Calcium in PDB 1rit: Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose

The structure of Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose, PDB code: 1rit was solved by M.Goel, K.J.Kaur, B.G.Maiya, M.J.Swamy, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.85
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	94.900, 94.900, 144.100, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 26

The structure of Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose (pdb code 1rit). 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 Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose, PDB code: 1rit:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose


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 Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca248 b:43.0 occ:1.00 OD1 A:ASN127 2.5 44.9 1.0 OD2 A:ASP123 2.6 53.3 1.0 O A:TYR125 2.8 63.5 1.0 OD2 A:ASP132 3.0 94.4 1.0 OD1 A:ASP123 3.0 51.3 1.0 CG A:ASP123 3.1 52.4 1.0 CG A:ASN127 3.3 43.3 1.0 ND2 A:ASN127 3.5 42.9 1.0 CG A:ASP132 3.6 94.1 1.0 OD1 A:ASP132 3.6 94.1 1.0 C A:TYR125 4.0 63.5 1.0 OD1 A:ASP83 4.0 58.5 1.0 O A:GLY104 4.2 54.9 1.0 O A:ASP83 4.5 48.8 1.0 CB A:ASP123 4.5 52.6 1.0 MN A:MN249 4.6 62.5 1.0 CB A:ASN127 4.7 44.1 1.0 N A:TYR125 4.8 60.4 1.0 CA A:TYR125 4.8 62.0 1.0 CD1 A:TYR125 4.8 74.9 1.0 CA A:GLY104 4.8 61.2 1.0 N A:ASN127 4.9 53.3 1.0 C A:GLY104 4.9 55.8 1.0 CB A:TYR125 4.9 74.2 1.0 CG A:ASP83 4.9 57.0 1.0 CB A:ASP132 4.9 92.5 1.0 N A:SER126 5.0 56.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose


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 Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca250 b:40.0 occ:1.00 OD1 B:ASN127 2.7 44.3 1.0 OD2 B:ASP123 2.7 52.7 1.0 O B:TYR125 2.9 62.9 1.0 OD1 B:ASP123 3.0 50.6 1.0 CG B:ASP123 3.1 51.7 1.0 OD2 B:ASP132 3.2 93.8 1.0 CG B:ASN127 3.5 42.6 1.0 ND2 B:ASN127 3.6 42.3 1.0 OD1 B:ASP83 3.8 57.8 1.0 CG B:ASP132 3.9 93.5 1.0 OD1 B:ASP132 3.9 93.5 1.0 C B:TYR125 4.0 62.9 1.0 O B:GLY104 4.1 54.3 1.0 O B:ASP83 4.3 48.1 1.0 CB B:ASP123 4.5 52.0 1.0 N B:TYR125 4.7 59.8 1.0 CG B:ASP83 4.7 56.3 1.0 CA B:GLY104 4.7 60.6 1.0 CD1 B:TYR125 4.7 74.2 1.0 CA B:TYR125 4.8 61.4 1.0 CB B:TYR125 4.8 73.6 1.0 MN B:MN251 4.9 58.0 1.0 C B:GLY104 4.9 55.1 1.0 CB B:ASP83 4.9 56.0 1.0 CB B:ASN127 4.9 43.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose


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 Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca252 b:51.0 occ:1.00 OD1 C:ASP123 2.5 42.9 1.0 O C:TYR125 2.6 58.3 1.0 OD1 C:ASN127 2.8 83.4 1.0 OD2 C:ASP132 3.0 59.9 1.0 OD2 C:ASP123 3.1 44.6 1.0 CG C:ASP123 3.2 40.4 1.0 CG C:ASN127 3.6 82.7 1.0 C C:TYR125 3.7 59.0 1.0 OD1 C:ASP83 4.1 81.8 1.0 CA C:GLY104 4.2 62.7 1.0 CG C:ASP132 4.2 64.0 1.0 CB C:TYR125 4.2 79.6 1.0 N C:TYR125 4.2 55.2 1.0 CA C:TYR125 4.3 56.1 1.0 O C:ASP83 4.4 66.2 1.0 CB C:ASN127 4.4 82.8 1.0 ND2 C:ASN127 4.4 86.3 1.0 O C:GLY104 4.5 65.8 1.0 N C:ASN127 4.5 80.9 1.0 CB C:ASP83 4.6 77.8 1.0 CB C:ASP123 4.6 37.4 1.0 CD2 C:TYR125 4.7 84.5 1.0 OD1 C:ASP132 4.7 60.5 1.0 N C:SER126 4.8 66.9 1.0 C C:GLY104 4.8 64.0 1.0 CG C:ASP83 4.8 80.3 1.0 CG C:TYR125 5.0 81.8 1.0 C C:SER126 5.0 73.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose


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 Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca254 b:57.6 occ:1.00 OD1 D:ASP123 2.5 50.9 1.0 O D:TYR125 2.6 64.3 1.0 OD2 D:ASP132 2.7 51.1 1.0 OD1 D:ASN127 2.8 88.6 1.0 OD2 D:ASP123 2.8 54.9 1.0 CG D:ASP123 3.0 53.2 1.0 CG D:ASP132 3.6 49.6 1.0 CG D:ASN127 3.8 86.6 1.0 C D:TYR125 3.8 66.5 1.0 OD1 D:ASP132 3.9 46.5 1.0 CB D:ASN127 4.3 88.2 1.0 OD1 D:ASP83 4.4 58.3 1.0 N D:ASN127 4.4 58.1 1.0 O D:GLY104 4.4 90.2 1.0 CB D:ASP123 4.5 53.0 1.0 CA D:GLY104 4.5 89.9 1.0 N D:TYR125 4.6 63.1 1.0 CA D:TYR125 4.6 64.6 1.0 O D:ASP83 4.6 77.6 1.0 MN D:MN255 4.8 75.2 1.0 CB D:TYR125 4.8 87.0 1.0 N D:SER126 4.9 67.1 1.0 CB D:ASP132 5.0 49.8 1.0 C D:GLY104 5.0 89.4 1.0 ND2 D:ASN127 5.0 86.4 1.0

M.Goel, R.S.Damai, D.K.Sethi, K.J.Kaur, B.G.Maiya, M.J.Swamy, D.M.Salunke. Crystal Structures of the Pna-Porphyrin Complex in the Presence and Absence of Lactose: Mapping the Conformational Changes on Lactose Binding, Interacting Surfaces, and Supramolecular Aggregations. Biochemistry V. 44 5588 2005.
ISSN: ISSN 0006-2960
PubMed: 15823017
DOI: 10.1021/BI047377S