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Manganese in PDB 1v6j: Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH

Protein crystallography data

The structure of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH, PDB code: 1v6j 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 / 2.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.733, 125.531, 76.050, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 22

Other elements in 1v6j:

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

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH (pdb code 1v6j). 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 Crystallized in Orthorhombic Form at Acidic pH, PDB code: 1v6j:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1v6j

Go back to Manganese Binding Sites List in 1v6j
Manganese binding site 1 out of 4 in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at 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 Crystallized in Orthorhombic Form at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn238

b:46.2
occ:1.00
OD1 A:ASP132 2.2 41.5 1.0
OE2 A:GLU121 2.3 28.7 1.0
OD2 A:ASP123 2.4 24.5 1.0
NE2 A:HIS137 2.5 26.0 1.0
CD A:GLU121 3.2 27.7 1.0
CG A:ASP132 3.3 41.0 1.0
OE1 A:GLU121 3.4 29.8 1.0
CG A:ASP123 3.4 23.1 1.0
CD2 A:HIS137 3.4 20.4 1.0
CE1 A:HIS137 3.5 22.7 1.0
OG A:SER147 3.7 38.1 1.0
CB A:ASP123 3.8 21.0 1.0
OD2 A:ASP132 3.8 36.2 1.0
O A:VAL145 3.9 19.9 1.0
O A:HOH243 4.0 31.4 1.0
CB A:ASP132 4.5 39.2 1.0
OD1 A:ASP123 4.5 21.8 1.0
CG A:GLU121 4.5 23.8 1.0
CG A:HIS137 4.6 25.9 1.0
ND1 A:HIS137 4.6 23.9 1.0
CD A:PRO133 4.7 22.7 1.0
CA A:ASP132 4.7 29.8 1.0
CA A:CA237 4.8 26.6 1.0
CB A:SER147 4.8 38.3 1.0

Manganese binding site 2 out of 4 in 1v6j

Go back to Manganese Binding Sites List in 1v6j
Manganese binding site 2 out of 4 in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at 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 Crystallized in Orthorhombic Form at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn238

b:45.3
occ:1.00
OD1 B:ASP132 2.3 38.0 1.0
OE2 B:GLU121 2.3 25.2 1.0
OD2 B:ASP123 2.5 26.7 1.0
NE2 B:HIS137 2.6 20.4 1.0
CD B:GLU121 3.1 24.9 1.0
OE1 B:GLU121 3.3 22.5 1.0
CG B:ASP132 3.4 37.6 1.0
CD2 B:HIS137 3.5 16.2 1.0
CG B:ASP123 3.5 27.3 1.0
CE1 B:HIS137 3.6 14.8 1.0
O B:VAL145 3.7 20.5 1.0
OG B:SER147 3.7 24.4 1.0
OD2 B:ASP132 3.8 35.0 1.0
O B:HOH241 3.8 33.5 1.0
CB B:ASP123 3.9 27.5 1.0
CG B:GLU121 4.5 19.5 1.0
CB B:ASP132 4.6 35.2 1.0
OD1 B:ASP123 4.6 26.5 1.0
CG B:HIS137 4.7 17.8 1.0
CA B:CA237 4.7 27.3 1.0
ND1 B:HIS137 4.7 16.2 1.0
CA B:ASP132 4.8 29.8 1.0
C B:VAL145 4.8 16.2 1.0
CD B:PRO133 4.9 22.8 1.0
CB B:SER147 5.0 22.5 1.0

Manganese binding site 3 out of 4 in 1v6j

Go back to Manganese Binding Sites List in 1v6j
Manganese binding site 3 out of 4 in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at 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 Crystallized in Orthorhombic Form at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn238

b:48.3
occ:1.00
OE2 C:GLU121 2.2 31.7 1.0
OD1 C:ASP132 2.2 39.6 1.0
OD2 C:ASP123 2.5 40.2 1.0
NE2 C:HIS137 2.6 30.8 1.0
CD C:GLU121 3.1 31.7 1.0
CG C:ASP132 3.3 43.2 1.0
OE1 C:GLU121 3.3 29.5 1.0
CD2 C:HIS137 3.5 25.7 1.0
CG C:ASP123 3.5 36.0 1.0
CE1 C:HIS137 3.7 27.2 1.0
OG C:SER147 3.7 22.2 1.0
OD2 C:ASP132 3.7 39.1 1.0
CB C:ASP123 3.9 33.0 1.0
O C:VAL145 3.9 22.9 1.0
CG C:GLU121 4.4 29.4 1.0
CB C:ASP132 4.6 40.6 1.0
OD1 C:ASP123 4.7 38.5 1.0
CG C:HIS137 4.7 27.4 1.0
ND1 C:HIS137 4.7 29.4 1.0
CA C:CA237 4.8 29.3 1.0
CD C:PRO133 4.8 34.4 1.0
CB C:SER147 4.8 19.8 1.0
CA C:ASP132 4.9 27.4 1.0

Manganese binding site 4 out of 4 in 1v6j

Go back to Manganese Binding Sites List in 1v6j
Manganese binding site 4 out of 4 in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at 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 Crystallized in Orthorhombic Form at Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn238

b:45.8
occ:1.00
OE2 D:GLU121 2.2 21.9 1.0
OD1 D:ASP132 2.5 33.0 1.0
NE2 D:HIS137 2.5 29.1 1.0
OD2 D:ASP123 2.8 24.4 1.0
CD D:GLU121 3.1 20.9 1.0
CG D:ASP132 3.4 36.2 1.0
OE1 D:GLU121 3.4 21.9 1.0
CD2 D:HIS137 3.4 26.1 1.0
CE1 D:HIS137 3.5 24.3 1.0
OG D:SER147 3.7 30.3 1.0
OD2 D:ASP132 3.7 37.6 1.0
CG D:ASP123 3.7 22.8 1.0
O D:HOH254 3.8 38.1 1.0
O D:VAL145 3.8 19.5 1.0
CB D:ASP123 3.9 22.5 1.0
CG D:GLU121 4.5 18.8 1.0
CD D:PRO133 4.5 22.5 1.0
CB D:ASP132 4.6 36.4 1.0
CG D:HIS137 4.6 26.8 1.0
ND1 D:HIS137 4.6 27.4 1.0
CB D:SER147 4.7 34.0 1.0
CA D:ASP132 4.7 23.4 1.0
OD1 D:ASP123 4.9 20.5 1.0
CG2 D:THR150 4.9 14.9 1.0
CA D:CA237 5.0 28.2 1.0

Reference:

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
Page generated: Tue Dec 15 03:56:45 2020

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