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Calcium in PDB 3ilf: Crystal Structure of Porphyranase A (Pora) in Complex with Neo- Porphyrotetraose

Protein crystallography data

The structure of Crystal Structure of Porphyranase A (Pora) in Complex with Neo- Porphyrotetraose, PDB code: 3ilf was solved by J.H.Hehemann, G.Correc, T.Barbeyron, W.Helbert, G.Michel, M.Czjzek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.34 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.090, 68.378, 71.268, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20.5

Other elements in 3ilf:

The structure of Crystal Structure of Porphyranase A (Pora) in Complex with Neo- Porphyrotetraose also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Porphyranase A (Pora) in Complex with Neo- Porphyrotetraose (pdb code 3ilf). 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 Porphyranase A (Pora) in Complex with Neo- Porphyrotetraose, PDB code: 3ilf:

Calcium binding site 1 out of 1 in 3ilf

Go back to Calcium Binding Sites List in 3ilf
Calcium binding site 1 out of 1 in the Crystal Structure of Porphyranase A (Pora) in Complex with Neo- Porphyrotetraose


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 Porphyranase A (Pora) in Complex with Neo- Porphyrotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca278

b:8.1
occ:1.00
O A:GLU38 2.3 9.1 1.0
O A:GLY74 2.3 7.9 1.0
OD1 A:ASP265 2.4 12.7 1.0
O A:ASP265 2.4 6.8 1.0
O A:HOH372 2.4 9.7 1.0
O A:HOH356 2.5 9.6 1.0
OD1 A:ASP40 2.5 14.3 1.0
C A:ASP265 3.4 5.8 1.0
C A:GLY74 3.4 8.9 1.0
CG A:ASP265 3.5 9.5 1.0
CG A:ASP40 3.5 17.0 1.0
C A:GLU38 3.5 7.3 1.0
CA A:ASP265 3.8 5.9 1.0
OD2 A:ASP40 3.9 17.9 1.0
CA A:GLY74 4.0 8.6 1.0
CB A:ASP265 4.3 5.0 1.0
CA A:GLU38 4.3 9.1 1.0
O A:HOH407 4.3 24.0 1.0
O A:HOH463 4.4 20.2 1.0
C A:PHE39 4.4 11.7 1.0
O A:PHE39 4.4 10.8 1.0
OD2 A:ASP265 4.5 14.1 1.0
N A:PHE75 4.5 8.7 1.0
N A:TRP266 4.6 5.0 1.0
N A:PHE39 4.6 7.3 1.0
CB A:GLU38 4.6 8.3 1.0
CB A:PHE39 4.6 10.0 1.0
N A:ASP40 4.7 14.3 1.0
CB A:TRP266 4.7 4.3 1.0
OE1 A:GLU38 4.7 10.8 1.0
CA A:PHE39 4.8 9.5 1.0
CB A:ASP40 4.8 15.8 1.0
O A:HOH558 4.8 18.2 1.0
CA A:PHE75 4.8 8.9 1.0
CD1 A:TRP266 4.8 8.5 1.0
CA A:ASP40 4.9 16.3 1.0
CA A:TRP266 4.9 5.7 1.0
O A:HOH373 4.9 41.7 1.0

Reference:

J.H.Hehemann, G.Correc, T.Barbeyron, W.Helbert, M.Czjzek, G.Michel. Transfer of Carbohydrate-Active Enzymes From Marine Bacteria to Japanese Gut Microbiota. Nature V. 464 908 2010.
ISSN: ISSN 0028-0836
PubMed: 20376150
DOI: 10.1038/NATURE08937
Page generated: Sat Dec 12 04:15:39 2020

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