Calcium in PDB 3ipv: Crystal Structure of Spatholobus Parviflorus Seed Lectin

The structure of Crystal Structure of Spatholobus Parviflorus Seed Lectin, PDB code: 3ipv was solved by K.Geethanandan, S.R.Bharath, J.Abhilash, C.Sadasivan, M.Haridas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.82 / 2.04
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.998, 60.792, 78.179, 101.32, 91.38, 104.32
R / Rfree (%)	19.9 / 26.4

The structure of Crystal Structure of Spatholobus Parviflorus Seed Lectin also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Spatholobus Parviflorus Seed Lectin (pdb code 3ipv). 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 Spatholobus Parviflorus Seed Lectin, PDB code: 3ipv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Spatholobus Parviflorus Seed Lectin


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 Spatholobus Parviflorus Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca252 b:22.3 occ:1.00 OD2 A:ASP137 2.3 16.2 1.0 O A:HOH321 2.3 10.2 1.0 OD1 A:ASP128 2.4 14.6 1.0 O A:HOH314 2.4 8.9 1.0 O A:TYR130 2.4 13.0 1.0 OD1 A:ASN132 2.4 11.2 1.0 OD2 A:ASP128 2.6 7.3 1.0 CG A:ASP128 2.8 11.7 1.0 CG A:ASP137 3.3 14.2 1.0 CG A:ASN132 3.5 15.2 1.0 C A:TYR130 3.6 14.3 1.0 OD1 A:ASP137 3.8 12.8 1.0 N A:ASN132 4.0 14.2 1.0 CB A:ASN132 4.1 14.4 1.0 MN A:MN253 4.2 24.6 1.0 O A:HOH332 4.2 8.0 1.0 CB A:ASP128 4.3 11.5 1.0 N A:TYR130 4.3 14.3 1.0 CA A:TYR130 4.4 14.0 1.0 O A:GLY106 4.6 11.3 1.0 CB A:ASP137 4.6 13.8 1.0 O A:ASP88 4.6 14.1 1.0 N A:GLU131 4.6 13.4 1.0 ND2 A:ASN132 4.7 14.1 1.0 OD1 A:ASP88 4.7 13.6 1.0 CA A:ASN132 4.7 14.5 1.0 C A:GLU131 4.7 14.2 1.0 CA A:GLU131 4.7 14.2 1.0 CB A:TYR130 4.7 13.5 1.0 CA A:GLY106 4.7 11.7 1.0 CD1 A:TYR130 4.8 10.6 1.0 CE1 A:HIS142 4.9 12.5 1.0 CD2 A:PHE135 4.9 14.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Spatholobus Parviflorus Seed Lectin


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 Spatholobus Parviflorus Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca240 b:25.5 occ:1.00 O B:HOH295 2.3 13.9 1.0 O B:TYR130 2.3 13.4 1.0 OD1 B:ASN132 2.4 7.3 1.0 OD1 B:ASP128 2.5 13.1 1.0 OD2 B:ASP137 2.6 12.8 1.0 OD2 B:ASP128 2.7 12.8 1.0 O B:HOH527 2.7 11.0 1.0 CG B:ASP128 2.9 13.7 1.0 C B:TYR130 3.5 14.7 1.0 CG B:ASN132 3.6 13.8 1.0 CG B:ASP137 3.7 14.5 1.0 N B:ASN132 4.1 14.0 1.0 OD1 B:ASP137 4.1 13.2 1.0 N B:TYR130 4.2 16.0 1.0 CA B:TYR130 4.3 14.3 1.0 CB B:ASN132 4.3 13.7 1.0 MN B:MN241 4.3 29.8 1.0 CB B:TYR130 4.4 13.4 1.0 CB B:ASP128 4.4 13.6 1.0 CD2 B:TYR130 4.4 15.3 1.0 O B:ASP88 4.5 13.7 1.0 O B:HOH291 4.6 12.2 1.0 N B:GLU131 4.6 14.1 1.0 ND2 B:ASN132 4.6 6.2 1.0 OD1 B:ASP88 4.6 9.3 1.0 O B:GLY106 4.6 11.2 1.0 CA B:GLU131 4.7 14.6 1.0 CA B:GLY106 4.7 11.4 1.0 C B:GLU131 4.7 14.9 1.0 CA B:ASN132 4.8 14.6 1.0 CB B:ASP137 4.9 14.7 1.0 CG B:TYR130 4.9 14.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Spatholobus Parviflorus Seed Lectin


