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Manganese in PDB 2zmk: Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene

Protein crystallography data

The structure of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene, PDB code: 2zmk was solved by K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 156.921, 89.958, 73.321, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.6

Other elements in 2zmk:

The structure of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene (pdb code 2zmk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene, PDB code: 2zmk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2zmk

Go back to Manganese Binding Sites List in 2zmk
Manganese binding site 1 out of 4 in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:49.0
occ:1.00
NE2 A:HIS136 2.2 30.6 1.0
O A:HOH401 2.2 17.9 1.0
OD1 A:ASP131 2.2 42.3 1.0
OE2 A:GLU122 2.3 31.8 1.0
OD2 A:ASP124 2.3 36.8 1.0
O A:HOH447 2.3 35.0 1.0
CE1 A:HIS136 3.0 33.3 1.0
CG A:ASP131 3.2 40.5 1.0
CG A:ASP124 3.2 36.5 1.0
CD2 A:HIS136 3.3 32.2 1.0
CD A:GLU122 3.4 31.3 1.0
CB A:ASP124 3.5 36.1 1.0
OD2 A:ASP131 3.7 38.7 1.0
OE1 A:GLU122 3.8 31.4 1.0
OG A:SER146 4.2 37.4 1.0
ND1 A:HIS136 4.2 32.6 1.0
O A:HOH402 4.2 33.5 1.0
CB A:ASP131 4.3 40.9 1.0
OD1 A:ASP124 4.3 36.8 1.0
CG A:HIS136 4.4 32.8 1.0
CA A:CA302 4.5 34.6 1.0
O A:VAL144 4.5 35.4 1.0
CG A:GLU122 4.6 30.9 1.0
O A:HOH448 4.7 45.6 1.0
CD A:PRO132 4.8 39.2 1.0
NE1 A:TRP130 4.8 43.2 1.0
CA A:ASP131 4.8 39.5 1.0
CD1 A:TRP130 4.9 43.5 1.0

Manganese binding site 2 out of 4 in 2zmk

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Manganese binding site 2 out of 4 in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:40.7
occ:1.00
OD2 B:ASP124 2.2 37.4 1.0
OD1 B:ASP131 2.2 35.5 1.0
O B:HOH401 2.3 29.9 1.0
O B:HOH402 2.3 19.8 1.0
OE2 B:GLU122 2.3 27.5 1.0
NE2 B:HIS136 2.4 29.9 1.0
CG B:ASP131 3.0 36.6 1.0
CG B:ASP124 3.1 36.7 1.0
CE1 B:HIS136 3.1 29.4 1.0
OD2 B:ASP131 3.2 40.1 1.0
CD B:GLU122 3.4 28.1 1.0
CB B:ASP124 3.5 35.8 1.0
CD2 B:HIS136 3.5 29.4 1.0
OE1 B:GLU122 3.8 29.8 1.0
O B:HOH403 4.0 21.6 1.0
OD1 B:ASP124 4.2 37.7 1.0
CB B:ASP131 4.2 37.0 1.0
OG B:SER146 4.3 32.2 1.0
CA B:CA302 4.3 40.0 1.0
ND1 B:HIS136 4.3 28.9 1.0
O B:VAL144 4.4 34.1 1.0
CG B:HIS136 4.5 31.1 1.0
NE1 B:TRP130 4.7 41.6 1.0
CG B:GLU122 4.7 26.3 1.0
CD1 B:TRP130 4.8 41.4 1.0
CA B:ASP131 4.8 37.2 1.0
CD B:PRO132 4.8 34.3 1.0
CZ B:PHE107 5.0 31.1 1.0
CA B:ASP124 5.0 34.5 1.0

Manganese binding site 3 out of 4 in 2zmk

Go back to Manganese Binding Sites List in 2zmk
Manganese binding site 3 out of 4 in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:50.8
occ:1.00
O C:HOH401 2.2 27.7 1.0
OE2 C:GLU122 2.2 31.2 1.0
OD1 C:ASP131 2.3 42.6 1.0
NE2 C:HIS136 2.3 30.3 1.0
OD2 C:ASP124 2.3 45.5 1.0
CE1 C:HIS136 3.1 34.1 1.0
CG C:ASP124 3.2 41.0 1.0
CG C:ASP131 3.2 43.9 1.0
CD C:GLU122 3.3 31.6 1.0
CD2 C:HIS136 3.4 32.9 1.0
CB C:ASP124 3.5 38.5 1.0
OD2 C:ASP131 3.7 45.8 1.0
OE1 C:GLU122 3.7 31.7 1.0
OG C:SER146 4.1 38.7 1.0
ND1 C:HIS136 4.3 33.4 1.0
OD1 C:ASP124 4.3 41.4 1.0
CA C:CA302 4.3 40.1 1.0
CB C:ASP131 4.3 42.9 1.0
O C:VAL144 4.4 36.4 1.0
O C:HOH402 4.4 36.6 1.0
O C:HOH418 4.4 51.1 1.0
CG C:HIS136 4.5 34.0 1.0
CG C:GLU122 4.6 32.1 1.0
NE1 C:TRP130 4.8 45.4 1.0
CD C:PRO132 4.8 39.4 1.0
CA C:ASP131 4.9 41.6 1.0
CD1 C:TRP130 4.9 45.7 1.0
CA C:ASP124 5.0 36.3 1.0
CZ C:PHE107 5.0 34.7 1.0

Manganese binding site 4 out of 4 in 2zmk

Go back to Manganese Binding Sites List in 2zmk
Manganese binding site 4 out of 4 in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:44.9
occ:1.00
OD1 D:ASP131 2.2 40.8 1.0
NE2 D:HIS136 2.2 32.5 1.0
O D:HOH401 2.3 29.2 1.0
O D:HOH402 2.3 36.4 1.0
OE2 D:GLU122 2.4 31.4 1.0
OD2 D:ASP124 2.4 40.7 1.0
CE1 D:HIS136 3.0 31.7 1.0
CG D:ASP131 3.3 40.2 1.0
CG D:ASP124 3.3 41.1 1.0
CD2 D:HIS136 3.4 33.0 1.0
CD D:GLU122 3.4 29.9 1.0
CB D:ASP124 3.6 39.2 1.0
OE1 D:GLU122 3.8 29.2 1.0
OD2 D:ASP131 4.0 41.9 1.0
OG D:SER146 4.1 38.2 1.0
CB D:ASP131 4.2 40.4 1.0
O D:HOH403 4.2 22.7 1.0
ND1 D:HIS136 4.2 32.5 1.0
OD1 D:ASP124 4.4 41.3 1.0
O D:VAL144 4.4 34.1 1.0
CG D:HIS136 4.4 33.4 1.0
CA D:CA302 4.5 44.4 1.0
CD D:PRO132 4.7 37.7 1.0
CG D:GLU122 4.7 29.1 1.0
CA D:ASP131 4.8 41.2 1.0
NE1 D:TRP130 4.8 41.9 1.0
CD1 D:TRP130 4.8 42.0 1.0

Reference:

K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Structure and Sugar-Specificity of Basic Winged-Bean Lectin: Structures of New Disaccharide Complexes and A Comparative Study with Other Known Disaccharide Complexes of the Lectin. Acta Crystallogr.,Sect.D V. 64 730 2008.
ISSN: ISSN 0907-4449
PubMed: 18566508
DOI: 10.1107/S0907444908011323
Page generated: Tue Dec 15 04:07:09 2020

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