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Manganese in PDB 2dvd: Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex

Protein crystallography data

The structure of Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex, PDB code: 2dvd was solved by S.K.Natchiar, O.Srinivas, N.Mitra, A.Surolia, N.Jayaraman, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 126.440, 124.640, 75.690, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.2

Other elements in 2dvd:

The structure of Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex (pdb code 2dvd). 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 Gal-Alpha-1,3-Gal Complex, PDB code: 2dvd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2dvd

Go back to Manganese Binding Sites List in 2dvd
Manganese binding site 1 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex


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 Gal-Alpha-1,3-Gal Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn238

b:47.4
occ:1.00
OD1 A:ASP132 2.1 30.8 1.0
OD2 A:ASP123 2.2 31.0 1.0
OE2 A:GLU121 2.2 23.0 1.0
O A:HOH1245 2.3 22.2 1.0
O A:HOH1244 2.4 19.9 1.0
NE2 A:HIS137 2.4 23.1 1.0
CG A:ASP132 3.1 31.0 1.0
CG A:ASP123 3.2 31.4 1.0
CD A:GLU121 3.2 22.7 1.0
CE1 A:HIS137 3.3 22.0 1.0
CD2 A:HIS137 3.5 24.4 1.0
OE1 A:GLU121 3.5 22.1 1.0
CB A:ASP123 3.6 29.6 1.0
OD2 A:ASP132 3.6 31.0 1.0
O A:HOH1242 3.7 20.0 1.0
CA A:CA237 4.1 28.7 1.0
O A:VAL145 4.1 24.5 1.0
CB A:ASP132 4.2 30.8 1.0
O A:HOH1333 4.2 17.9 1.0
OD1 A:ASP123 4.2 34.5 1.0
OG A:SER147 4.2 23.0 1.0
ND1 A:HIS137 4.5 22.7 1.0
CG A:GLU121 4.6 23.9 1.0
CG A:HIS137 4.6 24.5 1.0
CA A:ASP132 4.7 31.0 1.0
CD A:PRO133 4.9 30.0 1.0

Manganese binding site 2 out of 4 in 2dvd

Go back to Manganese Binding Sites List in 2dvd
Manganese binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex


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 Gal-Alpha-1,3-Gal Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn238

b:43.3
occ:1.00
OD2 B:ASP123 2.1 21.2 1.0
OD1 B:ASP132 2.2 26.1 1.0
OE2 B:GLU121 2.2 20.9 1.0
O B:HOH2245 2.3 20.2 1.0
O B:HOH2244 2.4 22.1 1.0
NE2 B:HIS137 2.4 28.7 1.0
CG B:ASP132 3.0 26.0 1.0
CG B:ASP123 3.1 21.3 1.0
CE1 B:HIS137 3.2 25.9 1.0
CD B:GLU121 3.2 21.1 1.0
OD2 B:ASP132 3.4 24.1 1.0
OE1 B:GLU121 3.5 19.7 1.0
CD2 B:HIS137 3.5 27.6 1.0
CB B:ASP123 3.5 23.3 1.0
O B:HOH2242 3.8 24.8 1.0
CA B:CA237 4.1 28.3 1.0
O B:VAL145 4.1 24.9 1.0
CB B:ASP132 4.2 26.4 1.0
OG B:SER147 4.2 23.5 1.0
OD1 B:ASP123 4.2 23.9 1.0
O B:HOH2311 4.3 25.5 1.0
ND1 B:HIS137 4.4 27.4 1.0
CG B:GLU121 4.6 20.9 1.0
CG B:HIS137 4.6 28.5 1.0
CA B:ASP132 4.7 27.6 1.0
CD B:PRO133 4.8 28.9 1.0

Manganese binding site 3 out of 4 in 2dvd

Go back to Manganese Binding Sites List in 2dvd
Manganese binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex


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 Gal-Alpha-1,3-Gal Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn238

b:48.0
occ:1.00
OD2 C:ASP123 2.2 33.0 1.0
OD1 C:ASP132 2.2 30.6 1.0
OE2 C:GLU121 2.3 24.7 1.0
O C:HOH3245 2.3 25.8 1.0
NE2 C:HIS137 2.3 29.1 1.0
O C:HOH3244 2.6 22.3 1.0
CG C:ASP132 3.1 32.0 1.0
CG C:ASP123 3.2 32.8 1.0
CE1 C:HIS137 3.2 28.9 1.0
CD2 C:HIS137 3.3 29.0 1.0
CD C:GLU121 3.3 26.0 1.0
OD2 C:ASP132 3.5 28.3 1.0
CB C:ASP123 3.6 32.1 1.0
OE1 C:GLU121 3.7 26.2 1.0
O C:HOH3242 4.0 27.4 1.0
CA C:CA237 4.1 30.6 1.0
O C:VAL145 4.2 29.9 1.0
O C:HOH3334 4.2 29.1 1.0
CB C:ASP132 4.2 32.6 1.0
OG C:SER147 4.2 27.1 1.0
OD1 C:ASP123 4.2 32.7 1.0
ND1 C:HIS137 4.3 28.7 1.0
CG C:HIS137 4.4 28.6 1.0
CG C:GLU121 4.6 25.2 1.0
CD C:PRO133 4.7 33.6 1.0
CA C:ASP132 4.7 33.9 1.0

Manganese binding site 4 out of 4 in 2dvd

Go back to Manganese Binding Sites List in 2dvd
Manganese binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex


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 Gal-Alpha-1,3-Gal Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn238

b:48.1
occ:1.00
OD1 D:ASP132 2.2 35.1 1.0
OE2 D:GLU121 2.2 22.0 1.0
OD2 D:ASP123 2.2 25.8 1.0
O D:HOH4245 2.3 24.7 1.0
O D:HOH4244 2.4 24.3 1.0
NE2 D:HIS137 2.4 27.5 1.0
CD D:GLU121 3.2 21.5 1.0
CG D:ASP123 3.2 26.9 1.0
CE1 D:HIS137 3.2 26.9 1.0
CG D:ASP132 3.3 32.9 1.0
CD2 D:HIS137 3.4 24.8 1.0
OE1 D:GLU121 3.5 20.0 1.0
CB D:ASP123 3.6 25.4 1.0
OD2 D:ASP132 4.0 33.3 1.0
OG D:SER147 4.1 24.7 1.0
O D:HOH4242 4.1 20.8 1.0
O D:VAL145 4.2 25.3 1.0
CA D:CA237 4.3 28.1 1.0
OD1 D:ASP123 4.3 26.0 1.0
O D:HOH4312 4.3 25.2 1.0
CB D:ASP132 4.4 30.6 1.0
ND1 D:HIS137 4.4 26.3 1.0
CG D:GLU121 4.5 20.5 1.0
CG D:HIS137 4.5 25.8 1.0
CA D:ASP132 4.7 29.0 1.0
CD D:PRO133 4.7 29.7 1.0

Reference:

S.K.Natchiar, O.Srinivas, N.Mitra, A.Surolia, N.Jayaraman, M.Vijayan. Structural Studies on Peanut Lectin Complexed with Disaccharides Involving Different Linkages: Further Insights Into the Structure and Interactions of the Lectin Acta Crystallogr.,Sect.D V. 62 1413 2006.
ISSN: ISSN 0907-4449
PubMed: 17057347
DOI: 10.1107/S0907444906035712
Page generated: Tue Dec 15 04:01:08 2020

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