Atomistry » Calcium » PDB 5tua-5ue5 » 5ubj
Atomistry »
  Calcium »
    PDB 5tua-5ue5 »
      5ubj »

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

Go back to Calcium Binding Sites List in 5ubj
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

Go back to Calcium Binding Sites List in 5ubj
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

Go back to Calcium Binding Sites List in 5ubj
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

Go back to Calcium Binding Sites List in 5ubj
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: Mon Jul 15 11:28:28 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy