
O A:GLY466 2.3 32.0 1.0
OG A:SER518 2.4 46.1 1.0
OD1 A:ASP464 2.5 38.3 1.0
OE1 A:GLN519 2.5 59.3 1.0
CB A:SER518 3.3 48.1 1.0
CG A:ASP464 3.3 40.5 1.0
C A:GLY466 3.3 29.8 1.0
OD2 A:ASP464 3.4 42.7 1.0
O A:HOH2327 3.4 38.6 1.0
CA A:GLY466 3.8 30.8 1.0
CD A:GLN519 3.8 64.5 1.0
N A:GLY466 4.0 31.1 1.0
OD1 A:ASP469 4.4 30.6 1.0
N A:LEU467 4.5 33.6 1.0
NE2 A:GLN519 4.6 66.1 1.0
CA A:SER518 4.6 44.0 1.0
CB A:ASP464 4.7 36.6 1.0
C A:SER518 4.9 49.2 1.0
O A:SER518 4.9 46.2 1.0
CG A:GLN519 4.9 56.4 1.0

Sodium binding site 2 out of 17 in 4d1i

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Sodium binding site 2 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na600

b:35.7
occ:1.00
 O B:GLY466 2.3 30.2 1.0
O B:HOH2356 2.3 44.9 1.0
OG B:SER518 2.3 39.4 1.0
O B:HOH2358 2.5 52.1 1.0
OD1 B:ASP464 2.5 39.8 1.0
CB B:SER518 3.2 37.9 1.0
O B:HOH2383 3.3 40.3 1.0
CG B:ASP464 3.3 37.7 1.0
OD2 B:ASP464 3.4 45.0 1.0
C B:GLY466 3.4 28.5 1.0
CA B:GLY466 3.9 30.5 1.0
N B:GLY466 4.0 32.2 1.0
OE1 B:GLN519 4.3 76.2 1.0
O B:HOH2360 4.3 47.9 1.0
OD1 B:ASP469 4.3 33.3 1.0
CA B:SER518 4.5 38.9 1.0
N B:LEU467 4.6 31.4 1.0
CB B:ASP464 4.7 35.4 1.0
O B:SER518 4.8 45.4 1.0
C B:SER518 4.8 41.7 1.0

Sodium binding site 3 out of 17 in 4d1i

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Sodium binding site 3 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na600

b:46.4
occ:1.00
 O C:HOH2363 2.1 39.7 1.0
O C:HOH2385 2.2 41.5 1.0
O C:SER518 2.6 49.0 1.0
OG C:SER518 2.6 41.8 1.0
NA C:NA601 3.0 50.2 1.0
C C:SER518 3.4 47.5 1.0
CB C:SER518 3.6 41.4 1.0
CA C:SER518 3.9 43.5 1.0
N C:GLN519 4.3 51.8 1.0
OD2 C:ASP464 4.4 47.7 1.0
OD2 C:ASP469 4.7 36.8 1.0
OD1 C:ASP469 4.7 33.9 1.0
OD1 C:ASP464 4.7 35.3 1.0
CA C:GLN519 4.7 57.5 1.0
CG C:ASP464 4.7 38.7 1.0
CB C:GLN519 4.9 52.6 1.0
O C:GLY466 5.0 35.7 1.0

Sodium binding site 4 out of 17 in 4d1i

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Sodium binding site 4 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:50.2
occ:1.00
 OG C:SER518 2.5 41.8 1.0
OD1 C:ASP464 2.5 35.3 1.0
O C:GLY466 2.6 35.7 1.0
NA C:NA600 3.0 46.4 1.0
OD2 C:ASP464 3.1 47.7 1.0
CG C:ASP464 3.1 38.7 1.0
CB C:SER518 3.4 41.4 1.0
C C:GLY466 3.7 32.3 1.0
CA C:GLY466 4.1 33.0 1.0
O C:HOH2363 4.2 39.7 1.0
N C:GLY466 4.2 32.1 1.0
OD1 C:ASP469 4.4 33.9 1.0
CB C:ASP464 4.6 34.9 1.0
CA C:SER518 4.7 43.5 1.0
O C:SER518 4.8 49.0 1.0
N C:LEU467 4.8 32.1 1.0
C C:SER518 4.9 47.5 1.0
O C:HOH2385 4.9 41.5 1.0

