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Manganese in PDB 1fay: Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)

Protein crystallography data

The structure of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form), PDB code: 1fay was solved by N.Manoj, V.R.Srinivas, 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) 20.00 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.530, 125.910, 138.790, 90.00, 95.89, 90.00
R / Rfree (%) 20.4 / 24.2

Other elements in 1fay:

The structure of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) (pdb code 1fay). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form), PDB code: 1fay:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1fay

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Manganese binding site 1 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic 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 Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:35.3
occ:1.00
 OD1 A:ASP132 2.1 24.1 1.0
NE2 A:HIS137 2.1 20.8 1.0
O A:HOH507 2.2 21.2 1.0
O A:HOH506 2.2 43.7 1.0
OE2 A:GLU123 2.3 6.9 1.0
OD2 A:ASP125 2.3 4.9 1.0
CE1 A:HIS137 3.1 20.8 1.0
CD2 A:HIS137 3.1 20.8 1.0
CG A:ASP132 3.2 24.1 1.0
CG A:ASP125 3.3 4.9 1.0
CD A:GLU123 3.3 6.9 1.0
CB A:ASP125 3.5 4.9 1.0
OE1 A:GLU123 3.7 6.9 1.0
OG A:SER147 3.7 29.6 1.0
OD2 A:ASP132 3.9 24.1 1.0
O A:HOH508 4.2 18.1 1.0
ND1 A:HIS137 4.2 20.8 1.0
CB A:ASP132 4.2 24.1 1.0
CG A:HIS137 4.3 20.8 1.0
OD1 A:ASP125 4.4 4.9 1.0
O A:ILE145 4.5 18.3 1.0
CD A:PRO133 4.6 28.5 1.0
CG A:GLU123 4.6 6.9 1.0
CA A:ASP132 4.7 15.8 1.0
CA A:CA303 4.8 35.3 1.0
NE1 A:TRP131 4.9 31.1 1.0
CD1 A:TRP131 4.9 31.1 1.0

Manganese binding site 2 out of 8 in 1fay

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Manganese binding site 2 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic 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 Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:35.3
occ:1.00
 O B:HOH505 2.1 43.7 1.0
O B:HOH514 2.1 19.1 1.0
OE2 B:GLU123 2.1 21.1 1.0
NE2 B:HIS137 2.2 12.6 1.0
OD1 B:ASP132 2.3 30.4 1.0
OD2 B:ASP125 2.4 19.2 1.0
CD2 B:HIS137 3.1 12.6 1.0
CD B:GLU123 3.1 21.1 1.0
CE1 B:HIS137 3.2 12.6 1.0
CG B:ASP125 3.3 19.2 1.0
CG B:ASP132 3.4 30.4 1.0
CB B:ASP125 3.5 19.2 1.0
OE1 B:GLU123 3.6 21.1 1.0
OG B:SER147 3.6 9.2 1.0
OD2 B:ASP132 4.0 30.4 1.0
ND1 B:HIS137 4.3 12.6 1.0
CG B:HIS137 4.3 12.6 1.0
CG B:GLU123 4.4 21.1 1.0
CB B:ASP132 4.4 30.4 1.0
O B:ILE145 4.5 20.0 1.0
OD1 B:ASP125 4.5 19.2 1.0
CD B:PRO133 4.7 18.7 1.0
CA B:CA303 4.7 35.3 1.0
CA B:ASP132 4.9 14.6 1.0
NE1 B:TRP131 4.9 14.8 1.0
CB B:SER147 5.0 9.2 1.0
CD1 B:TRP131 5.0 14.8 1.0
CA B:ASP125 5.0 7.2 1.0

