Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Peanut Lectin in Complex with Meso- Tetrasulphonatophenylporphyrin and Lactose, PDB code: 1rit:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn249 b:62.5 occ:1.00 NE2 A:HIS137 2.3 43.3 1.0 OE2 A:GLU121 2.6 48.5 1.0 OD2 A:ASP123 2.8 53.3 1.0 OD2 A:ASP132 3.1 94.4 1.0 CE1 A:HIS137 3.2 44.4 1.0 OD1 A:ASP132 3.2 94.1 1.0 CG A:ASP132 3.3 94.1 1.0 CD2 A:HIS137 3.3 45.7 1.0 CD A:GLU121 3.6 47.8 1.0 CG A:ASP123 3.8 52.4 1.0 OE1 A:GLU121 3.9 47.9 1.0 O A:VAL145 4.0 42.8 1.0 CB A:ASP123 4.0 52.6 1.0 CA A:ASP132 4.2 74.0 1.0 OG A:SER147 4.2 89.9 1.0 CB A:ASP132 4.3 92.5 1.0 ND1 A:HIS137 4.4 46.0 1.0 CD A:PRO133 4.4 52.0 1.0 CG A:HIS137 4.4 46.2 1.0 CA A:CA248 4.6 43.0 1.0 N A:ASP132 4.9 72.0 1.0 CG A:GLU121 4.9 48.1 1.0 OD1 A:ASP123 4.9 51.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn251 b:58.0 occ:1.00 NE2 B:HIS137 2.4 42.6 1.0 OE2 B:GLU121 2.4 47.9 1.0 OD2 B:ASP123 2.8 52.7 1.0 OD2 B:ASP132 3.3 93.8 1.0 CE1 B:HIS137 3.3 43.7 1.0 CD2 B:HIS137 3.3 45.1 1.0 OD1 B:ASP132 3.3 93.5 1.0 CD B:GLU121 3.4 47.2 1.0 CG B:ASP132 3.4 93.5 1.0 OE1 B:GLU121 3.7 47.3 1.0 CG B:ASP123 3.8 51.7 1.0 O B:VAL145 3.9 42.2 1.0 CB B:ASP123 4.0 52.0 1.0 OG B:SER147 4.1 89.3 1.0 CA B:ASP132 4.4 73.3 1.0 ND1 B:HIS137 4.5 45.3 1.0 CB B:ASP132 4.5 91.8 1.0 CG B:HIS137 4.5 45.6 1.0 CD B:PRO133 4.6 51.4 1.0 CG B:GLU121 4.7 47.5 1.0 CA B:CA250 4.9 40.0 1.0 CB B:SER147 5.0 89.5 1.0 OD1 B:ASP123 5.0 50.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn253 b:70.0 occ:1.00 OE2 C:GLU121 2.0 60.9 1.0 OD2 C:ASP123 2.3 44.6 1.0 O C:HOH256 2.4 65.8 1.0 OD1 C:ASP132 2.4 60.5 1.0 NE2 C:HIS137 2.5 68.2 1.0 CD C:GLU121 3.0 60.9 1.0 OE1 C:GLU121 3.3 58.6 1.0 CG C:ASP123 3.3 40.4 1.0 CD2 C:HIS137 3.4 63.2 1.0 CG C:ASP132 3.5 64.0 1.0 CE1 C:HIS137 3.6 64.7 1.0 OG C:SER147 3.7 42.8 1.0 CB C:ASP123 3.7 37.4 1.0 OD2 C:ASP132 3.9 59.9 1.0 O C:VAL145 4.1 46.7 1.0 CG C:GLU121 4.3 58.5 1.0 OD1 C:ASP123 4.4 42.9 1.0 CG C:HIS137 4.6 64.9 1.0 ND1 C:HIS137 4.6 66.9 1.0 CD C:PRO133 4.8 62.3 1.0 CB C:ASP132 4.8 61.5 1.0 CG2 C:THR150 4.9 53.1 1.0 CA C:ASP132 4.9 72.5 1.0 CB C:SER147 4.9 40.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn255 b:75.2 occ:1.00 OE2 D:GLU121 2.3 76.3 1.0 OD1 D:ASP132 2.5 46.5 1.0 OD2 D:ASP123 2.7 54.9 1.0 NE2 D:HIS137 2.7 65.7 1.0 CD D:GLU121 3.0 75.2 1.0 OE1 D:GLU121 3.2 76.3 1.0 OG D:SER147 3.4 62.0 1.0 CD2 D:HIS137 3.4 62.8 1.0 CG D:ASP132 3.7 49.6 1.0 O D:VAL145 3.7 68.3 1.0 CE1 D:HIS137 3.8 60.9 1.0 CG D:ASP123 3.8 53.2 1.0 CB D:ASP123 4.3 53.0 1.0 OD2 D:ASP132 4.3 51.1 1.0 CG D:GLU121 4.3 73.2 1.0 CB D:SER147 4.5 65.7 1.0 CD D:PRO133 4.6 57.7 1.0 CG D:HIS137 4.7 63.5 1.0 CA D:ASP132 4.8 81.4 1.0 CB D:ASP132 4.8 49.8 1.0 CA D:CA254 4.8 57.6 1.0 N D:SER147 4.8 63.1 1.0 ND1 D:HIS137 4.8 64.1 1.0 CG2 D:THR150 4.8 64.3 1.0 C D:VAL145 4.9 69.7 1.0 OD1 D:ASP123 4.9 50.9 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