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 Spatholobus Parviflorus Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca252 b:20.3 occ:1.00 OD2 C:ASP137 2.2 14.0 1.0 O C:TYR130 2.4 15.7 1.0 OD1 C:ASN132 2.4 10.1 1.0 OD1 C:ASP128 2.4 8.8 1.0 O C:HOH310 2.4 4.8 1.0 O C:HOH316 2.4 13.7 1.0 OD2 C:ASP128 2.5 6.2 1.0 CG C:ASP128 2.8 11.9 1.0 CG C:ASP137 3.3 13.2 1.0 CG C:ASN132 3.5 12.0 1.0 C C:TYR130 3.6 15.5 1.0 OD1 C:ASP137 3.8 11.5 1.0 N C:ASN132 4.0 15.3 1.0 O C:HOH266 4.1 18.0 1.0 MN C:MN253 4.1 28.2 1.0 CB C:ASN132 4.2 13.4 1.0 CB C:ASP128 4.3 10.9 1.0 CA C:TYR130 4.5 14.7 1.0 N C:TYR130 4.5 15.1 1.0 CB C:ASP137 4.5 11.4 1.0 N C:GLU131 4.6 14.9 1.0 ND2 C:ASN132 4.6 8.8 1.0 CA C:GLU131 4.6 15.6 1.0 O C:GLY106 4.6 10.0 1.0 OD1 C:ASP88 4.6 12.0 1.0 C C:GLU131 4.7 15.7 1.0 CB C:TYR130 4.7 14.7 1.0 CA C:GLY106 4.7 11.2 1.0 O C:ASP88 4.7 15.0 1.0 CA C:ASN132 4.7 14.1 1.0 CE1 C:HIS142 4.7 12.8 1.0 CD2 C:TYR130 4.8 15.4 1.0 CD2 C:PHE135 4.9 14.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Spatholobus Parviflorus Seed Lectin


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 Spatholobus Parviflorus Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca240 b:25.7 occ:1.00 O D:HOH321 2.3 11.6 1.0 OD1 D:ASN132 2.3 13.7 1.0 OD2 D:ASP137 2.3 18.2 1.0 O D:HOH307 2.4 10.8 1.0 O D:TYR130 2.5 10.5 1.0 OD2 D:ASP128 2.5 8.5 1.0 OD1 D:ASP128 2.5 13.0 1.0 CG D:ASP128 2.9 9.1 1.0 CG D:ASP137 3.4 16.4 1.0 CG D:ASN132 3.5 14.1 1.0 C D:TYR130 3.7 13.0 1.0 OD1 D:ASP137 3.8 13.8 1.0 N D:ASN132 3.9 15.4 1.0 MN D:MN241 4.2 29.2 1.0 CB D:ASN132 4.2 14.9 1.0 O D:HOH287 4.2 13.4 1.0 CB D:ASP128 4.4 10.7 1.0 N D:TYR130 4.4 13.2 1.0 O D:GLY106 4.4 10.0 1.0 CA D:TYR130 4.5 12.9 1.0 CA D:GLY106 4.5 12.5 1.0 ND2 D:ASN132 4.5 8.9 1.0 CB D:TYR130 4.6 13.1 1.0 C D:GLU131 4.6 15.5 1.0 CB D:ASP137 4.6 16.0 1.0 N D:GLU131 4.7 13.4 1.0 CA D:ASN132 4.7 15.7 1.0 CA D:GLU131 4.7 14.4 1.0 CD2 D:TYR130 4.7 14.7 1.0 OD1 D:ASP88 4.8 13.6 1.0 O D:ASP88 4.8 11.3 1.0 CD2 D:PHE135 4.8 15.1 1.0 CE1 D:HIS142 4.9 10.9 1.0 C D:GLY106 5.0 13.1 1.0

K.Geethanandan, J.Abhilash, S.R.Bharath, C.Sadasivan, M.Haridas. X-Ray Structure of A Galactose-Specific Lectin From Spatholobous Parviflorous Int.J.Biol.Macromol. V. 49 992 2011.
ISSN: ISSN 0141-8130
PubMed: 21889532
DOI: 10.1016/J.IJBIOMAC.2011.08.021