Manganese binding site 3 out of 8 in 1fay

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Manganese binding site 3 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn300

b:35.3
occ:1.00
 O C:HOH506 2.0 21.2 1.0
NE2 C:HIS137 2.1 21.0 1.0
O C:HOH505 2.1 43.7 1.0
OE2 C:GLU123 2.1 33.2 1.0
OD1 C:ASP132 2.2 25.3 1.0
OD2 C:ASP125 2.3 24.8 1.0
CD2 C:HIS137 3.1 21.0 1.0
CE1 C:HIS137 3.1 21.0 1.0
CD C:GLU123 3.2 33.2 1.0
CG C:ASP125 3.2 24.8 1.0
CG C:ASP132 3.3 25.3 1.0
CB C:ASP125 3.4 24.8 1.0
OE1 C:GLU123 3.6 33.2 1.0
OG C:SER147 3.7 39.1 1.0
OD2 C:ASP132 4.0 25.3 1.0
ND1 C:HIS137 4.2 21.0 1.0
CG C:HIS137 4.2 21.0 1.0
CB C:ASP132 4.3 25.3 1.0
OD1 C:ASP125 4.4 24.8 1.0
CG C:GLU123 4.4 33.2 1.0
O C:ILE145 4.5 32.2 1.0
CD C:PRO133 4.7 16.1 1.0
CA C:CA303 4.8 35.3 1.0
CA C:ASP132 4.8 12.9 1.0
O C:HOH504 4.8 26.8 1.0
CA C:ASP125 4.9 10.9 1.0
NE1 C:TRP131 5.0 21.9 1.0

Manganese binding site 4 out of 8 in 1fay

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Manganese binding site 4 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn300

b:35.3
occ:1.00
 OE2 D:GLU123 2.1 14.8 1.0
NE2 D:HIS137 2.2 18.9 1.0
O D:HOH505 2.2 43.7 1.0
OD1 D:ASP132 2.2 51.9 1.0
O D:HOH506 2.2 18.1 1.0
OD2 D:ASP125 2.3 14.5 1.0
CE1 D:HIS137 3.1 18.9 1.0
CD2 D:HIS137 3.1 18.9 1.0
CD D:GLU123 3.2 14.8 1.0
CG D:ASP125 3.2 14.5 1.0
CG D:ASP132 3.3 51.9 1.0
CB D:ASP125 3.5 14.5 1.0
OE1 D:GLU123 3.6 14.8 1.0
OG D:SER147 3.7 30.9 1.0
OD2 D:ASP132 3.9 51.9 1.0
ND1 D:HIS137 4.3 18.9 1.0
CG D:HIS137 4.3 18.9 1.0
CB D:ASP132 4.3 51.9 1.0
OD1 D:ASP125 4.4 14.5 1.0
CG D:GLU123 4.4 14.8 1.0
O D:ILE145 4.4 19.2 1.0
CD D:PRO133 4.7 28.6 1.0
CA D:CA303 4.8 35.3 1.0
O D:HOH504 4.8 26.8 1.0
CA D:ASP132 4.8 28.8 1.0
NE1 D:TRP131 4.9 50.7 1.0
CD1 D:TRP131 5.0 50.7 1.0
CA D:ASP125 5.0 4.3 1.0

Manganese binding site 5 out of 8 in 1fay

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Manganese binding site 5 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn300

b:35.3
occ:1.00
 OD1 E:ASP132 2.1 40.0 1.0
O E:HOH504 2.1 26.8 1.0
OD2 E:ASP125 2.2 15.1 1.0
OE2 E:GLU123 2.2 33.3 1.0
NE2 E:HIS137 2.2 20.3 1.0
O E:HOH506 2.3 21.2 1.0
CE1 E:HIS137 3.2 20.3 1.0
CG E:ASP132 3.2 40.0 1.0
CG E:ASP125 3.2 15.1 1.0
CD E:GLU123 3.2 33.3 1.0
CD2 E:HIS137 3.3 20.3 1.0
CB E:ASP125 3.5 15.1 1.0
OE1 E:GLU123 3.6 33.3 1.0
OD2 E:ASP132 3.8 40.0 1.0
OG E:SER147 3.8 33.1 1.0
CB E:ASP132 4.2 40.0 1.0
ND1 E:HIS137 4.3 20.3 1.0
OD1 E:ASP125 4.3 15.1 1.0
CG E:HIS137 4.4 20.3 1.0
O E:ILE145 4.4 30.9 1.0
CG E:GLU123 4.5 33.3 1.0
CA E:CA303 4.7 35.3 1.0
CD E:PRO133 4.7 44.1 1.0
CA E:ASP132 4.7 50.1 1.0
NE1 E:TRP131 4.7 30.8 1.0
O E:HOH513 4.8 18.9 1.0
CD1 E:TRP131 4.8 30.8 1.0
CA E:ASP125 5.0 13.6 1.0

