Calcium in PDB 1sfy: Crystal Structure of Recombinant Erythrina Corallodandron Lectin

The structure of Crystal Structure of Recombinant Erythrina Corallodandron Lectin, PDB code: 1sfy was solved by K.A.Kulkarni, A.Srivastava, N.Mitra, A.Surolia, M.Vijayan, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.66 / 2.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.240, 144.890, 127.660, 90.00, 93.29, 90.00
R / Rfree (%)	18 / 20.8

The structure of Crystal Structure of Recombinant Erythrina Corallodandron Lectin also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Calcium atom in the Crystal Structure of Recombinant Erythrina Corallodandron Lectin (pdb code 1sfy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Recombinant Erythrina Corallodandron Lectin, PDB code: 1sfy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Recombinant Erythrina Corallodandron 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 Recombinant Erythrina Corallodandron Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1290 b:36.9 occ:1.00 O A:HOH1502 2.4 15.8 1.0 OD2 A:ASP136 2.6 36.6 1.0 O A:PHE131 2.6 33.2 1.0 OD2 A:ASP129 2.7 29.4 1.0 OD1 A:ASP129 2.7 28.6 1.0 O A:HOH1503 2.7 44.9 1.0 OD1 A:ASN133 2.8 44.2 1.0 CG A:ASP129 3.0 27.6 1.0 CG A:ASN133 3.6 41.8 1.0 CG A:ASP136 3.6 37.7 1.0 C A:PHE131 3.7 33.7 1.0 OD1 A:ASP136 4.0 39.8 1.0 CB A:ASN133 4.0 41.3 1.0 N A:ASN133 4.1 38.5 1.0 CA A:GLY107 4.3 29.8 1.0 O A:HOH1500 4.3 21.6 1.0 CB A:PHE131 4.4 32.6 1.0 NE1 A:TRP135 4.4 37.4 1.0 O A:GLY107 4.4 29.5 1.0 CA A:PHE131 4.4 32.5 1.0 MN A:MN1289 4.5 22.8 1.0 N A:PHE131 4.5 30.5 1.0 CB A:ASP129 4.5 26.0 1.0 OD1 A:ASP89 4.6 25.9 1.0 ND2 A:ASN133 4.6 43.4 1.0 N A:SER132 4.6 35.6 1.0 CD2 A:PHE131 4.7 32.3 1.0 CA A:ASN133 4.7 40.2 1.0 CA A:SER132 4.8 36.2 1.0 O A:ASP89 4.8 21.4 1.0 C A:SER132 4.8 37.2 1.0 CZ2 A:TRP135 4.8 35.3 1.0 C A:GLY107 4.9 29.6 1.0 CB A:ASP136 4.9 38.0 1.0 CE2 A:TRP135 4.9 36.7 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Recombinant Erythrina Corallodandron 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 Recombinant Erythrina Corallodandron Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2290 b:29.4 occ:1.00 OD2 B:ASP136 2.5 35.7 1.0 O B:PHE131 2.6 33.7 1.0 O B:HOH2502 2.6 25.6 1.0 OD2 B:ASP129 2.6 27.4 1.0 O B:HOH2503 2.6 44.8 1.0 OD1 B:ASP129 2.7 28.9 1.0 OD1 B:ASN133 2.9 42.0 1.0 CG B:ASP129 3.0 27.3 1.0 CG B:ASP136 3.6 37.7 1.0 CG B:ASN133 3.7 40.7 1.0 C B:PHE131 3.7 34.4 1.0 OD1 B:ASP136 4.0 39.9 1.0 N B:ASN133 4.1 39.1 1.0 CB B:ASN133 4.1 40.8 1.0 O B:HOH2500 4.2 18.7 1.0 MN B:MN2289 4.3 25.6 1.0 NE1 B:TRP135 4.4 38.3 1.0 CA B:GLY107 