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Sodium in PDB 8hhv: Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum

Protein crystallography data

The structure of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum, PDB code: 8hhv was solved by C.Nakashima, J.Li, T.Arakawa, C.Yamada, A.Ishiwata, K.Fujita, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.18 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.285, 128.296, 104.019, 90, 109.38, 90
R / Rfree (%) 17.7 / 21.1

Other elements in 8hhv:

The structure of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum (pdb code 8hhv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum, PDB code: 8hhv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8hhv

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Sodium binding site 1 out of 8 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:11.3
occ:1.00
 OD1 A:ASP85 2.3 25.5 1.0
O A:ASP82 2.3 16.3 1.0
OD2 A:ASP80 2.4 14.2 1.0
O A:GLY86 2.4 16.9 1.0
O A:HOH951 2.5 25.1 1.0
OD1 A:ASP80 2.7 14.3 1.0
CG A:ASP80 2.8 17.5 1.0
C A:GLY86 3.3 15.2 1.0
C A:ASP82 3.4 15.8 1.0
CG A:ASP85 3.5 28.1 1.0
O A:HOH974 3.6 28.4 1.0
N A:GLY86 3.9 15.2 1.0
C A:ASP85 3.9 17.7 1.0
CA A:GLY86 4.1 13.9 1.0
OD2 A:ASP85 4.1 32.4 1.0
O A:ASP85 4.1 14.5 1.0
N A:MET87 4.2 12.6 1.0
CB A:ASP80 4.2 14.5 1.0
CA A:ASP82 4.3 18.3 0.5
CA A:ASP82 4.3 19.1 0.5
N A:LEU83 4.3 16.7 1.0
CB A:ASP82 4.4 21.6 0.5
CA A:LEU83 4.4 15.4 1.0
CB A:ASP82 4.4 19.7 0.5
CA A:MET87 4.4 12.7 1.0
OD2 A:ASP82 4.4 25.8 0.5
O A:HOH937 4.5 37.7 1.0
N A:ASP82 4.5 16.7 1.0
CA A:ASP85 4.6 17.9 1.0
CB A:ASP85 4.6 21.7 1.0
N A:ASP85 4.6 13.9 1.0
CG A:ASP82 4.6 20.5 0.5
N A:LEU88 4.7 11.7 1.0
C A:LEU83 4.8 14.9 1.0
O D:HOH800 4.8 18.6 1.0
O D:HOH890 4.9 35.6 1.0

Sodium binding site 2 out of 8 in 8hhv

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Sodium binding site 2 out of 8 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:16.6
occ:1.00
 O A:HOH643 2.2 21.4 1.0
OD2 A:ASP33 2.3 15.3 1.0
O A:HOH673 2.3 15.8 1.0
OH A:TYR316 2.4 12.4 1.0
O A:HOH985 3.1 34.8 1.0
CG A:ASP33 3.1 11.7 1.0
OD1 A:ASP33 3.4 13.3 1.0
CZ A:TYR316 3.4 12.2 1.0
CE1 A:TYR316 3.5 11.3 1.0
O A:HOH1030 3.7 18.6 1.0
CB A:ASP51 4.2 14.1 1.0
OD2 A:ASP51 4.2 13.9 1.0
OH A:TYR293 4.3 12.1 1.0
N A:ASP51 4.3 10.5 1.0
CB A:ASP33 4.5 10.4 1.0
O A:ASP51 4.6 12.9 1.0
CE2 A:TYR316 4.7 12.1 1.0
CG A:ASP51 4.7 13.2 1.0
CA A:ASP51 4.8 12.6 1.0
CD1 A:TYR316 4.9 14.3 1.0
CZ3 A:TRP313 4.9 16.5 1.0

Sodium binding site 3 out of 8 in 8hhv

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Sodium binding site 3 out of 8 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:11.3
occ:1.00
 OD1 B:ASP85 2.2 26.2 1.0
O B:ASP82 2.4 17.4 1.0
OD2 B:ASP80 2.4 16.4 1.0
O B:GLY86 2.5 14.4 1.0
OD1 B:ASP80 2.6 15.4 1.0
O B:HOH946 2.6 17.6 1.0
CG B:ASP80 2.8 13.5 1.0
O B:HOH996 3.3 25.1 1.0
C B:GLY86 3.4 14.1 1.0
CG B:ASP85 3.4 26.0 1.0
C B:ASP82 3.4 16.5 1.0
N B:GLY86 3.9 12.5 1.0
C B:ASP85 4.0 15.2 1.0
OD2 B:ASP85 4.0 31.1 1.0
CA B:GLY86 4.2 12.2 1.0
O B:ASP85 4.2 15.6 1.0
CB B:ASP82 4.2 22.9 1.0
CA B:ASP82 4.2 17.1 1.0
N B:MET87 4.2 13.8 1.0
CB B:ASP80 4.3 12.8 1.0
N B:LEU83 4.4 13.6 1.0
CA B:LEU83 4.4 14.8 1.0
CA B:MET87 4.5 13.2 1.0
N B:ASP82 4.5 17.7 1.0
O B:HOH968 4.5 29.1 1.0
CB B:ASP85 4.6 22.2 1.0
N B:ASP85 4.6 15.6 1.0
CA B:ASP85 4.6 15.6 1.0
N B:LEU88 4.7 13.7 1.0
CG B:ASP82 4.7 34.1 1.0
C B:LEU83 4.8 12.8 1.0
OD2 B:ASP82 5.0 44.4 1.0

