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Calcium in PDB 2bwr: Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution

Protein crystallography data

The structure of Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution, PDB code: 2bwr was solved by G.Cioci, E.P.Mitchell, V.Chazalet, C.Gautier, S.Oscarson, H.Debray, S.Perez, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.13 / 1.5
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.828, 142.219, 52.161, 90.00, 92.10, 90.00
R / Rfree (%) 15.8 / 18.2

Other elements in 2bwr:

The structure of Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution (pdb code 2bwr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution, PDB code: 2bwr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2bwr

Go back to Calcium Binding Sites List in 2bwr
Calcium binding site 1 out of 4 in the Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution


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 Psathyrella Velutina Lectin at 1.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:6.6
occ:1.00
O A:CYS349 2.3 7.7 1.0
O A:HOH2400 2.4 8.0 1.0
OG1 A:THR345 2.4 6.7 1.0
OD2 A:ASP351 2.4 5.4 1.0
OD1 A:ASP347 2.4 5.9 1.0
OD1 A:ASP343 2.4 5.3 1.0
OD1 A:ASP351 2.7 4.7 1.0
CG A:ASP351 2.9 4.9 1.0
CG A:ASP347 3.5 8.7 1.0
C A:CYS349 3.5 6.6 1.0
CG A:ASP343 3.5 7.3 1.0
CB A:THR345 3.6 7.8 1.0
CG2 A:THR345 3.9 7.8 1.0
OD2 A:ASP347 3.9 9.3 1.0
N A:THR345 4.0 5.7 1.0
O A:HOH2397 4.1 11.8 1.0
N A:CYS349 4.1 6.2 1.0
CA A:THR345 4.2 7.0 1.0
CA A:CYS349 4.3 7.2 1.0
OD2 A:ASP343 4.3 6.3 1.0
N A:LEU344 4.3 5.5 1.0
CB A:ASP351 4.4 5.0 1.0
C A:ALA350 4.4 4.2 1.0
N A:ASP351 4.4 4.2 1.0
CA A:ASP343 4.4 4.7 1.0
CB A:CYS349 4.5 7.4 1.0
N A:ALA350 4.5 4.8 1.0
CB A:ASN365 4.5 5.2 1.0
CB A:ASP343 4.5 4.9 1.0
N A:ASP347 4.5 7.3 1.0
CA A:ALA350 4.5 4.2 1.0
N A:GLY346 4.6 6.8 1.0
C A:THR345 4.6 6.8 1.0
CB A:ASP347 4.7 9.0 1.0
O A:ASN365 4.9 8.8 1.0
C A:ASP343 4.9 4.6 1.0
N A:GLY348 4.9 6.5 1.0
CA A:ASP351 4.9 4.0 1.0
O A:ALA350 4.9 5.8 1.0
CA A:ASP347 5.0 8.0 1.0

Calcium binding site 2 out of 4 in 2bwr

Go back to Calcium Binding Sites List in 2bwr
Calcium binding site 2 out of 4 in the Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution


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 Psathyrella Velutina Lectin at 1.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:11.6
occ:0.50
O A:LEU183 2.5 10.6 1.0
OD2 A:ASP185 2.5 8.7 1.0
OD1 A:ASP177 2.5 8.6 1.0
OD1 A:ASP181 2.5 14.6 1.0
OG1 A:THR179 2.7 15.1 1.0
O A:HOH2250 2.9 20.0 1.0
OD1 A:ASP185 3.1 9.6 1.0
CG A:ASP185 3.1 10.1 1.0
CG A:ASP177 3.4 9.4 1.0
CG A:ASP181 3.5 19.3 1.0
C A:LEU183 3.5 8.8 1.0
OD2 A:ASP181 3.8 19.2 1.0
CB A:THR179 3.8 13.8 1.0
N A:THR179 3.9 11.1 1.0
N A:LEU183 3.9 10.3 1.0
CB A:LEU183 4.0 10.0 1.0
CA A:ASP177 4.0 7.5 1.0
CA A:LEU183 4.0 9.8 1.0
CB A:ASP177 4.1 8.0 1.0
N A:VAL178 4.2 9.0 1.0
CG2 A:THR179 4.2 14.9 1.0
OD2 A:ASP177 4.2 10.9 1.0
CA A:THR179 4.3 13.4 1.0
N A:GLY180 4.4 14.8 1.0
N A:ASP181 4.4 16.1 1.0
C A:ASP177 4.5 9.3 1.0
CB A:ASP185 4.5 8.4 1.0
N A:ASP185 4.6 6.8 1.0
N A:LEU184 4.6 8.6 1.0
N A:GLY182 4.7 13.6 1.0
CB A:ASP181 4.8 17.3 1.0
C A:THR179 4.8 14.3 1.0
C A:VAL178 4.9 11.0 1.0
C A:LEU184 4.9 7.7 1.0
CA A:ASP181 5.0 16.6 1.0
CA A:LEU184 5.0 8.1 1.0
C A:GLY182 5.0 13.4 1.0

