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Calcium in PDB 6b7k: GH43 Endo-Arabinanase From Bacillus Licheniformis

Enzymatic activity of GH43 Endo-Arabinanase From Bacillus Licheniformis

All present enzymatic activity of GH43 Endo-Arabinanase From Bacillus Licheniformis:
3.2.1.99;

Protein crystallography data

The structure of GH43 Endo-Arabinanase From Bacillus Licheniformis, PDB code: 6b7k was solved by E.G.S.Farro, A.S.Nascimento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.52 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.558, 124.178, 69.231, 90.00, 91.16, 90.00
R / Rfree (%) 23 / 27.4

Calcium Binding Sites:

The binding sites of Calcium atom in the GH43 Endo-Arabinanase From Bacillus Licheniformis (pdb code 6b7k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the GH43 Endo-Arabinanase From Bacillus Licheniformis, PDB code: 6b7k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6b7k

Go back to Calcium Binding Sites List in 6b7k
Calcium binding site 1 out of 8 in the GH43 Endo-Arabinanase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of GH43 Endo-Arabinanase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:69.5
occ:1.00
 O A:HOH419 2.5 35.0 1.0
CE1 A:HIS252 2.9 45.2 1.0
O A:PRO131 3.4 30.1 1.0
NE2 A:HIS252 3.7 43.4 1.0
ND1 A:HIS252 3.7 43.0 1.0
OD1 A:ASP132 3.8 34.7 1.0
O A:HOH404 3.8 47.7 1.0
O A:PRO184 4.2 37.1 1.0
O A:GLN253 4.3 34.4 1.0
O A:PRO73 4.4 62.1 1.0
CB A:ASP132 4.4 34.0 1.0
OD2 A:ASP254 4.4 35.1 1.0
C A:PRO131 4.5 31.1 1.0
CG A:ASP132 4.5 34.4 1.0
CD2 A:HIS252 4.8 43.3 1.0
CG A:ASP254 4.8 34.8 1.0
CG A:HIS252 4.8 40.7 1.0
CB A:ASP74 4.9 42.4 1.0
OD1 A:ASP74 4.9 42.1 1.0
C A:ASP130 4.9 32.9 1.0
O A:PRO14 4.9 33.1 1.0
O A:ASP130 5.0 33.1 1.0

Calcium binding site 2 out of 8 in 6b7k

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Calcium binding site 2 out of 8 in the GH43 Endo-Arabinanase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of GH43 Endo-Arabinanase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:34.1
occ:1.00
 OD1 A:ASP132 2.4 34.7 1.0
OD1 A:ASP74 2.4 42.1 1.0
OD2 A:ASP254 2.5 35.1 1.0
O A:HOH417 2.6 23.6 1.0
OD1 A:ASP254 2.7 35.0 1.0
CG A:ASP254 3.0 34.8 1.0
CG A:ASP132 3.2 34.4 1.0
OD2 A:ASP132 3.4 34.9 1.0
CG A:ASP74 3.4 42.2 1.0
OD2 A:ASP74 3.8 43.0 1.0
OG A:SER15 4.2 30.3 1.0
O A:LEU133 4.2 38.7 1.0
CB A:ASP132 4.5 34.0 1.0
CB A:ASP254 4.5 34.7 1.0
CB A:ASN185 4.7 39.0 1.0
O A:VAL255 4.7 39.3 1.0
CB A:ASP74 4.7 42.4 1.0
N A:LEU133 4.7 35.8 1.0
CA A:ASP132 4.8 33.4 1.0
O A:ILE75 4.9 32.4 1.0

