Manganese in PDB 1v6k: Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva)

The structure of Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva), PDB code: 1v6k 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 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.030, 124.030, 75.710, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.9

The structure of Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva) 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 Peptide(Iwssagnva) (pdb code 1v6k). 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 Peptide(Iwssagnva), PDB code: 1v6k:
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 Peptide(Iwssagnva)


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 Peptide(Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn234 b:39.0 occ:1.00 OD2 A:ASP123 2.2 22.3 1.0 OD1 A:ASP132 2.2 30.2 1.0 OE2 A:GLU121 2.3 21.9 1.0 NE2 A:HIS137 2.3 19.5 1.0 O A:HOH240 2.3 21.3 1.0 O A:HOH239 2.4 14.1 1.0 CG A:ASP123 3.0 22.6 1.0 CE1 A:HIS137 3.1 17.2 1.0 CG A:ASP132 3.1 30.3 1.0 CD A:GLU121 3.3 17.4 1.0 CD2 A:HIS137 3.4 18.1 1.0 CB A:ASP123 3.4 22.8 1.0 OD2 A:ASP132 3.6 31.5 1.0 OE1 A:GLU121 3.7 14.3 1.0 O A:HOH237 4.0 13.6 1.0 CA A:CA233 4.1 18.7 1.0 OD1 A:ASP123 4.1 24.6 1.0 O A:HOH249 4.2 20.0 1.0 CB A:ASP132 4.2 30.1 1.0 ND1 A:HIS137 4.3 19.1 1.0 O A:VAL145 4.3 22.3 1.0 CG A:HIS137 4.4 18.9 1.0 OG A:SER147 4.4 21.7 1.0 CG A:GLU121 4.6 18.5 1.0 CA A:ASP132 4.7 29.8 1.0 CD A:PRO133 4.8 30.0 1.0 CA A:ASP123 4.9 22.0 1.0

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


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 Peptide(Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn234 b:33.7 occ:1.00 OD1 B:ASP132 2.1 27.7 1.0 OE2 B:GLU121 2.2 17.4 1.0 OD2 B:ASP123 2.2 22.2 1.0 NE2 B:HIS137 2.3 21.2 1.0 O B:HOH240 2.3 18.1 1.0 O B:HOH239 2.3 13.2 1.0 CD B:GLU121 3.2 17.6 1.0 CE1 B:HIS137 3.2 18.5 1.0 CG B:ASP132 3.2 27.6 1.0 CG B:ASP123 3.2 21.3 1.0 CD2 B:HIS137 3.3 19.2 1.0 OE1 B:GLU121 3.5 14.0 1.0 CB B:ASP123 3.6 21.7 1.0 OD2 B:ASP132 3.9 29.6 1.0 O B:HOH237 4.0 17.4 1.0 OG B:SER147 4.0 23.7 1.0 O B:VAL145 4.1 22.6 1.0 CB B:ASP132 4.2 27.6 1.0 OD1 B:ASP123 4.3 21.4 1.0 ND1 B:HIS137 4.3 19.9 1.0 CA B:CA233 4.4 18.1 1.0 CG B:HIS137 4.4 19.5 1.0 CG B:GLU121 4.5 17.2 1.0 CD B:PRO133 4.6 28.2 1.0 CA B:ASP132 4.6 28.9 1.0

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


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 Peptide(Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn234 b:40.1 occ:1.00 OD1 C:ASP132 2.1 29.5 1.0 OD2 C:ASP123 2.1 23.3 1.0 OE2 C:GLU121 2.2 22.9 1.0 O C:HOH240 2.3 25.6 1.0 O C:HOH239 2.4 12.8 1.0 NE2 C:HIS137 2.4 22.6 1.0 CG C:ASP123 3.2 22.2 1.0 CG C:ASP132 3.2 29.9 1.0 CE1 C:HIS137 3.2 20.9 1.0 CD C:GLU121 3.2 21.4 1.0 CD2 C:HIS137 3.4 20.7 1.0 OE1 C:GLU121 3.5 18.4 1.0 CB C:ASP123 3.6 22.7 1.0 OD2 C:ASP132 3.8 29.5 1.0 O C:HOH237 4.0 17.4 1.0 CA C:CA233 4.1 25.6 1.0 OG C:SER147 4.1 24.2 1.0 O C:VAL145 4.1 24.7 1.0 CB C:ASP132 4.2 29.8 1.0 OD1 C:ASP123 4.2 24.6 1.0 ND1 C:HIS137 4.4 21.8 1.0 CG C:HIS137 4.5 22.1 1.0 CG C:GLU121 4.6 19.8 1.0 CA C:ASP132 4.6 30.5 1.0 CD C:PRO133 4.6 30.4 1.0

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


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 Peptide(Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn234 b:41.8 occ:1.00 OD1 D:ASP132 2.2 30.4 1.0 OE2 D:GLU121 2.2 18.5 1.0 O D:HOH240 2.3 22.7 1.0 NE2 D:HIS137 2.3 19.6 1.0 OD2 D:ASP123 2.3 21.8 1.0 O D:HOH239 2.5 18.9 1.0 CG D:ASP132 3.2 29.3 1.0 CD D:GLU121 3.2 19.4 1.0 CE1 D:HIS137 3.2 17.4 1.0 CG D:ASP123 3.2 21.9 1.0 CD2 D:HIS137 3.3 17.4 1.0 OE1 D:GLU121 3.5 16.2 1.0 CB D:ASP123 3.6 22.2 1.0 OD2 D:ASP132 3.7 29.7 1.0 O D:HOH237 4.0 18.0 1.0 O D:VAL145 4.1 21.7 1.0 CA D:CA233 4.2 22.9 1.0 OG D:SER147 4.2 21.4 1.0 OD1 D:ASP123 4.3 24.5 1.0 CB D:ASP132 4.3 29.9 1.0 ND1 D:HIS137 4.4 20.9 1.0 CG D:HIS137 4.5 19.9 1.0 CG D:GLU121 4.5 18.8 1.0 CD D:PRO133 4.6 30.0 1.0 CA D:ASP132 4.7 29.9 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