Sodium binding site 4 out of 8 in 8hhv

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Sodium binding site 4 out of 8 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:18.9
occ:1.00
 O B:HOH681 2.3 20.2 1.0
OD2 B:ASP33 2.3 16.9 1.0
O B:HOH742 2.4 20.6 1.0
OH B:TYR316 2.4 15.4 1.0
O B:HOH982 2.8 40.9 1.0
CG B:ASP33 3.1 11.8 1.0
CZ B:TYR316 3.4 16.4 1.0
OD1 B:ASP33 3.4 14.0 1.0
CE1 B:TYR316 3.5 13.4 1.0
O B:HOH1059 3.8 19.6 1.0
CB B:ASP51 4.1 17.4 1.0
OH B:TYR293 4.2 14.3 1.0
OD2 B:ASP51 4.4 16.7 1.0
N B:ASP51 4.4 13.1 1.0
CB B:ASP33 4.4 12.7 1.0
O B:ASP51 4.6 14.9 1.0
CE2 B:TYR316 4.7 14.6 1.0
CA B:ASP51 4.7 14.1 1.0
CG B:ASP51 4.7 16.1 1.0
CD1 B:TYR316 4.8 14.8 1.0
CZ3 B:TRP313 4.9 21.0 1.0

Sodium binding site 5 out of 8 in 8hhv

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Sodium binding site 5 out of 8 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:15.3
occ:1.00
 OD2 C:ASP80 2.3 15.6 1.0
OD1 C:ASP85 2.3 29.4 1.0
O C:ASP82 2.3 19.1 1.0
O C:GLY86 2.4 20.2 1.0
OD1 C:ASP80 2.6 18.9 1.0
O C:HOH867 2.7 24.9 1.0
CG C:ASP80 2.7 17.8 1.0
O C:HOH888 3.4 30.0 1.0
C C:GLY86 3.4 18.3 1.0
C C:ASP82 3.4 20.2 1.0
CG C:ASP85 3.5 25.2 1.0
N C:GLY86 3.9 18.6 1.0
C C:ASP85 4.0 17.6 1.0
O C:HOH656 4.1 42.4 1.0
CA C:GLY86 4.2 17.4 1.0
O C:ASP85 4.2 18.6 1.0
OD2 C:ASP85 4.2 31.4 1.0
CA C:ASP82 4.2 22.4 1.0
CB C:ASP80 4.2 15.7 1.0
CB C:ASP82 4.2 24.3 1.0
N C:MET87 4.3 15.9 1.0
N C:LEU83 4.3 20.3 1.0
N C:ASP82 4.4 20.2 1.0
CA C:LEU83 4.4 18.2 1.0
CA C:MET87 4.5 15.6 1.0
CA C:ASP85 4.6 18.0 1.0
N C:ASP85 4.6 16.3 1.0
CB C:ASP85 4.6 19.6 1.0
N C:LEU88 4.7 14.3 1.0
C C:LEU83 4.9 20.6 1.0
CG C:ASP82 4.9 33.9 1.0

Sodium binding site 6 out of 8 in 8hhv

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Sodium binding site 6 out of 8 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:20.7
occ:1.00
 OD2 C:ASP33 2.3 16.3 1.0
O C:HOH658 2.4 19.0 1.0
O2 C:GOL505 2.4 41.2 1.0
O C:HOH631 2.4 16.4 1.0
OH C:TYR316 2.4 12.2 1.0
CG C:ASP33 3.1 13.8 1.0
OD1 C:ASP33 3.3 14.8 1.0
CZ C:TYR316 3.4 14.3 1.0
CE1 C:TYR316 3.6 12.8 1.0
C2 C:GOL505 3.6 40.8 1.0
O3 C:GOL505 3.7 23.4 1.0
CB C:ASP51 4.1 12.4 1.0
C3 C:GOL505 4.2 33.2 1.0
OH C:TYR293 4.2 14.6 1.0
OD2 C:ASP51 4.3 13.1 1.0
N C:ASP51 4.3 11.8 1.0
CB C:ASP33 4.4 12.6 1.0
O C:ASP51 4.5 14.1 1.0
CA C:ASP51 4.7 11.9 1.0
CG C:ASP51 4.7 12.5 1.0
CE2 C:TYR316 4.7 13.6 1.0
C1 C:GOL505 4.8 37.0 1.0
CD1 C:TYR316 4.9 13.7 1.0
CZ3 C:TRP313 4.9 20.9 1.0