Calcium binding site 3 out of 8 in 6b7k

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Calcium binding site 3 out of 8 in the GH43 Endo-Arabinanase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of GH43 Endo-Arabinanase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:74.2
occ:1.00
 O B:HOH412 2.3 77.0 1.0
O B:HOH406 2.8 36.5 1.0
CE1 B:HIS252 2.9 46.3 1.0
ND1 B:HIS252 3.2 45.9 1.0
O B:GLN253 3.5 42.3 1.0
NE2 B:HIS252 4.1 47.4 1.0
O B:PRO184 4.3 38.5 1.0
CG B:HIS252 4.4 45.1 1.0
O B:PRO131 4.4 34.7 1.0
O B:PRO14 4.6 34.1 1.0
C B:GLN253 4.6 41.8 1.0
O B:ALA183 4.7 36.0 1.0
CB B:ASP254 4.7 37.6 1.0
O B:PRO73 4.7 35.2 1.0
C B:ALA183 4.7 36.6 1.0
CG B:ASP254 4.8 37.6 1.0
CD2 B:HIS252 4.8 46.9 1.0
CB B:ALA183 4.8 37.5 1.0
CA B:ALA183 4.9 37.6 1.0
O B:HIS252 4.9 43.3 1.0
C B:HIS252 4.9 43.1 1.0
OD1 B:ASP132 5.0 39.9 1.0

Calcium binding site 4 out of 8 in 6b7k

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Calcium binding site 4 out of 8 in the GH43 Endo-Arabinanase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of GH43 Endo-Arabinanase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:40.4
occ:1.00
 OD1 B:ASP254 2.4 38.2 1.0
OD1 B:ASP74 2.5 34.3 1.0
OD1 B:ASP132 2.5 39.9 1.0
OD2 B:ASP254 2.7 37.4 1.0
CG B:ASP254 2.9 37.6 1.0
O B:HOH406 3.3 36.5 1.0
CG B:ASP74 3.6 34.8 1.0
CG B:ASP132 3.7 40.2 1.0
OD2 B:ASP74 4.0 35.0 1.0
OD2 B:ASP132 4.3 41.8 1.0
O B:VAL255 4.3 39.8 1.0
O B:LEU133 4.4 34.0 1.0
CB B:ASP254 4.4 37.6 1.0
OG B:SER15 4.4 33.8 1.0
O B:ILE75 4.6 35.5 1.0
CB B:ASN185 4.7 40.9 1.0
CB B:ASP132 4.8 39.0 1.0
CB B:ASP74 4.8 35.5 1.0
N B:VAL255 4.9 37.9 1.0

Calcium binding site 5 out of 8 in 6b7k

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Calcium binding site 5 out of 8 in the GH43 Endo-Arabinanase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of GH43 Endo-Arabinanase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:76.7
occ:1.00
 O C:HOH415 2.4 39.3 1.0
CE1 C:HIS252 3.0 51.7 1.0
ND1 C:HIS252 3.4 50.5 1.0
O C:GLN253 3.7 40.0 1.0
NE2 C:HIS252 4.0 52.2 1.0
O C:PRO131 4.2 40.6 1.0
O C:PRO14 4.4 31.3 1.0
O C:PRO184 4.4 41.2 1.0
O C:PRO73 4.5 31.6 1.0
CG C:ASP254 4.6 42.8 1.0
CG C:HIS252 4.6 49.0 1.0
CB C:ASP254 4.7 41.0 1.0
C C:GLN253 4.7 39.0 1.0
OD2 C:ASP254 4.8 44.5 1.0
CD2 C:HIS252 4.8 50.9 1.0
OD1 C:ASP254 4.9 42.9 1.0
CB C:ALA183 5.0 38.1 1.0
O C:ALA183 5.0 39.1 1.0