Sodium binding site 5 out of 17 in 4d1i

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Sodium binding site 5 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na600

b:25.0
occ:1.00
 O D:HOH2538 2.1 31.1 1.0
O D:HOH2487 2.3 38.3 1.0
OG D:SER571 2.4 25.9 1.0
O D:SER571 2.4 23.5 1.0
O D:HOH2536 2.5 22.8 1.0
C D:SER571 3.2 23.3 1.0
CB D:SER571 3.6 24.5 1.0
N D:SER571 3.6 24.3 1.0
CA D:SER571 3.6 24.1 1.0
O D:HOH2537 3.8 30.3 1.0
O D:HOH2258 3.9 51.4 1.0
O D:HOH2263 4.1 41.3 1.0
NZ D:LYS524 4.1 41.3 1.0
N D:TYR572 4.2 24.4 1.0
O D:HOH2470 4.3 22.8 1.0
O D:HOH2264 4.4 42.0 1.0
CA D:TYR572 4.6 24.5 1.0
CD D:LYS524 4.7 35.1 1.0
C D:ALA570 4.8 23.1 1.0
O D:HOH2248 4.9 32.6 1.0
CE D:LYS524 4.9 36.4 1.0

Sodium binding site 6 out of 17 in 4d1i

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Sodium binding site 6 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:36.8
occ:1.00
 O D:HOH2442 2.2 28.8 1.0
O D:HOH2449 2.4 34.2 1.0
O D:HOH2477 2.4 36.1 1.0
OG D:SER518 2.5 26.1 1.0
O D:SER518 2.5 30.6 1.0
O D:HOH2446 2.7 33.0 1.0
NA D:NA602 3.1 27.3 1.0
C D:SER518 3.4 29.9 1.0
CB D:SER518 3.5 27.4 1.0
CA D:SER518 3.8 27.9 1.0
CG D:GLN519 3.9 39.2 0.5
O D:HOH2476 4.0 42.3 1.0
OD2 D:ASP464 4.3 29.1 1.0
OD2 D:ASP469 4.4 28.5 1.0
OD1 D:ASP469 4.4 25.0 1.0
N D:GLN519 4.4 30.9 1.0
OD1 D:ASP464 4.5 23.4 1.0
CG D:ASP464 4.5 25.9 1.0
CB D:GLN519 4.8 34.4 0.5
CG D:ASP469 4.8 24.2 1.0
CB D:GLN519 4.8 26.0 0.5
CA D:GLN519 4.8 32.5 0.5
CA D:GLN519 4.8 28.8 0.5
CD D:GLN519 4.8 42.1 0.5
OE1 D:GLN519 4.9 23.2 0.5
O D:HOH2445 4.9 31.2 1.0
O D:GLY466 4.9 24.1 1.0

Sodium binding site 7 out of 17 in 4d1i

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Sodium binding site 7 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:27.3
occ:1.00
 O D:HOH2442 2.3 28.8 1.0
O D:HOH2445 2.3 31.2 1.0
OG D:SER518 2.4 26.1 1.0
O D:GLY466 2.4 24.1 1.0
OD1 D:ASP464 2.4 23.4 1.0
O D:HOH2446 2.4 33.0 1.0
NA D:NA601 3.1 36.8 1.0
CG D:ASP464 3.1 25.9 1.0
CB D:SER518 3.2 27.4 1.0
OD2 D:ASP464 3.3 29.1 1.0
C D:GLY466 3.4 21.6 1.0
CA D:GLY466 3.9 24.1 1.0
N D:GLY466 4.0 22.7 1.0
O D:HOH2447 4.1 36.7 1.0
OD1 D:ASP469 4.3 25.0 1.0
OE1 D:GLN519 4.3 23.2 0.5
NE2 D:GLN519 4.4 42.2 0.5
CB D:ASP464 4.5 23.3 1.0
CA D:SER518 4.6 27.9 1.0
N D:LEU467 4.6 23.1 1.0
O D:HOH2449 4.7 34.2 1.0
CD D:GLN519 4.7 42.1 0.5
CG D:GLN519 4.7 39.2 0.5
O D:SER518 4.8 30.6 1.0
C D:SER518 4.9 29.9 1.0

