Calcium in PDB 5ubj: Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans

Enzymatic activity of Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans

All present enzymatic activity of Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans:
3.2.1.55;

Protein crystallography data

The structure of Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans, PDB code: 5ubj was solved by M.V.Liberato, F.J.Contesini, A.R.Damasio, F.M.Squina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.76 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.562, 57.529, 49.371, 90.00, 104.98, 90.00
R / Rfree (%) 14.4 / 17.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans (pdb code 5ubj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans, PDB code: 5ubj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5ubj

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Calcium binding site 1 out of 5 in the Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:12.5
occ:1.00
 NE2 A:GLN213 2.4 10.9 1.0
O A:HOH536 2.4 14.4 1.0
O A:HOH585 2.5 11.7 1.0
O A:HOH591 2.5 12.4 1.0
NE2 A:HIS278 2.5 13.8 1.0
O A:HOH579 2.5 11.8 1.0
O A:HOH570 2.5 12.8 1.0
CD A:GLN213 3.4 12.2 1.0
CE1 A:HIS278 3.4 14.3 1.0
CD2 A:HIS278 3.5 13.9 1.0
OE1 A:GLN213 3.7 14.9 1.0
O A:GLN159 3.9 13.3 1.0
O A:PRO102 4.1 11.6 1.0
O A:HOH646 4.2 13.3 1.0
O A:GLY279 4.4 12.2 1.0
O A:VAL212 4.5 13.0 1.0
OG1 A:THR103 4.6 11.2 1.0
ND1 A:HIS278 4.6 14.0 1.0
CG A:HIS278 4.6 13.1 1.0
O A:ALA101 4.6 14.4 1.0
CG A:GLN213 4.7 12.6 1.0
O A:ASP50 4.7 12.4 1.0
O A:HOH671 4.9 12.4 1.0
O A:PHE51 4.9 13.0 1.0
C A:ALA101 5.0 13.4 1.0

Calcium binding site 2 out of 5 in 5ubj

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Calcium binding site 2 out of 5 in the Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:14.6
occ:1.00
 OD2 A:ASP111 2.3 18.1 1.0
O A:GLU108 2.3 15.7 1.0
O A:HOH690 2.3 16.7 1.0
OE2 A:GLU108 2.4 17.9 1.0
CD A:GLU108 3.2 18.5 1.0
CG A:ASP111 3.5 18.6 1.0
C A:GLU108 3.5 14.8 1.0
CG A:GLU108 3.7 15.8 1.0
OE1 A:GLU108 4.1 18.1 1.0
OD1 A:ASP111 4.1 17.2 1.0
C A:PRO109 4.3 15.3 1.0
N A:ASP111 4.3 15.1 1.0
CA A:GLU108 4.3 14.3 1.0
CA A:PRO109 4.3 16.1 1.0
O A:PRO109 4.3 16.0 1.0
N A:PRO109 4.4 15.5 1.0
OH A:TYR106 4.6 15.0 1.0
CA A:ASP111 4.6 15.6 1.0
CB A:GLU108 4.6 14.8 1.0
CB A:ASP111 4.6 16.3 1.0
O A:HOH578 4.6 15.2 1.0
N A:LYS110 4.7 14.6 1.0

Calcium binding site 3 out of 5 in 5ubj

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Calcium binding site 3 out of 5 in the Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:20.0
occ:1.00
 O A:HOH546 2.3 29.6 1.0
O A:HOH636 2.4 19.0 1.0
O A:HOH726 2.4 25.2 1.0
O A:HOH773 2.4 30.1 1.0
O A:HOH555 2.5 22.1 1.0
O A:HOH564 2.5 14.6 1.0
O A:HOH567 2.6 15.5 1.0
O A:HOH534 2.6 29.7 1.0
O A:HOH798 3.9 38.2 1.0
NZ A:LYS49 3.9 14.5 1.0
OD2 A:ASP50 4.1 13.2 1.0
OD1 A:ASP50 4.2 12.5 1.0
O A:HOH575 4.4 15.2 1.0
OE2 A:GLU210 4.4 14.6 1.0
OE1 A:GLU210 4.4 13.9 1.0
O A:HOH688 4.4 25.1 1.0
OD1 A:ASP158 4.5 13.0 1.0
CG A:ASP50 4.5 13.1 1.0
CD A:GLU210 4.6 14.2 1.0
OD2 A:ASP158 4.6 12.7 1.0
O A:HOH682 4.7 25.8 1.0
ND1 A:HIS278 4.8 14.0 1.0
CE A:LYS49 4.8 12.6 1.0

Calcium binding site 4 out of 5 in 5ubj

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Calcium binding site 4 out of 5 in the Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:29.8
occ:1.00
 O A:SER197 2.3 17.4 1.0
O A:HOH657 2.4 31.5 1.0
O A:HOH784 2.4 26.3 1.0
O A:HOH722 2.4 28.1 1.0
O A:HOH789 2.4 34.9 1.0
O A:HOH748 2.5 27.0 1.0
O A:HOH651 2.6 26.6 1.0
C A:SER197 3.5 17.2 1.0
N A:SER197 4.1 17.8 1.0
N A:GLU198 4.4 17.6 1.0
CA A:SER197 4.4 17.4 1.0
CA A:GLU198 4.4 20.1 1.0
OG A:SER197 4.5 18.3 1.0
OE1 A:GLU196 4.6 30.8 1.0
O A:HOH747 4.6 8.7 1.0
O A:HOH593 4.9 22.6 1.0

Calcium binding site 5 out of 5 in 5ubj

Go back to Calcium Binding Sites List in 5ubj
Calcium binding site 5 out of 5 in the Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of An Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:33.6
occ:1.00
 O A:HOH764 2.4 54.1 1.0
O A:HOH749 2.4 44.5 1.0
OE2 A:GLU196 2.4 30.1 1.0
OE1 A:GLU196 2.8 30.8 1.0
CD A:GLU196 2.9 30.1 1.0
O A:HOH722 4.1 28.1 1.0
O A:HOH739 4.3 42.4 1.0
O A:HOH544 4.4 39.5 1.0
CG A:GLU196 4.5 28.0 1.0
OG1 A:THR195 4.7 22.3 1.0
O A:THR195 4.7 22.4 1.0
O A:HOH789 5.0 34.9 1.0

Reference:

F.J.Contesini, M.V.Liberato, M.V.Rubio, F.Calzado, M.P.Zubieta, D.M.Riano-Pachon, F.M.Squina, F.Bracht, M.S.Skaf, A.R.Damasio. Structural and Functional Characterization of A Highly Secreted Alpha-L-Arabinofuranosidase (GH62) From Aspergillus Nidulans Grown on Sugarcane Bagasse. Biochim. Biophys. Acta V.1865 1758 2017.
ISSN: ISSN 0006-3002
PubMed: 28890404
DOI: 10.1016/J.BBAPAP.2017.09.001
Page generated: Sat Dec 12 05:45:47 2020

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