Calcium in PDB 1rir: Crystal Structure of Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut Lectin.

The structure of Crystal Structure of Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut Lectin., PDB code: 1rir 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 / 2.90
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	94.800, 94.800, 144.000, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 28.2

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

Manganese

(Mn)

4 atoms

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

Calcium binding site 1 out of 4 in the Crystal Structure of Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut 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 Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut Lectin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca246 b:20.8 occ:1.00 O A:TYR125 2.6 57.4 1.0 OD2 A:ASP123 2.6 47.1 1.0 OD1 A:ASN127 2.7 38.7 1.0 OD1 A:ASP123 2.8 45.1 1.0 OD2 A:ASP132 3.0 88.3 1.0 CG A:ASP123 3.0 46.2 1.0 CG A:ASN127 3.5 37.1 1.0 ND2 A:ASN127 3.6 36.8 1.0 CG A:ASP132 3.8 88.0 1.0 C A:TYR125 3.8 57.4 1.0 OD1 A:ASP132 3.8 88.0 1.0 OD1 A:ASP83 3.9 52.3 1.0 O A:ASP83 4.2 42.6 1.0 O A:GLY104 4.4 48.8 1.0 CB A:ASP123 4.4 46.4 1.0 N A:TYR125 4.4 54.3 1.0 CA A:TYR125 4.5 55.9 1.0 CD1 A:TYR125 4.6 68.7 1.0 CB A:TYR125 4.6 68.1 1.0 CG A:ASP83 4.8 50.8 1.0 N A:SER126 4.8 50.3 1.0 MN A:MN247 4.8 51.8 1.0 CB A:ASN127 4.9 38.0 1.0 N A:ASN127 4.9 47.1 1.0 CA A:GLY104 4.9 55.0 1.0 CB A:ASP83 4.9 50.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut 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 Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut Lectin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca250 b:19.1 occ:1.00 OD1 B:ASN127 2.6 51.2 1.0 OD2 B:ASP123 2.7 43.2 1.0 O B:TYR125 2.8 40.7 1.0 OD1 B:ASP123 3.0 41.2 1.0 OD2 B:ASP132 3.1 62.8 1.0 CG B:ASP123 3.2 42.2 1.0 CG B:ASN127 3.4 49.5 1.0 ND2 B:ASN127 3.4 49.2 1.0 CG B:ASP132 3.8 62.5 1.0 OD1 B:ASP132 3.8 62.6 1.0 OD1 B:ASP83 3.8 49.6 1.0 C B:TYR125 4.0 40.7 1.0 O B:GLY104 4.1 46.5 1.0 O B:ASP83 4.4 54.9 1.0 CB B:ASP123 4.6 42.5 1.0 CD1 B:TYR125 4.7 56.1 1.0 CA B:GLY104 4.7 52.8 1.0 N B:TYR125 4.7 37.5 1.0 CA B:TYR125 4.7 39.2 1.0 CG B:ASP83 4.7 48.1 1.0 CB B:ASN127 4.8 50.4 1.0 MN B:MN251 4.8 48.4 1.0 CB B:TYR125 4.8 55.4 1.0 C B:GLY104 4.9 47.4 1.0 N B:ASN127 4.9 40.0 1.0 CB B:ASP83 4.9 47.7 1.0 N B:SER126 5.0 51.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut 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 Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut Lectin. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca252 b:31.9 occ:1.00 OD2 C:ASP123 2.7 57.0 1.0 OD1 C:ASN127 2.7 94.2 1.0 OD1 C:ASP123 3.0 55.0 1.0 O C:TYR125 3.0 55.1 1.0 OD2 C:ASP132 3.1 75.0 1.0 CG C:ASP123 3.1 56.1 1.0 CG C:ASN127 3.4 92.5 1.0 ND2 C:ASN127 3.5 92.2 1.0 OD1 C:ASP132 3.7 74.7 1.0 CG C:ASP132 3.8 74.7 1.0 OD1 C:ASP83 3.8 84.3 1.0 O C:GLY104 3.9 59.3 1.0 C C:TYR125 4.2 55.2 1.0 O C:ASP83 4.4 84.0 1.0 CB C:ASP123 4.5 56.3 1.0 CA C:GLY104 4.6 65.6 1.0 MN C:MN253 4.7 51.5 1.0 C C:GLY104 4.7 60.2 1.0 CG C:ASP83 4.7 82.8 1.0 CB C:ASN127 4.9 93.4 1.0 CB C:ASP83 4.9 82.5 1.0 N C:TYR125 4.9 52.0 1.0 CA C:TYR125 5.0 53.7 1.0 CD1 C:TYR125 5.0 89.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut 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 Meso-Tetrasulphonatophenylporphyrin in Complex with Peanut Lectin. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca248 b:28.5 occ:1.00 OD2 D:ASP123 2.6 61.5 1.0 OD1 D:ASN127 2.7 0.1 1.0 OD1 D:ASP123 2.8 59.5 1.0 O D:TYR125 2.9 61.4 1.0 CG D:ASP123 3.0 60.6 1.0 OD2 D:ASP132 3.1 83.9 1.0 CG D:ASN127 3.5 0.5 1.0 ND2 D:ASN127 3.6 0.1 1.0 OD1 D:ASP132 3.7 83.6 1.0 CG D:ASP132 3.7 83.6 1.0 OD1 D:ASP83 3.9 86.6 1.0 C D:TYR125 4.1 61.4 1.0 O D:GLY104 4.1 59.8 1.0 O D:ASP83 4.3 63.6 1.0 CB D:ASP123 4.5 60.8 1.0 MN D:MN249 4.6 54.1 1.0 CA D:GLY104 4.7 66.1 1.0 N D:TYR125 4.8 58.3 1.0 CG D:ASP83 4.8 85.1 1.0 CA D:TYR125 4.8 59.9 1.0 CD1 D:TYR125 4.9 71.0 1.0 C D:GLY104 4.9 60.7 1.0 CB D:TYR125 4.9 70.3 1.0 CB D:ASP83 4.9 84.8 1.0 CB D:ASN127 4.9 0.4 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