Manganese in PDB 1v6i: Peanut Lectin-Lactose Complex in Acidic pH

The structure of Peanut Lectin-Lactose Complex in Acidic pH, PDB code: 1v6i 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 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.609, 125.749, 76.049, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.8

The structure of Peanut Lectin-Lactose Complex in Acidic pH also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Peanut Lectin-Lactose Complex in Acidic pH (pdb code 1v6i). 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 Acidic pH, PDB code: 1v6i:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Peanut Lectin-Lactose Complex in Acidic pH


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 Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1238 b:37.9 occ:1.00 OE2 A:GLU121 2.2 20.7 1.0 OD1 A:ASP132 2.2 23.8 1.0 OD2 A:ASP123 2.2 19.2 1.0 NE2 A:HIS137 2.3 19.9 1.0 O A:HOH1242 2.3 22.9 1.0 O A:HOH1241 2.3 14.1 1.0 CG A:ASP123 3.2 20.9 1.0 CG A:ASP132 3.2 25.2 1.0 CD A:GLU121 3.2 17.4 1.0 CE1 A:HIS137 3.2 20.1 1.0 CD2 A:HIS137 3.3 19.4 1.0 OE1 A:GLU121 3.5 15.5 1.0 CB A:ASP123 3.6 20.9 1.0 OD2 A:ASP132 3.7 25.7 1.0 O A:HOH1239 4.0 20.0 1.0 CA A:CA1237 4.1 21.8 1.0 O A:VAL145 4.2 23.2 1.0 OG A:SER147 4.2 18.9 1.0 OD1 A:ASP123 4.3 22.2 1.0 O A:HOH1251 4.3 18.6 1.0 CB A:ASP132 4.4 25.3 1.0 ND1 A:HIS137 4.4 19.1 1.0 CG A:HIS137 4.4 20.5 1.0 CG A:GLU121 4.5 17.8 1.0 CD A:PRO133 4.6 29.3 1.0 CA A:ASP132 4.8 27.6 1.0

Manganese binding site 2 out of 4 in the Peanut Lectin-Lactose Complex in Acidic pH


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 Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2238 b:34.0 occ:1.00 OD1 B:ASP132 2.1 24.3 1.0 OE2 B:GLU121 2.2 16.3 1.0 OD2 B:ASP123 2.2 19.1 1.0 O B:HOH2241 2.3 19.4 1.0 O B:HOH2242 2.3 18.0 1.0 NE2 B:HIS137 2.4 20.9 1.0 CG B:ASP132 3.1 22.8 1.0 CD B:GLU121 3.2 15.4 1.0 CG B:ASP123 3.3 20.1 1.0 CD2 B:HIS137 3.3 19.6 1.0 CE1 B:HIS137 3.4 19.1 1.0 OE1 B:GLU121 3.5 17.1 1.0 OD2 B:ASP132 3.7 22.8 1.0 CB B:ASP123 3.7 18.9 1.0 O B:HOH2239 4.0 17.2 1.0 O B:VAL145 4.0 24.4 1.0 OG B:SER147 4.1 17.7 1.0 O B:HOH2247 4.2 20.4 1.0 CA B:CA2237 4.2 18.7 1.0 CB B:ASP132 4.3 23.7 1.0 OD1 B:ASP123 4.4 20.2 1.0 ND1 B:HIS137 4.5 20.1 1.0 CG B:HIS137 4.5 20.2 1.0 CG B:GLU121 4.5 15.3 1.0 CA B:ASP132 4.7 25.8 1.0 CD B:PRO133 4.7 26.9 1.0

Manganese binding site 3 out of 4 in the Peanut Lectin-Lactose Complex in Acidic pH


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 Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn3238 b:42.0 occ:1.00 OD1 C:ASP132 2.2 26.1 1.0 OE2 C:GLU121 2.2 22.7 1.0 OD2 C:ASP123 2.2 23.2 1.0 O C:HOH3242 2.3 22.4 1.0 NE2 C:HIS137 2.4 23.8 1.0 O C:HOH3241 2.4 20.8 1.0 CG C:ASP132 3.2 27.3 1.0 CG C:ASP123 3.2 22.5 1.0 CD C:GLU121 3.3 21.3 1.0 CE1 C:HIS137 3.3 22.4 1.0 CD2 C:HIS137 3.3 20.4 1.0 CB C:ASP123 3.6 21.8 1.0 OD2 C:ASP132 3.7 25.5 1.0 OE1 C:GLU121 3.7 19.4 1.0 O C:HOH3239 4.1 25.4 1.0 OG C:SER147 4.1 19.8 1.0 CA C:CA3237 4.2 26.7 1.0 O C:VAL145 4.3 26.3 1.0 OD1 C:ASP123 4.3 24.1 1.0 CB C:ASP132 4.3 28.0 1.0 O C:HOH3260 4.3 27.1 1.0 ND1 C:HIS137 4.4 22.4 1.0 CG C:HIS137 4.5 22.6 1.0 CG C:GLU121 4.6 20.4 1.0 CD C:PRO133 4.7 31.0 1.0 CA C:ASP132 4.8 29.8 1.0

Manganese binding site 4 out of 4 in the Peanut Lectin-Lactose Complex in Acidic pH


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 Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn4238 b:37.1 occ:1.00 O D:HOH4242 2.2 18.2 1.0 OD2 D:ASP123 2.2 21.9 1.0 OE2 D:GLU121 2.2 18.4 1.0 OD1 D:ASP132 2.2 28.4 1.0 NE2 D:HIS137 2.3 21.1 1.0 O D:HOH4241 2.4 26.5 1.0 CE1 D:HIS137 3.2 19.2 1.0 CG D:ASP132 3.2 27.1 1.0 CD D:GLU121 3.2 17.8 1.0 CG D:ASP123 3.2 22.1 1.0 CD2 D:HIS137 3.4 18.3 1.0 OE1 D:GLU121 3.5 16.2 1.0 CB D:ASP123 3.6 20.6 1.0 OD2 D:ASP132 3.6 25.8 1.0 O D:HOH4239 4.0 24.6 1.0 OG D:SER147 4.1 21.0 1.0 O D:VAL145 4.2 25.0 1.0 CA D:CA4237 4.2 23.7 1.0 OD1 D:ASP123 4.3 22.7 1.0 CB D:ASP132 4.3 27.9 1.0 ND1 D:HIS137 4.3 21.1 1.0 CG D:HIS137 4.5 19.8 1.0 CG D:GLU121 4.6 17.7 1.0 CD D:PRO133 4.7 30.4 1.0 CA D:ASP132 4.7 28.5 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