Calcium in PDB 2yfs: Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose

All present enzymatic activity of Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose:
2.4.1.9;

The structure of Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose, PDB code: 2yfs was solved by T.Pijning, M.A.Anwar, H.Leemhuis, S.Kralj, L.Dijkhuizen, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.45 / 2.60
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	171.951, 171.951, 116.503, 90.00, 90.00, 90.00
R / Rfree (%)	17.971 / 22.397

The binding sites of Calcium atom in the Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose (pdb code 2yfs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose, PDB code: 2yfs:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose


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 Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1711 b:78.6 occ:1.00 OD1 A:ASN489 2.4 46.2 1.0 O A:TRP487 2.4 50.5 1.0 OE1 A:GLN450 2.5 62.7 1.0 OD1 A:ASP419 2.5 70.9 1.0 OD1 A:ASP521 2.9 54.1 1.0 OD2 A:ASP521 3.1 56.3 1.0 CG A:ASP521 3.4 51.5 1.0 CG A:ASN489 3.4 45.5 1.0 CG A:ASP419 3.5 69.6 1.0 CD A:GLN450 3.5 62.4 1.0 C A:TRP487 3.6 50.5 1.0 OD2 A:ASP419 3.7 69.2 1.0 N A:ASN489 3.9 44.6 1.0 ND2 A:ASN489 4.2 47.2 1.0 NE2 A:GLN450 4.2 64.1 1.0 O A:ASN420 4.3 59.0 1.0 CA A:TRP487 4.4 51.9 1.0 OG A:SER443 4.4 39.5 1.0 CB A:ASN489 4.5 44.1 1.0 C A:SER488 4.5 46.3 1.0 CG A:GLN450 4.5 60.3 1.0 N A:SER488 4.6 48.7 1.0 CB A:GLN450 4.6 57.8 1.0 CA A:ASN489 4.6 43.5 1.0 CA A:SER488 4.7 47.3 1.0 N A:ASN420 4.7 64.8 1.0 CB A:TRP487 4.7 52.9 1.0 CB A:ASP419 4.9 69.8 1.0 CB A:ASP521 4.9 46.8 1.0 CB A:SER443 4.9 37.4 1.0 OE1 A:GLN406 5.0 44.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose


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 Inulosucrase From Lactobacillus Johnsonii NCC533 in Complex with Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1712 b:35.9 occ:1.00 OD1 A:ASN317 2.1 39.8 1.0 O A:HOH2029 2.4 33.0 1.0 O A:HOH2092 2.4 27.1 1.0 OG A:SER667 2.4 42.4 1.0 OD2 A:ASP660 2.4 33.8 1.0 O A:ILE662 2.4 37.9 1.0 OD1 A:ASP660 2.4 34.6 1.0 CG A:ASP660 2.7 33.7 1.0 CG A:ASN317 3.3 36.5 1.0 C A:ILE662 3.5 37.8 1.0 CB A:SER667 3.7 43.6 1.0 O A:GLY315 3.9 37.1 1.0 ND2 A:ASN317 4.0 35.9 1.0 CB A:ILE662 4.2 36.8 1.0 CA A:ILE662 4.2 36.6 1.0 CB A:ASP660 4.2 33.3 1.0 OD1 A:ASP664 4.3 46.7 1.0 N A:ILE662 4.3 35.3 1.0 CA A:SER667 4.4 44.0 1.0 OD2 A:ASP664 4.5 47.6 1.0 CB A:ASN317 4.5 35.1 1.0 O A:HOH2089 4.5 37.6 1.0 N A:TRP663 4.5 39.2 1.0 CG A:ASP664 4.6 46.3 1.0 CG2 A:ILE662 4.6 36.9 1.0 O A:ASP316 4.7 36.1 1.0 C A:GLY315 4.7 36.9 1.0 CA A:ASN317 4.8 34.8 1.0 CA A:TRP663 4.8 41.1 1.0 N A:ASP664 4.8 44.4 1.0 C A:ASP316 5.0 36.0 1.0

T.Pijning, M.A.Anwar, M.Boger, J.M.Dobruchowska, H.Leemhuis, S.Kralj, L.Dijkhuizen, B.W.Dijkstra. Crystal Structure of Inulosucrase From Lactobacillus: Insights Into the Substrate Specificity and Product Specificity of GH68 Fructansucrases. J.Mol.Biol. V. 412 80 2011.
ISSN: ISSN 0022-2836
PubMed: 21801732
DOI: 10.1016/J.JMB.2011.07.031