Calcium in PDB 3a0k: Crystal Structure of An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds

The structure of Crystal Structure of An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds, PDB code: 3a0k was solved by B.A.M.Rocha, P.Delatorre, E.S.Marinho, R.G.Benevides, T.R.Moura, L.A.G.Souza, K.S.Nascimento, A.H.Sampaio, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.12 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.034, 103.074, 122.334, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.5

The structure of Crystal Structure of An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds (pdb code 3a0k). 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 An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds, PDB code: 3a0k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds


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 An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:10.8 occ:1.00 O A:TYR12 2.3 11.2 1.0 O A:HOH503 2.3 7.0 1.0 O A:HOH259 2.3 8.3 1.0 OD1 A:ASN14 2.3 12.4 1.0 OD2 A:ASP19 2.3 11.3 1.0 OD1 A:ASP10 2.4 7.7 1.0 OD2 A:ASP10 2.4 8.8 1.0 CG A:ASP10 2.7 11.3 1.0 CG A:ASP19 3.4 11.3 1.0 CG A:ASN14 3.5 10.9 1.0 C A:TYR12 3.5 10.6 1.0 N A:ASN14 3.8 12.5 1.0 OD1 A:ASP19 3.8 10.1 1.0 CB A:ASN14 4.1 12.1 1.0 MN A:MN238 4.1 11.9 1.0 CB A:ASP10 4.2 9.1 1.0 CA A:TYR12 4.3 9.4 1.0 N A:TYR12 4.3 9.6 1.0 CB A:ARG228 4.4 8.5 1.0 CA A:PRO13 4.4 13.0 1.0 O A:ASP208 4.5 9.2 1.0 N A:PRO13 4.5 12.7 1.0 CB A:TYR12 4.5 9.0 1.0 CE1 A:HIS24 4.5 10.2 1.0 C A:PRO13 4.5 13.8 1.0 ND2 A:ASN14 4.5 7.0 1.0 O A:HOH289 4.6 9.6 1.0 OD1 A:ASP208 4.6 9.6 1.0 CA A:ARG228 4.6 10.2 1.0 O A:ARG228 4.6 9.1 1.0 CA A:ASN14 4.6 11.6 1.0 CB A:ASP19 4.6 13.6 1.0 NE2 A:HIS24 4.8 9.4 1.0 CD2 A:TYR12 4.9 12.4 1.0 CA A:ASP10 4.9 8.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds


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 An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca239 b:15.0 occ:1.00 OD2 C:ASP19 2.2 15.7 1.0 O C:HOH536 2.3 15.6 1.0 O C:TYR12 2.3 19.1 1.0 O C:HOH256 2.3 14.2 1.0 OD1 C:ASP10 2.3 15.2 1.0 OD1 C:ASN14 2.4 14.4 1.0 OD2 C:ASP10 2.4 10.9 1.0 CG C:ASP10 2.7 9.2 1.0 CG C:ASP19 3.3 16.6 1.0 CG C:ASN14 3.5 18.0 1.0 C C:TYR12 3.5 17.2 1.0 OD1 C:ASP19 3.8 14.7 1.0 N C:ASN14 3.9 18.3 1.0 MN C:MN238 4.1 14.5 1.0 CB C:ASN14 4.1 18.2 1.0 CB C:ASP10 4.2 10.0 1.0 CA C:TYR12 4.3 17.3 1.0 N C:TYR12 4.3 15.6 1.0 CE1 C:HIS24 4.4 12.8 1.0 CA C:PRO13 4.4 19.0 1.0 C C:PRO13 4.5 19.6 1.0 N C:PRO13 4.5 18.4 1.0 O C:HOH537 4.5 12.5 1.0 CB C:TYR12 4.5 16.5 1.0 O C:ASP208 4.6 13.2 1.0 CB C:ARG228 4.6 16.9 1.0 CB C:ASP19 4.6 15.7 1.0 OD1 C:ASP208 4.6 16.4 1.0 O C:ARG228 4.6 16.5 1.0 ND2 C:ASN14 4.6 17.2 1.0 CA C:ASN14 4.7 18.9 1.0 CA C:ARG228 4.7 16.5 1.0 NE2 C:HIS24 4.8 13.1 1.0 CD1 C:TYR12 4.9 19.8 1.0 CA C:ASP10 4.9 10.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds


