Calcium in PDB 1v00: Erythrina Cristagalli Lectin

The structure of Erythrina Cristagalli Lectin, PDB code: 1v00 was solved by K.Turton, R.Natesh, N.Thiyagarajan, J.A.Chaddock, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.12 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.900, 167.230, 55.130, 90.00, 97.08, 90.00
R / Rfree (%)	17.2 / 19.5

The structure of Erythrina Cristagalli Lectin also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Erythrina Cristagalli Lectin (pdb code 1v00). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Erythrina Cristagalli Lectin, PDB code: 1v00:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Erythrina Cristagalli Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Erythrina Cristagalli Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1242 b:10.4 occ:1.00 O A:PHE131 2.4 10.6 1.0 OD2 A:ASP136 2.4 12.3 1.0 OD1 A:ASN133 2.5 15.1 1.0 OD1 A:ASP129 2.5 11.4 1.0 O A:HOH2162 2.5 12.4 1.0 OD2 A:ASP129 2.5 9.5 1.0 O A:HOH2149 2.6 10.5 1.0 CG A:ASP129 2.9 12.6 1.0 CG A:ASP136 3.5 11.4 1.0 C A:PHE131 3.6 11.6 1.0 CG A:ASN133 3.6 14.5 1.0 OD1 A:ASP136 3.9 11.1 1.0 N A:ASN133 4.0 11.3 1.0 MN A:MN1241 4.2 10.2 1.0 CB A:ASN133 4.2 13.7 1.0 CB A:ASP129 4.4 9.7 1.0 N A:PHE131 4.4 11.0 1.0 O A:HOH2295 4.4 10.6 1.0 CA A:PHE131 4.4 11.6 1.0 NE1 A:TRP135 4.5 14.6 1.0 CB A:PHE131 4.6 11.7 1.0 O A:ASP89 4.6 10.2 1.0 O A:GLY107 4.6 12.4 1.0 N A:SER132 4.6 11.2 1.0 CA A:SER132 4.6 11.0 1.0 CB A:ASP136 4.7 12.1 1.0 CA A:GLY107 4.7 12.0 1.0 OD2 A:ASP89 4.7 10.7 1.0 ND2 A:ASN133 4.7 12.1 1.0 CA A:ASN133 4.8 12.5 1.0 C A:SER132 4.8 12.8 1.0 CD2 A:PHE131 4.8 11.9 1.0 CZ2 A:TRP135 4.9 14.7 1.0 CE2 A:TRP135 5.0 13.4 1.0 CE1 A:HIS142 5.0 13.2 1.0

Calcium binding site 2 out of 4 in the Erythrina Cristagalli Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Erythrina Cristagalli Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1242 b:18.6 occ:1.00 O B:PHE131 2.4 19.7 1.0 OD2 B:ASP136 2.5 17.9 1.0 OD1 B:ASP129 2.5 15.9 1.0 OD1 B:ASN133 2.6 21.7 1.0 O B:HOH2118 2.6 19.7 1.0 O B:HOH2105 2.6 15.6 1.0 OD2 B:ASP129 2.6 15.9 1.0 CG B:ASP129 2.9 15.7 1.0 CG B:ASP136 3.5 18.3 1.0 C B:PHE131 3.6 19.8 1.0 CG B:ASN133 3.7 20.6 1.0 OD1 B:ASP136 3.8 17.5 1.0 N B:ASN133 4.0 19.9 1.0 CB B:ASN133 4.2 21.2 1.0 MN B:MN1241 4.3 17.2 1.0 N B:PHE131 4.3 18.9 1.0 CA B:PHE131 4.3 20.0 1.0 O B:HOH2223 4.4 15.6 1.0 CB B:ASP129 4.4 14.7 1.0 CB B:PHE131 4.4 20.2 1.0 NE1 B:TRP135 4.4 18.1 1.0 O B:GLY107 4.5 16.9 1.0 N B:SER132 4.6 18.8 1.0 CA B:GLY107 4.6 17.8 1.0 OD2 B:ASP89 4.6 17.1 1.0 O B:ASP89 4.7 17.0 1.0 CA B:SER132 4.7 18.3 1.0 CB B:ASP136 4.7 17.7 1.0 CD2 B:PHE131 4.8 23.0 1.0 CA B:ASN133 4.8 20.8 1.0 ND2 B:ASN133 4.8 23.1 1.0 C B:SER132 4.8 20.2 1.0 CZ2 B:TRP135 4.8 20.9 1.0 CE2 B:TRP135 4.9 20.0 1.0