Sodium binding site 7 out of 8 in 8hhv

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Sodium binding site 7 out of 8 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:18.1
occ:1.00
 OD2 D:ASP33 2.3 14.8 1.0
O2 D:GOL506 2.3 38.3 1.0
O D:HOH649 2.3 21.1 1.0
OH D:TYR316 2.4 12.8 1.0
O D:HOH708 2.5 15.3 1.0
CG D:ASP33 3.1 10.7 1.0
C2 D:GOL506 3.3 39.7 1.0
CZ D:TYR316 3.4 15.3 1.0
OD1 D:ASP33 3.4 13.0 1.0
CE1 D:TYR316 3.5 14.3 1.0
O D:HOH988 3.6 36.3 1.0
C3 D:GOL506 3.6 33.5 1.0
O3 D:GOL506 3.9 22.6 1.0
OH D:TYR293 4.1 14.1 1.0
CB D:ASP51 4.2 14.1 1.0
OD2 D:ASP51 4.2 13.6 1.0
N D:ASP51 4.4 12.3 1.0
CB D:ASP33 4.4 10.9 1.0
O D:ASP51 4.6 13.1 1.0
C1 D:GOL506 4.7 36.7 1.0
CE2 D:TYR316 4.7 12.7 1.0
CG D:ASP51 4.7 15.0 1.0
CA D:ASP51 4.8 13.3 1.0
CZ3 D:TRP313 4.8 16.6 1.0
CD1 D:TYR316 4.8 14.5 1.0
O1 D:GOL506 5.0 43.9 1.0

Sodium binding site 8 out of 8 in 8hhv

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Sodium binding site 8 out of 8 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:11.0
occ:1.00
 OD1 D:ASP85 2.3 30.8 1.0
O D:ASP82 2.3 17.3 1.0
O D:HOH645 2.4 40.0 1.0
OD2 D:ASP80 2.4 15.6 1.0
O D:GLY86 2.5 13.5 1.0
OD1 D:ASP80 2.6 13.9 1.0
O D:HOH885 2.7 20.9 1.0
CG D:ASP80 2.9 13.8 1.0
C D:GLY86 3.4 13.9 1.0
C D:ASP82 3.4 14.6 1.0
O D:HOH969 3.5 26.2 1.0
CG D:ASP85 3.5 30.1 1.0
N D:GLY86 3.9 13.5 1.0
C D:ASP85 3.9 16.2 1.0
CA D:GLY86 4.1 13.2 1.0
O D:ASP85 4.1 15.7 1.0
OD2 D:ASP85 4.2 32.2 1.0
CA D:ASP82 4.2 17.8 1.0
CB D:ASP82 4.2 22.7 1.0
N D:MET87 4.3 13.8 1.0
N D:LEU83 4.3 14.4 1.0
CB D:ASP80 4.3 11.1 1.0
CA D:LEU83 4.4 15.8 1.0
CG D:ASP82 4.4 29.6 1.0
O D:HOH924 4.4 31.1 1.0
N D:ASP82 4.4 15.7 1.0
OD2 D:ASP82 4.4 36.9 1.0
CA D:MET87 4.5 13.3 1.0
N D:ASP85 4.5 15.5 1.0
CA D:ASP85 4.5 15.8 1.0
CB D:ASP85 4.6 22.9 1.0
C D:LEU83 4.8 15.4 1.0
N D:LEU88 4.8 11.4 1.0
O A:HOH713 4.8 20.8 1.0
O A:HOH760 4.9 25.2 1.0

Reference:

M.Shimokawa, A.Ishiwata, T.Kashima, C.Nakashima, J.Li, R.Fukushima, M.Sawai, M.Nakamori, Y.Tanaka, A.Kudoh, S.Morigami, G.Akai, N.Shimizu, T.Arakawa, C.Yamada, K.Tanaka, Y.Ito, S.Fushinobu, K.Fujita. Identification and Characterization of Endo- and Exo-Hydrolases Cleaving the Alpha- and Beta-D-Arabinofuranosidic Bonds of Lipoarabinomannan and Arabinogalactan of Mycobacteria To Be Published.
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