Calcium in PDB 4kc8: Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris

All present enzymatic activity of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris:
3.2.1.99;

The structure of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris, PDB code: 4kc8 was solved by A.F.Z.Nascimento, C.C.Polo, C.R.Santos, M.C.M.F.Costa, A.N.Mesa, R.A.Prade, R.Ruller, F.M.Squina, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.38 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.673, 86.770, 194.372, 90.00, 90.07, 90.00
R / Rfree (%)	15.3 / 19.7

The binding sites of Calcium atom in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris (pdb code 4kc8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris, PDB code: 4kc8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:53.8 occ:1.00 O A:PRO171 2.6 25.8 1.0 O A:ALA96 2.7 30.8 1.0 N A:PRO171 3.2 25.2 1.0 C A:ASP170 3.3 25.8 1.0 CB A:ALA96 3.3 31.1 1.0 O A:HOH840 3.3 24.0 1.0 C A:PRO171 3.5 25.4 1.0 CA A:ASP170 3.5 28.7 1.0 CD A:PRO171 3.5 25.3 1.0 C A:ALA96 3.6 28.8 1.0 O A:ASP170 3.9 26.0 1.0 CA A:PRO171 3.9 22.5 1.0 CA A:ALA96 3.9 27.8 1.0 CG A:PRO171 4.0 23.7 1.0 NE2 A:HIS314 4.4 29.4 1.0 CB A:ASP170 4.4 25.1 1.0 N A:GLY172 4.5 26.6 1.0 CB A:PRO171 4.5 23.1 1.0 N A:ASP170 4.5 27.9 1.0 OG A:SER34 4.6 29.3 1.0 N A:PRO97 4.8 25.1 1.0 OD1 A:ASP170 4.8 26.4 1.0 C A:PRO97 4.9 29.6 1.0 CE1 A:HIS314 4.9 27.1 1.0 N A:GLN98 4.9 27.0 1.0 CB A:GLN98 4.9 30.8 1.0 CG A:ASP170 4.9 27.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:41.7 occ:1.00 O B:HOH906 2.2 20.5 1.0 O B:HOH910 2.3 24.0 1.0 O B:HOH907 2.3 27.9 1.0 O B:HOH908 2.6 23.7 1.0 O B:HOH645 2.7 22.4 1.0 NE2 B:HIS314 3.0 21.6 1.0 O B:PRO171 3.7 15.9 1.0 CD2 B:HIS314 3.8 17.2 1.0 CE1 B:HIS314 3.9 16.5 1.0 OG B:SER34 4.0 18.8 1.0 O B:PRO225 4.1 11.5 1.0 CD1 B:TYR226 4.4 11.9 1.0 C B:PRO171 4.5 12.7 1.0 O B:ASN315 4.6 13.0 1.0 O B:ASP170 4.6 10.6 1.0 O B:HOH901 4.8 24.1 1.0 C B:ASP170 4.8 12.6 1.0 C B:GLY224 4.8 9.6 1.0 O B:GLY224 4.9 12.5 1.0 CA B:GLY172 4.9 14.3 1.0 CA B:GLY224 4.9 10.7 1.0 CG B:HIS314 5.0 13.7 1.0 C B:PRO225 5.0 13.4 1.0 ND1 B:HIS314 5.0 15.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From Thermotoga Petrophila Rku-1 in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:51.7 occ:1.00 O C:HOH706 2.4 30.3 1.0 O C:HOH705 2.7 31.2 1.0 NE2 C:HIS314 2.8 33.3 1.0 CD2 C:HIS314 3.5 33.3 1.0 OG C:SER34 3.8 31.9 1.0 CE1 C:HIS314 3.8 35.4 1.0 O C:PRO171 4.0 35.8 1.0 O C:PRO225 4.3 29.2 1.0 CD2 C:TYR226 4.4 32.4 1.0 O C:ASN315 4.6 30.9 1.0 O C:GLY224 4.6 29.1 1.0 CG C:HIS314 4.6 28.4 1.0 C C:GLY224 4.8 27.5 1.0 ND1 C:HIS314 4.8 33.3 1.0 C C:PRO171 4.8 33.3 1.0 O C:ASP170 4.8 29.4 1.0 CA C:GLY224 4.8 27.7 1.0 CB C:ALA96 4.9 31.0 1.0 C C:ASP170 4.9 28.0 1.0

C.R.Santos, C.C.Polo, M.C.Costa, A.F.Nascimento, A.N.Meza, J.Cota, Z.B.Hoffmam, R.V.Honorato, P.S.Oliveira, G.H.Goldman, H.J.Gilbert, R.A.Prade, R.Ruller, F.M.Squina, D.W.Wong, M.T.Murakami. Mechanistic Strategies For Catalysis Adopted By Evolutionary Distinct Family 43 Arabinanases. J.Biol.Chem. V. 289 7362 2014.
ISSN: ISSN 0021-9258
PubMed: 24469445
DOI: 10.1074/JBC.M113.537167