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Manganese in PDB 1wbf: Winged Bean Lectin, Saccharide Free Form

Protein crystallography data

The structure of Winged Bean Lectin, Saccharide Free Form, PDB code: 1wbf was solved by N.Manoj, V.R.Srinivas, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.159, 75.161, 95.772, 90.00, 106.91, 90.00
R / Rfree (%) 19.7 / 25.7

Other elements in 1wbf:

The structure of Winged Bean Lectin, Saccharide Free Form also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Winged Bean Lectin, Saccharide Free Form (pdb code 1wbf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Winged Bean Lectin, Saccharide Free Form, PDB code: 1wbf:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 1wbf

Go back to Manganese Binding Sites List in 1wbf
Manganese binding site 1 out of 2 in the Winged Bean Lectin, Saccharide Free Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Winged Bean Lectin, Saccharide Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:37.7
occ:1.00
O A:HOH664 2.2 22.3 1.0
OE2 A:GLU122 2.2 13.2 1.0
OD1 A:ASP131 2.3 28.0 1.0
O A:HOH663 2.4 44.8 1.0
OD2 A:ASP124 2.6 28.3 1.0
NE2 A:HIS136 2.9 18.9 1.0
CG A:ASP131 3.2 21.3 1.0
CD A:GLU122 3.2 21.9 1.0
CG A:ASP124 3.3 22.0 1.0
OD2 A:ASP131 3.4 24.6 1.0
OE1 A:GLU122 3.5 20.4 1.0
CB A:ASP124 3.7 19.9 1.0
CE1 A:HIS136 3.8 20.1 1.0
CD2 A:HIS136 3.8 21.7 1.0
O A:HOH665 4.0 19.2 1.0
CA A:CA303 4.1 23.1 1.0
OD1 A:ASP124 4.1 29.7 1.0
O A:VAL144 4.2 18.2 1.0
OG A:SER146 4.3 23.8 1.0
CB A:ASP131 4.5 17.6 1.0
CG A:GLU122 4.5 13.8 1.0
O A:HOH662 4.6 27.9 1.0
NE1 A:TRP130 4.6 34.9 1.0
CZ A:PHE107 4.8 17.4 1.0
CD1 A:TRP130 4.9 30.5 1.0
ND1 A:HIS136 5.0 22.2 1.0
CG A:HIS136 5.0 16.9 1.0

Manganese binding site 2 out of 2 in 1wbf

Go back to Manganese Binding Sites List in 1wbf
Manganese binding site 2 out of 2 in the Winged Bean Lectin, Saccharide Free Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Winged Bean Lectin, Saccharide Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:39.0
occ:1.00
O B:HOH679 2.2 41.6 1.0
OE2 B:GLU122 2.3 17.5 1.0
OD1 B:ASP131 2.3 14.4 1.0
O B:HOH678 2.4 30.1 1.0
OD2 B:ASP124 2.6 37.8 1.0
NE2 B:HIS136 2.7 7.2 1.0
CD B:GLU122 3.0 19.2 1.0
OE1 B:GLU122 3.0 13.5 1.0
CG B:ASP131 3.3 16.7 1.0
CG B:ASP124 3.3 30.2 1.0
CB B:ASP124 3.6 27.4 1.0
CE1 B:HIS136 3.6 6.0 1.0
CD2 B:HIS136 3.6 10.8 1.0
OD2 B:ASP131 3.7 18.8 1.0
OG B:SER146 4.1 15.6 1.0
O B:HOH680 4.2 14.3 1.0
OD1 B:ASP124 4.4 47.5 1.0
CG B:GLU122 4.4 17.6 1.0
CA B:CA303 4.5 23.6 1.0
O B:VAL144 4.5 23.8 1.0
CB B:ASP131 4.5 8.9 1.0
O B:HOH677 4.6 22.1 1.0
ND1 B:HIS136 4.7 9.9 1.0
CG B:HIS136 4.8 6.4 1.0
NE1 B:TRP130 4.8 24.3 1.0
CZ B:PHE107 5.0 13.2 1.0

Reference:

N.Manoj, V.R.Srinivas, K.Suguna. Structure of Basic Winged-Bean Lectin and A Comparison with Its Saccharide-Bound Form. Acta Crystallogr.,Sect.D V. 55 794 1999.
ISSN: ISSN 0907-4449
PubMed: 10089310
DOI: 10.1107/S090744499900044X
Page generated: Tue Dec 15 03:57:20 2020

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