Manganese in PDB 1v6l: Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg)

The structure of Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg), PDB code: 1v6l was solved by S.Kundhavai Natchiar, A.Arockia Jeyaprakash, T.N.C.Ramya, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.278, 124.636, 75.752, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.9

The structure of Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg) (pdb code 1v6l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg), PDB code: 1v6l:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:38.2 occ:1.00 OE2 A:GLU121 2.2 26.0 1.0 OD1 A:ASP132 2.2 36.7 1.0 O A:HOH242 2.2 27.1 1.0 OD2 A:ASP123 2.3 18.9 1.0 NE2 A:HIS137 2.3 18.9 1.0 O A:HOH241 2.4 20.9 1.0 CE1 A:HIS137 3.1 18.5 1.0 CG A:ASP123 3.1 24.1 1.0 CG A:ASP132 3.2 37.7 1.0 CD A:GLU121 3.2 21.9 1.0 CD2 A:HIS137 3.4 18.5 1.0 CB A:ASP123 3.5 21.9 1.0 OE1 A:GLU121 3.6 19.1 1.0 OD2 A:ASP132 3.7 36.8 1.0 O A:HOH239 4.1 22.2 1.0 O A:VAL145 4.2 19.2 1.0 OD1 A:ASP123 4.2 25.8 1.0 CB A:ASP132 4.3 39.3 1.0 OG A:SER147 4.3 18.2 1.0 CA A:CA237 4.3 22.8 1.0 ND1 A:HIS137 4.3 20.4 1.0 O A:HOH251 4.4 28.8 1.0 CG A:HIS137 4.5 21.6 1.0 CG A:GLU121 4.5 21.4 1.0 CA A:ASP132 4.7 23.5 1.0 CD A:PRO133 4.7 24.0 1.0 CA A:ASP123 5.0 23.8 1.0

Manganese binding site 2 out of 4 in the Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:34.5 occ:1.00 OD1 B:ASP132 2.1 35.8 1.0 OE2 B:GLU121 2.2 17.2 1.0 OD2 B:ASP123 2.3 22.8 1.0 O B:HOH241 2.3 22.1 1.0 NE2 B:HIS137 2.4 18.1 1.0 O B:HOH242 2.4 25.6 1.0 CG B:ASP132 3.2 31.9 1.0 CG B:ASP123 3.2 21.0 1.0 CD B:GLU121 3.2 14.7 1.0 CE1 B:HIS137 3.3 16.9 1.0 CD2 B:HIS137 3.4 17.7 1.0 CB B:ASP123 3.5 19.2 1.0 OE1 B:GLU121 3.6 16.7 1.0 OD2 B:ASP132 3.7 31.4 1.0 O B:HOH239 3.9 22.5 1.0 O B:VAL145 4.1 23.7 1.0 OG B:SER147 4.1 17.8 1.0 OD1 B:ASP123 4.3 21.4 1.0 CA B:CA237 4.3 18.8 1.0 CB B:ASP132 4.3 33.0 1.0 ND1 B:HIS137 4.4 20.3 1.0 O B:HOH246 4.4 24.4 1.0 CG B:HIS137 4.5 18.5 1.0 CG B:GLU121 4.5 16.7 1.0 CD B:PRO133 4.6 19.8 1.0 CA B:ASP132 4.7 29.7 1.0

Manganese binding site 3 out of 4 in the Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:40.4 occ:1.00 OD1 C:ASP132 2.1 37.5 1.0 OE2 C:GLU121 2.1 29.4 1.0 OD2 C:ASP123 2.2 32.2 1.0 O C:HOH242 2.3 30.6 1.0 O C:HOH241 2.3 26.9 1.0 NE2 C:HIS137 2.4 28.4 1.0 CG C:ASP132 3.1 36.5 1.0 CD C:GLU121 3.2 26.6 1.0 CG C:ASP123 3.2 30.7 1.0 CE1 C:HIS137 3.2 28.6 1.0 CD2 C:HIS137 3.5 24.4 1.0 OD2 C:ASP132 3.5 32.9 1.0 CB C:ASP123 3.6 30.6 1.0 OE1 C:GLU121 3.6 24.0 1.0 O C:HOH239 3.9 23.5 1.0 OG C:SER147 4.0 20.6 1.0 O C:VAL145 4.0 22.0 1.0 CB C:ASP132 4.3 35.8 1.0 OD1 C:ASP123 4.3 33.9 1.0 ND1 C:HIS137 4.4 28.6 1.0 CA C:CA237 4.4 24.4 1.0 CG C:GLU121 4.5 25.2 1.0 CD C:PRO133 4.6 24.2 1.0 CG C:HIS137 4.6 26.8 1.0 CA C:ASP132 4.7 35.2 1.0

Manganese binding site 4 out of 4 in the Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Peanut Lectin-Lactose Complex in the Presence of 9MER Peptide (Pviwssatg) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:39.2 occ:1.00 OE2 D:GLU121 2.2 23.0 1.0 OD2 D:ASP123 2.2 24.0 1.0 OD1 D:ASP132 2.3 31.2 1.0 O D:HOH242 2.3 27.2 1.0 NE2 D:HIS137 2.4 18.9 1.0 O D:HOH241 2.4 34.2 1.0 CG D:ASP132 3.2 29.0 1.0 CG D:ASP123 3.2 24.7 1.0 CE1 D:HIS137 3.2 16.2 1.0 CD D:GLU121 3.3 23.7 1.0 CD2 D:HIS137 3.4 16.6 1.0 CB D:ASP123 3.6 25.5 1.0 OD2 D:ASP132 3.6 27.8 1.0 OE1 D:GLU121 3.7 21.3 1.0 O D:HOH239 3.9 22.2 1.0 O D:VAL145 4.1 20.1 1.0 OG D:SER147 4.1 19.0 1.0 O D:HOH286 4.2 18.1 1.0 OD1 D:ASP123 4.3 25.6 1.0 CA D:CA237 4.3 25.3 1.0 CB D:ASP132 4.4 29.9 1.0 ND1 D:HIS137 4.4 19.3 1.0 CG D:HIS137 4.5 17.4 1.0 CG D:GLU121 4.6 21.4 1.0 CD D:PRO133 4.6 34.5 1.0 CA D:ASP132 4.7 27.8 1.0

S.Kundhavai Natchiar, A.Arockia Jeyaprakash, T.N.Ramya, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan. Structural Plasticity of Peanut Lectin: An X-Ray Analysis Involving Variation in pH, Ligand Binding and Crystal Structure. Acta Crystallogr.,Sect.D V. 60 211 2004.
ISSN: ISSN 0907-4449
PubMed: 14747696
DOI: 10.1107/S090744490302849X