Calcium binding site 3 out of 4 in the Erythrina Cristagalli Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Erythrina Cristagalli Lectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1242 b:11.0 occ:1.00 O C:PHE131 2.4 11.8 1.0 OD1 C:ASN133 2.4 11.5 1.0 OD2 C:ASP136 2.5 15.1 1.0 OD2 C:ASP129 2.5 12.2 1.0 O C:HOH2196 2.5 12.3 1.0 O C:HOH2181 2.5 12.4 1.0 OD1 C:ASP129 2.6 10.6 1.0 CG C:ASP129 2.9 13.3 1.0 CG C:ASP136 3.5 15.6 1.0 CG C:ASN133 3.6 13.2 1.0 C C:PHE131 3.6 13.1 1.0 OD1 C:ASP136 3.9 12.3 1.0 N C:ASN133 4.0 12.9 1.0 CB C:ASN133 4.2 14.8 1.0 MN C:MN1241 4.2 11.2 1.0 N C:PHE131 4.3 11.4 1.0 CB C:ASP129 4.4 12.1 1.0 CA C:PHE131 4.4 13.0 1.0 O C:HOH2330 4.4 10.0 1.0 NE1 C:TRP135 4.5 13.9 1.0 OD2 C:ASP89 4.5 21.2 1.0 O C:GLY107 4.5 11.9 1.0 O C:ASP89 4.5 14.7 1.0 CB C:PHE131 4.5 13.9 1.0 N C:SER132 4.6 12.2 1.0 CA C:SER132 4.6 13.0 1.0 CA C:GLY107 4.6 14.2 1.0 ND2 C:ASN133 4.7 13.2 1.0 CB C:ASP136 4.7 13.7 1.0 CA C:ASN133 4.7 13.4 1.0 C C:SER132 4.8 13.4 1.0 CD2 C:PHE131 4.8 14.4 1.0 CZ2 C:TRP135 4.8 15.8 1.0 CE2 C:TRP135 4.9 14.1 1.0

Calcium binding site 4 out of 4 in the Erythrina Cristagalli Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Erythrina Cristagalli Lectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1242 b:12.8 occ:1.00 O D:PHE131 2.4 13.7 1.0 OD2 D:ASP136 2.5 15.8 1.0 OD1 D:ASN133 2.5 16.4 1.0 OD2 D:ASP129 2.5 12.8 1.0 O D:HOH2149 2.5 15.4 1.0 OD1 D:ASP129 2.6 12.5 1.0 O D:HOH2136 2.6 15.6 1.0 CG D:ASP129 2.9 11.9 1.0 CG D:ASP136 3.5 13.9 1.0 CG D:ASN133 3.6 16.9 1.0 C D:PHE131 3.6 13.6 1.0 OD1 D:ASP136 3.9 14.1 1.0 N D:ASN133 4.0 14.1 1.0 MN D:MN1241 4.1 12.3 1.0 CB D:ASN133 4.2 14.7 1.0 CB D:ASP129 4.4 11.2 1.0 O D:HOH2269 4.4 13.8 1.0 N D:PHE131 4.4 12.7 1.0 NE1 D:TRP135 4.4 16.3 1.0 CA D:PHE131 4.4 13.0 1.0 O D:GLY107 4.6 16.6 1.0 CB D:PHE131 4.6 12.9 1.0 N D:SER132 4.6 13.4 1.0 CA D:SER132 4.6 14.2 1.0 O D:ASP89 4.6 12.7 1.0 CA D:GLY107 4.7 15.8 1.0 CB D:ASP136 4.7 13.8 1.0 OD2 D:ASP89 4.7 14.6 1.0 ND2 D:ASN133 4.7 16.4 1.0 CA D:ASN133 4.7 16.1 1.0 C D:SER132 4.7 15.0 1.0 CD2 D:PHE131 4.8 14.3 1.0 CZ2 D:TRP135 4.9 17.4 1.0 CE2 D:TRP135 4.9 17.3 1.0 CE1 D:HIS142 5.0 13.0 1.0

K.Turton, R.Natesh, N.Thiyagarajan, J.A.Chaddock, K.R.Acharya. Crystal Structures of Erythrina Cristagalli Lectin with Bound N-Linked Oligosaccharide and Lactose Glycobiology V. 14 923 2004.
ISSN: ISSN 0959-6658
PubMed: 15201215
DOI: 10.1093/GLYCOB/CWH114