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Manganese in PDB 2du1: Crystal Structure of Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine

Protein crystallography data

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine, PDB code: 2du1 was solved by K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 157.619, 90.960, 73.430, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25.1

Other elements in 2du1:

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine (pdb code 2du1). 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 Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine, PDB code: 2du1:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2du1

Go back to Manganese Binding Sites List in 2du1
Manganese binding site 1 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine


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 Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1300

b:41.1
occ:1.00
NE2 A:HIS136 2.3 29.3 1.0
O A:HOH1403 2.3 16.5 1.0
OE2 A:GLU122 2.3 29.5 1.0
OD2 A:ASP124 2.3 31.1 1.0
OD1 A:ASP131 2.4 40.8 1.0
O A:HOH1402 2.4 29.8 1.0
CG A:ASP131 3.0 38.8 1.0
CG A:ASP124 3.1 30.9 1.0
CE1 A:HIS136 3.2 30.4 1.0
CD2 A:HIS136 3.4 30.0 1.0
CD A:GLU122 3.4 30.1 1.0
OD2 A:ASP131 3.4 39.5 1.0
CB A:ASP124 3.5 29.7 1.0
OE1 A:GLU122 3.8 28.1 1.0
CB A:ASP131 4.1 38.2 1.0
OD1 A:ASP124 4.1 30.7 1.0
O A:HOH1404 4.3 24.6 1.0
ND1 A:HIS136 4.3 31.4 1.0
CA A:CA1303 4.3 33.5 1.0
OG A:SER146 4.4 37.1 1.0
CG A:HIS136 4.5 31.8 1.0
O A:VAL144 4.5 32.7 1.0
CA A:ASP131 4.7 38.4 1.0
CD A:PRO132 4.7 37.6 1.0
NE1 A:TRP130 4.7 45.7 1.0
O A:HOH1438 4.7 44.6 1.0
CG A:GLU122 4.7 28.0 1.0
CD1 A:TRP130 4.8 44.5 1.0

Manganese binding site 2 out of 4 in 2du1

Go back to Manganese Binding Sites List in 2du1
Manganese binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine


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 Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2300

b:34.0
occ:1.00
OD2 B:ASP124 2.2 31.4 1.0
OD1 B:ASP131 2.2 27.9 1.0
OE2 B:GLU122 2.3 23.8 1.0
O B:HOH2403 2.3 16.7 1.0
O B:HOH2402 2.4 19.7 1.0
NE2 B:HIS136 2.5 27.4 1.0
CG B:ASP131 3.2 28.4 1.0
CG B:ASP124 3.2 31.6 1.0
CE1 B:HIS136 3.3 24.9 1.0
CD B:GLU122 3.3 21.2 1.0
CD2 B:HIS136 3.5 25.1 1.0
CB B:ASP124 3.5 29.9 1.0
OE1 B:GLU122 3.6 23.1 1.0
OD2 B:ASP131 3.8 31.6 1.0
CB B:ASP131 4.1 29.8 1.0
OG B:SER146 4.2 22.6 1.0
CA B:CA2303 4.2 32.6 1.0
OD1 B:ASP124 4.3 30.6 1.0
O B:VAL144 4.4 30.0 1.0
ND1 B:HIS136 4.5 24.2 1.0
CG B:HIS136 4.6 25.5 1.0
CG B:GLU122 4.7 20.3 1.0
NE1 B:TRP130 4.7 38.1 1.0
CA B:ASP131 4.8 33.1 1.0
CD1 B:TRP130 4.8 37.2 1.0
CD B:PRO132 4.9 29.9 1.0

Manganese binding site 3 out of 4 in 2du1

Go back to Manganese Binding Sites List in 2du1
Manganese binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine


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 Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3300

b:50.6
occ:1.00
OD1 C:ASP131 2.2 43.2 1.0
O C:HOH3402 2.3 19.1 1.0
OD2 C:ASP124 2.3 40.1 1.0
OE2 C:GLU122 2.3 29.8 1.0
OE1 C:GLU122 2.9 30.9 1.0
CD C:GLU122 2.9 30.4 1.0
NE2 C:HIS136 3.0 31.7 1.0
CG C:ASP131 3.3 43.0 1.0
CG C:ASP124 3.3 39.1 1.0
CB C:ASP124 3.7 36.4 1.0
OD2 C:ASP131 3.7 47.0 1.0
CE1 C:HIS136 3.7 31.2 1.0
O C:HOH3403 3.8 20.9 1.0
O C:VAL144 3.9 38.1 1.0
CD2 C:HIS136 4.0 31.9 1.0
CA C:CA3303 4.1 41.5 1.0
OG C:SER146 4.1 44.4 1.0
CG C:GLU122 4.4 31.4 1.0
OD1 C:ASP124 4.4 42.2 1.0
NE1 C:TRP130 4.5 49.6 1.0
CB C:ASP131 4.6 42.0 1.0
O C:HOH3433 4.6 53.8 1.0
CD1 C:TRP130 4.7 48.3 1.0
CZ C:PHE107 4.7 38.0 1.0
CE2 C:PHE107 4.9 36.0 1.0
CG2 C:VAL144 4.9 41.9 1.0
ND1 C:HIS136 5.0 33.1 1.0

Manganese binding site 4 out of 4 in 2du1

Go back to Manganese Binding Sites List in 2du1
Manganese binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine


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 Basic Winged Bean Lectin in Complex with Methyl- Alpha-N-Acetyl-D Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn4300

b:40.9
occ:1.00
OD1 D:ASP131 2.2 33.4 1.0
O D:HOH4402 2.2 23.1 1.0
O D:HOH4403 2.3 28.6 1.0
NE2 D:HIS136 2.3 30.9 1.0
OE2 D:GLU122 2.3 32.9 1.0
OD2 D:ASP124 2.5 30.6 1.0
CE1 D:HIS136 3.1 29.6 1.0
CD D:GLU122 3.3 30.8 1.0
CG D:ASP124 3.4 32.1 1.0
CG D:ASP131 3.4 33.6 1.0
CD2 D:HIS136 3.5 29.5 1.0
CB D:ASP124 3.6 31.8 1.0
OE1 D:GLU122 3.6 27.3 1.0
O D:HOH4404 4.0 20.2 1.0
OG D:SER146 4.1 29.8 1.0
OD2 D:ASP131 4.2 32.0 1.0
CB D:ASP131 4.3 34.6 1.0
CA D:CA4303 4.3 36.2 1.0
ND1 D:HIS136 4.3 29.8 1.0
O D:VAL144 4.3 32.4 1.0
OD1 D:ASP124 4.5 33.8 1.0
CG D:HIS136 4.5 29.7 1.0
CG D:GLU122 4.7 28.7 1.0
CD D:PRO132 4.7 34.5 1.0
CA D:ASP131 4.8 37.7 1.0
NE1 D:TRP130 4.9 36.7 1.0
CD1 D:TRP130 4.9 36.5 1.0

Reference:

K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Structural Basis For the Carbohydrate-Specificity of Basic Winged-Bean Lectin and Its Differential Affinity For Gal and Galnac Acta Crystallogr.,Sect.D V. 62 1319 2006.
ISSN: ISSN 0907-4449
PubMed: 17057334
DOI: 10.1107/S0907444906028198
Page generated: Tue Dec 15 04:01:01 2020

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