4.4 29.3 1.0 CA B:PHE131 4.4 33.0 1.0 CB B:ASP129 4.5 26.7 1.0 CB B:PHE131 4.5 32.5 1.0 O B:GLY107 4.5 29.8 1.0 N B:PHE131 4.5 31.8 1.0 N B:SER132 4.6 35.4 1.0 OD1 B:ASP89 4.7 25.5 1.0 O B:ASP89 4.7 24.3 1.0 ND2 B:ASN133 4.7 43.1 1.0 CA B:SER132 4.7 36.8 1.0 CA B:ASN133 4.7 40.3 1.0 CD2 B:PHE131 4.7 31.0 1.0 C B:SER132 4.8 38.0 1.0 CB B:ASP136 4.8 37.0 1.0 CZ2 B:TRP135 4.9 37.6 1.0 CE2 B:TRP135 4.9 37.7 1.0 C B:GLY107 5.0 30.5 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Recombinant Erythrina Corallodandron 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 Recombinant Erythrina Corallodandron Lectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3290 b:27.3 occ:1.00 OD2 C:ASP136 2.6 36.3 1.0 OD2 C:ASP129 2.6 25.2 1.0 O C:HOH3503 2.7 20.6 1.0 O C:PHE131 2.7 34.4 1.0 O C:HOH3502 2.7 18.6 1.0 OD1 C:ASP129 2.7 28.3 1.0 OD1 C:ASN133 2.8 40.9 1.0 CG C:ASP129 3.0 26.3 1.0 CG C:ASN133 3.6 40.4 1.0 CG C:ASP136 3.7 37.4 1.0 C C:PHE131 3.8 33.3 1.0 CB C:ASN133 4.1 40.4 1.0 OD1 C:ASP136 4.1 36.8 1.0 N C:ASN133 4.1 38.9 1.0 CA C:GLY107 4.3 28.0 1.0 O C:GLY107 4.3 26.6 1.0 NE1 C:TRP135 4.4 36.3 1.0 MN C:MN3289 4.4 19.7 1.0 O C:HOH3500 4.4 6.3 1.0 CB C:PHE131 4.5 31.1 1.0 CA C:PHE131 4.5 32.1 1.0 CB C:ASP129 4.5 25.9 1.0 N C:PHE131 4.5 30.3 1.0 ND2 C:ASN133 4.6 42.9 1.0 OD1 C:ASP89 4.7 22.0 1.0 O C:ASP89 4.7 23.4 1.0 N C:SER132 4.7 34.4 1.0 CD2 C:PHE131 4.7 30.8 1.0 CA C:ASN133 4.7 40.7 1.0 CZ2 C:TRP135 4.8 36.0 1.0 CA C:SER132 4.8 35.6 1.0 C C:GLY107 4.8 27.1 1.0 CE2 C:TRP135 4.9 36.6 1.0 C C:SER132 4.9 37.0 1.0 CB C:ASP136 4.9 38.1 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Recombinant Erythrina Corallodandron 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 Recombinant Erythrina Corallodandron Lectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca4290 b:31.9 occ:1.00 OD2 D:ASP136 2.6 37.5 1.0 O D:PHE131 2.6 35.4 1.0 OD2 D:ASP129 2.6 26.6 1.0 O D:HOH4502 2.7 13.5 1.0 O D:HOH4503 2.7 28.2 1.0 OD1 D:ASP129 2.8 29.6 1.0 OD1 D:ASN133 2.8 46.1 1.0 CG D:ASP129 3.1 27.7 1.0 CG D:ASP136 3.5 38.5 1.0 CG D:ASN133 3.6 43.2 1.0 C D:PHE131 3.7 34.1 1.0 OD1 D:ASP136 3.8 38.6 1.0 CB D:ASN133 4.0 41.9 1.0 N D:ASN133 4.0 39.8 1.0 O D:HOH4500 4.3 10.2 1.0 NE1 D:TRP135 4.3 35.8 1.0 CA D:GLY107 4.4 29.1 1.0 MN D:MN4289 4.4 22.2 1.0 O D:GLY107 4.4 30.0 1.0 CB D:PHE131 4.5 32.0 1.0 CA D:PHE131 4.5 31.9 1.0 CB D:ASP129 4.5 26.2 1.0 N D:PHE131 4.5 29.9 1.0 OD1 D:ASP89 4.6 27.3 1.0 ND2 D:ASN133 4.6 43.0 1.0 N D:SER132 4.6 35.5 1.0 CA D:ASN133 4.6 40.9 1.0 CD2 D:PHE131 4.7 31.0 1.0 CA D:SER132 4.7 36.7 1.0 C D:SER132 4.7 38.2 1.0 CZ2 D:TRP135 4.8 37.8 1.0 CB D:ASP136 4.8 38.3 1.0 O D:ASP89 4.8 26.2 1.0 CE2 D:TRP135 4.8 36.6 1.0 C D:GLY107 4.9 30.