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Calcium in PDB 2yfr: Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533

Enzymatic activity of Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533

All present enzymatic activity of Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533:
2.4.1.9;

Protein crystallography data

The structure of Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533, PDB code: 2yfr 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) 121.63 / 1.75
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 172.007, 172.007, 114.581, 90.00, 90.00, 90.00
R / Rfree (%) 15.095 / 16.958

Other elements in 2yfr:

The structure of Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533 (pdb code 2yfr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533, PDB code: 2yfr:

Calcium binding site 1 out of 1 in 2yfr

Go back to Calcium Binding Sites List in 2yfr
Calcium binding site 1 out of 1 in the Crystal Structure of Inulosucrase From Lactobacillus Johnsonii NCC533


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1709

b:19.2
occ:0.50
 O A:TRP487 2.1 25.6 1.0
OE1 A:GLN450 2.2 33.1 1.0
OD1 A:ASP419 2.2 34.2 1.0
OD1 A:ASN489 2.4 29.1 1.0
OD1 A:ASP521 2.6 21.7 0.6
O A:HOH2276 2.7 39.5 1.0
OD2 A:ASP521 2.8 26.6 0.6
CG A:ASP521 3.0 24.1 0.6
C A:TRP487 3.3 25.0 1.0
CG A:ASP419 3.4 37.5 1.0
CD A:GLN450 3.4 30.5 1.0
CG A:ASN489 3.5 24.3 1.0
OD2 A:ASP419 3.9 37.3 1.0
N A:ASN489 3.9 20.7 1.0
NE2 A:GLN450 4.1 31.0 1.0
CA A:TRP487 4.2 26.1 1.0
ND2 A:ASN489 4.2 29.8 1.0
N A:SER488 4.3 22.8 1.0
O A:ASN420 4.3 32.4 1.0
C A:SER488 4.3 21.7 1.0
CA A:SER488 4.4 22.3 1.0
N A:ASN420 4.4 34.9 1.0
CB A:ASP521 4.4 24.0 0.4
CB A:GLN450 4.4 25.1 1.0
CB A:TRP487 4.5 27.5 1.0
CB A:ASN489 4.5 22.9 1.0
CG A:GLN450 4.5 27.5 1.0
CB A:ASP521 4.6 23.9 0.6
CA A:ASN489 4.6 20.9 1.0
CB A:ASP419 4.6 37.5 1.0
OG A:SER443 4.8 25.9 1.0
CA A:ASP419 4.8 37.0 1.0
O A:HOH2288 4.9 29.4 1.0

Reference:

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
Page generated: Fri Jul 12 19:28:53 2024

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