Calcium binding site 3 out of 4 in 2bwr

Go back to Calcium Binding Sites List in 2bwr
Calcium binding site 3 out of 4 in the Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution


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 Psathyrella Velutina Lectin at 1.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:7.1
occ:1.00
O B:CYS349 2.2 8.4 1.0
O B:HOH2386 2.4 11.2 1.0
OD2 B:ASP351 2.4 5.7 1.0
OD1 B:ASP347 2.4 7.7 1.0
OD1 B:ASP343 2.4 6.4 1.0
OG1 B:THR345 2.4 6.7 1.0
OD1 B:ASP351 2.7 6.6 1.0
CG B:ASP351 2.9 6.3 1.0
CG B:ASP347 3.4 8.2 1.0
C B:CYS349 3.4 8.8 1.0
CG B:ASP343 3.5 7.0 1.0
CB B:THR345 3.6 7.7 1.0
OD2 B:ASP347 3.9 9.9 1.0
CG2 B:THR345 3.9 9.2 1.0
N B:THR345 4.0 6.7 1.0
N B:CYS349 4.1 7.9 1.0
CA B:CYS349 4.2 8.7 1.0
O B:HOH2382 4.3 10.2 1.0
CA B:THR345 4.3 6.2 1.0
OD2 B:ASP343 4.3 7.8 1.0
CB B:ASP351 4.3 5.0 1.0
N B:LEU344 4.4 4.8 1.0
CB B:CYS349 4.4 10.2 1.0
CA B:ASP343 4.4 5.2 1.0
N B:ASP351 4.4 6.3 1.0
N B:ALA350 4.4 7.0 1.0
C B:ALA350 4.5 5.5 1.0
N B:ASP347 4.5 8.1 1.0
CB B:ASN365 4.5 6.6 1.0
CB B:ASP343 4.5 6.0 1.0
CA B:ALA350 4.6 6.7 1.0
N B:GLY346 4.6 6.5 1.0
CB B:ASP347 4.7 7.6 1.0
C B:THR345 4.7 6.7 1.0
O B:ALA350 4.9 6.7 1.0
CA B:ASP351 4.9 4.6 1.0
O B:ASN365 4.9 9.6 1.0
C B:ASP343 4.9 4.5 1.0
N B:GLY348 5.0 7.3 1.0

Calcium binding site 4 out of 4 in 2bwr

Go back to Calcium Binding Sites List in 2bwr
Calcium binding site 4 out of 4 in the Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Psathyrella Velutina Lectin at 1.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:12.7
occ:0.50
OD2 B:ASP185 2.3 13.6 1.0
OD1 B:ASP177 2.4 13.9 1.0
O B:LEU183 2.4 14.5 1.0
OD1 B:ASP181 2.4 20.4 1.0
OG1 B:THR179 2.6 17.9 1.0
OD1 B:ASP185 2.9 13.7 1.0
CG B:ASP185 3.0 11.8 1.0
O B:HOH2243 3.0 27.1 1.0
CG B:ASP177 3.3 13.2 1.0
CG B:ASP181 3.4 21.1 1.0
C B:LEU183 3.5 13.8 1.0
OD2 B:ASP181 3.8 22.1 1.0
CB B:THR179 3.8 17.2 1.0
N B:THR179 3.8 16.1 1.0
CA B:ASP177 3.9 11.4 1.0
N B:LEU183 3.9 15.4 1.0
CB B:ASP177 4.0 11.0 1.0
CA B:LEU183 4.1 14.2 1.0
N B:VAL178 4.1 12.7 1.0
OD2 B:ASP177 4.1 15.6 1.0
CB B:LEU183 4.1 14.1 1.0
CG2 B:THR179 4.2 18.7 1.0
N B:ASP181 4.2 18.4 1.0
CA B:THR179 4.3 16.9 1.0
N B:GLY180 4.3 17.1 1.0
C B:ASP177 4.4 12.4 1.0
CB B:ASP185 4.4 10.7 1.0
N B:ASP185 4.5 11.4 1.0
N B:LEU184 4.6 12.6 1.0
CB B:ASP181 4.6 19.2 1.0
N B:GLY182 4.6 17.1 1.0
C B:THR179 4.7 17.6 1.0
C B:LEU184 4.8 10.9 1.0
CA B:ASP181 4.8 18.9 1.0
CA B:LEU184 4.9 11.6 1.0
C B:VAL178 4.9 15.1 1.0
C B:ASP181 4.9 18.2 1.0

Reference:

G.Cioci, E.P.Mitchell, V.Chazalet, H.Debray, S.Oscarson, M.Lahmann, C.Gautier, C.Breton, S.Perez, A.Imberty. Beta-Propeller Crystal Structure of Psathyrella Velutina Lectin: An Integrin-Like Fungal Protein Interacting with Monosaccharides and Calcium. J.Mol.Biol. V. 357 1575 2006.
ISSN: ISSN 0022-2836
PubMed: 16497330
DOI: 10.1016/J.JMB.2006.01.066
Page generated: Sat Dec 12 03:33:04 2020

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