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 An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca239 b:13.1 occ:1.00 O E:TYR12 2.2 11.7 1.0 OD1 E:ASN14 2.3 14.2 1.0 O E:HOH269 2.3 8.6 1.0 OD2 E:ASP19 2.3 12.1 1.0 O E:HOH304 2.4 12.9 1.0 OD1 E:ASP10 2.4 11.4 1.0 OD2 E:ASP10 2.5 11.8 1.0 CG E:ASP10 2.8 9.2 1.0 CG E:ASP19 3.4 14.1 1.0 C E:TYR12 3.4 12.2 1.0 CG E:ASN14 3.4 14.6 1.0 OD1 E:ASP19 3.8 8.4 1.0 N E:ASN14 3.8 11.5 1.0 CB E:ASN14 4.0 14.0 1.0 MN E:MN238 4.1 11.7 1.0 CA E:TYR12 4.2 11.1 1.0 N E:TYR12 4.3 10.6 1.0 CB E:ASP10 4.3 12.5 1.0 N E:PRO13 4.4 12.4 1.0 CB E:TYR12 4.4 10.7 1.0 CA E:PRO13 4.4 12.5 1.0 C E:PRO13 4.5 13.1 1.0 CE1 E:HIS24 4.5 11.4 1.0 ND2 E:ASN14 4.5 12.8 1.0 O E:ASP208 4.5 9.9 1.0 O E:HOH545 4.5 11.4 1.0 CB E:ARG228 4.5 12.6 1.0 CA E:ASN14 4.6 13.5 1.0 CB E:ASP19 4.6 14.9 1.0 CA E:ARG228 4.6 10.5 1.0 OD1 E:ASP208 4.6 12.3 1.0 O E:ARG228 4.7 9.4 1.0 CD2 E:TYR12 4.7 12.5 1.0 NE2 E:HIS24 4.8 13.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds


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 An Antiflamatory Legume Lectin From Cymbosema Roseum Seeds within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca239 b:10.5 occ:1.00 O G:HOH538 2.3 9.0 1.0 OD1 G:ASP10 2.3 9.3 1.0 O G:TYR12 2.3 11.9 1.0 O G:HOH323 2.4 9.5 1.0 OD1 G:ASN14 2.4 10.9 1.0 OD2 G:ASP19 2.4 11.4 1.0 OD2 G:ASP10 2.4 9.3 1.0 CG G:ASP10 2.7 10.8 1.0 CG G:ASP19 3.4 12.3 1.0 C G:TYR12 3.5 10.7 1.0 CG G:ASN14 3.5 9.8 1.0 OD1 G:ASP19 3.9 10.1 1.0 N G:ASN14 3.9 11.4 1.0 CB G:ASN14 4.1 11.8 1.0 MN G:MN238 4.1 10.6 1.0 CB G:ASP10 4.2 9.3 1.0 N G:TYR12 4.2 8.7 1.0 CA G:TYR12 4.3 9.1 1.0 CE1 G:HIS24 4.4 7.9 1.0 CB G:TYR12 4.4 7.4 1.0 O G:ASP208 4.4 9.2 1.0 O G:HOH547 4.5 8.9 1.0 CB G:ARG228 4.5 7.7 1.0 N G:PRO13 4.5 11.8 1.0 CA G:PRO13 4.6 12.6 1.0 OD1 G:ASP208 4.6 10.8 1.0 C G:PRO13 4.6 12.9 1.0 CA G:ASN14 4.6 12.8 1.0 O G:ARG228 4.7 9.0 1.0 ND2 G:ASN14 4.7 9.4 1.0 CB G:ASP19 4.7 10.8 1.0 CA G:ARG228 4.7 7.9 1.0 NE2 G:HIS24 4.8 9.4 1.0 CD1 G:TYR12 4.9 12.0 1.0 CA G:ASP10 5.0 10.2 1.0

B.A.Rocha, P.Delatorre, T.M.Oliveira, R.G.Benevides, A.F.Pires, A.A.Sousa, L.A.Souza, S.A.Ana Maria, H.Debray, W.F.De Azevedo, A.H.Sampaio, B.S.Cavada. Structural Basis For Both Pro- and Anti-Inflammatory Response Induced By Mannose-Specific Legume Lectin From Cymbosema Roseum Biochimie 2011.
ISSN: ISSN 0300-9084
PubMed: 21277932
DOI: 10.1016/J.BIOCHI.2011.01.006