Sodium binding site 8 out of 17 in 4d1i

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Sodium binding site 8 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na600

b:26.2
occ:1.00
 O E:HOH2520 2.2 31.5 1.0
O E:HOH2513 2.4 18.9 1.0
OG E:SER571 2.4 26.3 1.0
O E:HOH2472 2.4 29.3 1.0
O E:SER571 2.5 22.6 1.0
O E:HOH2515 2.5 38.6 1.0
C E:SER571 3.2 23.2 1.0
CB E:SER571 3.6 24.1 1.0
N E:SER571 3.6 23.7 1.0
CA E:SER571 3.7 23.7 1.0
O E:HOH2514 3.8 36.1 1.0
O E:HOH2235 4.1 55.8 1.0
O E:HOH2237 4.1 39.5 1.0
NZ E:LYS524 4.2 37.6 1.0
O E:HOH2516 4.3 27.5 1.0
N E:TYR572 4.3 20.8 1.0
O E:HOH2449 4.3 22.5 1.0
O E:HOH2254 4.5 42.9 1.0
CA E:TYR572 4.8 21.5 1.0
C E:ALA570 4.8 23.2 1.0
CD E:LYS524 4.8 31.1 1.0

Sodium binding site 9 out of 17 in 4d1i

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Sodium binding site 9 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na601

b:26.5
occ:1.00
 O E:HOH2424 2.3 33.6 1.0
O E:GLY466 2.3 22.9 1.0
O E:HOH2426 2.4 31.1 1.0
OG E:SER518 2.4 27.3 1.0
O E:HOH2429 2.4 34.6 1.0
OD1 E:ASP464 2.5 27.6 1.0
CG E:ASP464 3.2 28.4 1.0
CB E:SER518 3.3 27.1 1.0
OD2 E:ASP464 3.3 31.6 1.0
NA E:NA602 3.3 29.7 1.0
C E:GLY466 3.4 23.3 1.0
CA E:GLY466 3.8 22.5 1.0
N E:GLY466 4.0 21.4 1.0
O E:HOH2425 4.0 50.8 1.0
OD1 E:ASP469 4.3 22.4 1.0
OE1 E:GLN519 4.3 36.1 1.0
N E:LEU467 4.6 22.9 1.0
CB E:ASP464 4.6 24.8 1.0
CA E:SER518 4.6 24.6 1.0
O E:HOH2431 4.6 40.2 1.0
O E:SER518 4.9 26.6 1.0
C E:SER518 4.9 26.6 1.0

Sodium binding site 10 out of 17 in 4d1i

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Sodium binding site 10 out of 17 in the The Structure of the GH35 Beta-Galactosidase BGL35A From Cellvibrio Japonicus


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 Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na602

b:29.7
occ:1.00
 O E:HOH2431 2.2 40.2 1.0
O E:HOH2459 2.3 33.6 1.0
O E:HOH2426 2.3 31.1 1.0
O E:SER518 2.4 26.6 1.0
OG E:SER518 2.5 27.3 1.0
O E:HOH2429 2.7 34.6 1.0
C E:SER518 3.3 26.6 1.0
NA E:NA601 3.3 26.5 1.0
CB E:SER518 3.5 27.1 1.0
CA E:SER518 3.7 24.6 1.0
O E:HOH2460 4.0 35.3 1.0
O E:HOH2458 4.1 39.5 1.0
N E:GLN519 4.3 25.6 1.0
OD2 E:ASP469 4.3 25.7 1.0
OD1 E:ASP469 4.4 22.4 1.0
OD2 E:ASP464 4.5 31.6 1.0
O E:HOH2209 4.5 41.1 1.0
OD1 E:ASP464 4.6 27.6 1.0
CG E:ASP464 4.7 28.4 1.0
CA E:GLN519 4.7 27.3 1.0
CB E:GLN519 4.8 27.2 1.0
CG E:ASP469 4.8 23.3 1.0
O E:HOH2432 4.8 33.7 1.0
OE1 E:GLN519 4.9 36.1 1.0
O E:HOH2424 4.9 33.6 1.0
O E:GLY466 5.0 22.9 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 14:49:44 2024

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