Calcium binding site 6 out of 8 in 6b7k

Go back to Calcium Binding Sites List in 6b7k
Calcium binding site 6 out of 8 in the GH43 Endo-Arabinanase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of GH43 Endo-Arabinanase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:47.8
occ:1.00
 OD1 C:ASP132 2.3 48.6 1.0
OD1 C:ASP254 2.5 42.9 1.0
OD1 C:ASP74 2.6 30.9 1.0
OD2 C:ASP254 2.6 44.5 1.0
CG C:ASP254 2.9 42.8 1.0
CG C:ASP132 3.4 48.2 1.0
CG C:ASP74 3.6 31.6 1.0
OD2 C:ASP74 3.9 31.8 1.0
O C:HOH415 3.9 39.3 1.0
OD2 C:ASP132 4.0 49.8 1.0
O C:VAL255 4.2 38.3 1.0
O C:LEU133 4.3 44.2 1.0
CB C:ASP254 4.4 41.0 1.0
CB C:ASP132 4.6 45.8 1.0
OG C:SER15 4.6 31.5 1.0
O C:ILE75 4.8 32.8 1.0
CB C:ASN185 4.8 40.2 1.0
N C:VAL255 4.8 37.4 1.0
CB C:ASP74 4.9 32.4 1.0
N C:LEU133 4.9 41.1 1.0
CA C:ASP132 5.0 43.0 1.0

Calcium binding site 7 out of 8 in 6b7k

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Calcium binding site 7 out of 8 in the GH43 Endo-Arabinanase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of GH43 Endo-Arabinanase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:44.8
occ:1.00
 OD1 D:ASP132 2.4 36.4 1.0
O D:HOH418 2.4 28.4 1.0
OD1 D:ASP74 2.4 34.6 1.0
OD2 D:ASP254 2.7 38.0 1.0
OD1 D:ASP254 2.7 35.9 1.0
CG D:ASP254 3.1 36.8 1.0
CG D:ASP74 3.4 34.8 1.0
CG D:ASP132 3.4 36.8 1.0
OD2 D:ASP74 3.6 36.0 1.0
OD2 D:ASP132 3.7 37.2 1.0
O D:VAL255 4.2 38.8 1.0
O D:LEU133 4.2 38.7 1.0
OG D:SER15 4.4 31.9 1.0
CB D:ASP254 4.6 37.3 1.0
O D:ILE75 4.6 32.2 1.0
CB D:ASP132 4.7 37.3 1.0
CB D:ASP74 4.7 33.9 1.0
N D:LEU133 4.9 37.9 1.0
CB D:ASN185 5.0 39.3 1.0

Calcium binding site 8 out of 8 in 6b7k

Go back to Calcium Binding Sites List in 6b7k
Calcium binding site 8 out of 8 in the GH43 Endo-Arabinanase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of GH43 Endo-Arabinanase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:75.7
occ:1.00
 O D:HOH405 2.4 42.2 1.0
O D:HOH407 2.6 24.9 1.0
NE2 D:HIS252 2.7 41.8 1.0
CD2 D:HIS252 3.0 41.6 1.0
CE1 D:HIS252 3.9 41.3 1.0
O D:PRO131 4.0 36.2 1.0
CG D:HIS252 4.2 41.2 1.0
O D:GLN253 4.3 37.9 1.0
O D:PRO73 4.3 33.1 1.0
O D:PRO14 4.5 34.0 1.0
O D:PRO184 4.6 36.7 1.0
CB D:ALA72 4.6 32.7 1.0
ND1 D:HIS252 4.6 41.0 1.0
OD2 D:ASP254 4.8 38.0 1.0
CB D:ALA183 4.9 35.7 1.0
O D:HIS252 4.9 38.3 1.0
CA D:ALA183 5.0 35.2 1.0

Reference:

E.G.S.Farro, A.E.T.Leite, I.A.Silva, J.G.Filgueiras, E.R.De Azevedo, I.Polikarpov, A.S.Nascimento. GH43 Endo-Arabinanase From Bacillus Licheniformis: Structure, Activity and Unexpected Synergistic Effect on Cellulose Enzymatic Hydrolysis. Int. J. Biol. Macromol. V. 117 7 2018.
ISSN: ISSN 1879-0003
PubMed: 29800670
DOI: 10.1016/J.IJBIOMAC.2018.05.157
Page generated: Mon Jul 15 16:43:18 2024

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