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Recombinant Erythrina Corallodandron Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Recombinant Erythrina Corallodandron Lectin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca5290 b:37.5 occ:1.00 O E:PHE131 2.6 34.4 1.0 OD2 E:ASP136 2.6 38.1 1.0 O E:HOH5503 2.7 20.3 1.0 OD2 E:ASP129 2.7 29.2 1.0 OD1 E:ASN133 2.7 43.1 1.0 OD1 E:ASP129 2.7 29.2 1.0 O E:HOH5502 2.8 20.1 1.0 CG E:ASP129 3.1 29.0 1.0 CG E:ASN133 3.6 42.7 1.0 C E:PHE131 3.7 34.1 1.0 CG E:ASP136 3.7 38.6 1.0 CB E:ASN133 4.0 42.6 1.0 N E:ASN133 4.0 40.4 1.0 OD1 E:ASP136 4.1 38.7 1.0 CA E:GLY107 4.3 30.7 1.0 CB E:PHE131 4.4 33.0 1.0 CA E:PHE131 4.4 32.9 1.0 O E:GLY107 4.4 32.0 1.0 NE1 E:TRP135 4.4 37.4 1.0 N E:PHE131 4.5 31.4 1.0 OD1 E:ASP89 4.5 29.4 1.0 CB E:ASP129 4.6 27.3 1.0 ND2 E:ASN133 4.6 43.8 1.0 O E:HOH5500 4.6 19.5 1.0 MN E:MN5289 4.6 27.6 1.0 CD2 E:PHE131 4.6 33.7 1.0 N E:SER132 4.6 36.6 1.0 CA E:ASN133 4.7 41.8 1.0 CA E:SER132 4.7 38.5 1.0 O E:ASP89 4.7 27.2 1.0 C E:SER132 4.8 39.8 1.0 CZ2 E:TRP135 4.8 37.7 1.0 C E:GLY107 4.9 31.6 1.0 CE2 E:TRP135 4.9 37.8 1.0 CB E:ASP136 4.9 38.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Recombinant Erythrina Corallodandron Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Recombinant Erythrina Corallodandron Lectin within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca6290 b:33.4 occ:1.00 OD2 F:ASP136 2.6 39.2 1.0 O F:PHE131 2.6 36.3 1.0 OD2 F:ASP129 2.7 25.9 1.0 O F:HOH6502 2.7 21.8 1.0 OD1 F:ASP129 2.8 32.6 1.0 OD1 F:ASN133 2.8 44.4 1.0 O F:HOH6503 2.8 26.0 1.0 CG F:ASP129 3.1 28.8 1.0 CG F:ASN133 3.6 43.5 1.0 CG F:ASP136 3.6 38.8 1.0 C F:PHE131 3.7 35.6 1.0 CB F:ASN133 4.0 42.4 1.0 N F:ASN133 4.0 41.0 1.0 OD1 F:ASP136 4.0 37.6 1.0 CA F:GLY107 4.3 30.0 1.0 MN F:MN6289 4.3 25.4 1.0 NE1 F:TRP135 4.4 38.2 1.0 O F:GLY107 4.4 30.3 1.0 CB F:PHE131 4.5 32.8 1.0 CA F:PHE131 4.5 33.2 1.0 N F:PHE131 4.5 31.1 1.0 CB F:ASP129 4.6 27.3 1.0 ND2 F:ASN133 4.6 44.2 1.0 N F:SER132 4.6 37.6 1.0 CA F:ASN133 4.6 42.6 1.0 OD1 F:ASP89 4.7 27.4 1.0 O F:HOH6500 4.7 10.6 1.0 CD2 F:PHE131 4.7 32.9 1.0 CA F:SER132 4.7 39.6 1.0 C F:SER132 4.8 40.6 1.0 CZ2 F:TRP135 4.8 38.8 1.0 O F:ASP89 4.8 28.4 1.0 CB F:ASP136 4.8 39.4 1.0 CE2 F:TRP135 4.8 38.5 1.0 C F:GLY107 4.9 30.2 1.0

K.A.Kulkarni, A.Srivastava, N.Mitra, N.Sharon, A.Surolia, M.Vijayan, K.Suguna. Effect of Glycosylation on the Structure of Erythrina Corallodendron Lectin. Proteins V. 56 821 2004.
ISSN: ISSN 0887-3585
PubMed: 15281133
DOI: 10.1002/PROT.20168