Manganese binding site 6 out of 8 in 1fay

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Manganese binding site 6 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn300

b:35.3
occ:1.00
 OE2 F:GLU123 2.1 53.1 1.0
OD1 F:ASP132 2.2 45.5 1.0
NE2 F:HIS137 2.2 9.7 1.0
OD2 F:ASP125 2.2 40.5 1.0
O F:HOH505 2.3 43.7 1.0
O F:HOH506 2.5 18.1 1.0
CD F:GLU123 3.2 53.1 1.0
CE1 F:HIS137 3.2 9.7 1.0
CG F:ASP125 3.2 40.5 1.0
CD2 F:HIS137 3.2 9.7 1.0
CG F:ASP132 3.3 45.5 1.0
CB F:ASP125 3.5 40.5 1.0
OE1 F:GLU123 3.6 53.1 1.0
OG F:SER147 3.8 25.6 1.0
OD2 F:ASP132 3.9 45.5 1.0
ND1 F:HIS137 4.3 9.7 1.0
CB F:ASP132 4.3 45.5 1.0
OD1 F:ASP125 4.3 40.5 1.0
CG F:HIS137 4.4 9.7 1.0
O F:ILE145 4.4 12.6 1.0
CG F:GLU123 4.4 53.1 1.0
CA F:CA303 4.7 35.3 1.0
CD F:PRO133 4.7 12.4 1.0
CA F:ASP132 4.8 18.4 1.0
NE1 F:TRP131 4.8 56.1 1.0
O F:HOH517 4.9 18.9 1.0
CD1 F:TRP131 4.9 56.1 1.0
CA F:ASP125 4.9 10.6 1.0

Manganese binding site 7 out of 8 in 1fay

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Manganese binding site 7 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn300

b:35.3
occ:1.00
 OE2 G:GLU123 2.1 54.2 1.0
OD2 G:ASP125 2.2 51.8 1.0
O G:HOH412 2.2 18.9 1.0
OD1 G:ASP132 2.2 82.9 1.0
NE2 G:HIS137 2.2 30.4 1.0
O G:HOH408 2.3 21.2 1.0
CD G:GLU123 3.1 54.2 1.0
CG G:ASP125 3.1 51.8 1.0
CE1 G:HIS137 3.2 30.4 1.0
CD2 G:HIS137 3.2 30.4 1.0
CG G:ASP132 3.3 82.9 1.0
CB G:ASP125 3.4 51.8 1.0
OE1 G:GLU123 3.5 54.2 1.0
OG G:SER147 3.8 52.9 1.0
OD2 G:ASP132 3.9 82.9 1.0
OD1 G:ASP125 4.3 51.8 1.0
ND1 G:HIS137 4.3 30.4 1.0
CG G:HIS137 4.4 30.4 1.0
CB G:ASP132 4.4 82.9 1.0
CG G:GLU123 4.4 54.2 1.0
O G:ILE145 4.5 39.5 1.0
CA G:CA303 4.6 35.3 1.0
O G:HOH407 4.7 43.7 1.0
CD G:PRO133 4.8 75.1 1.0
NE1 G:TRP131 4.8 59.0 1.0
O G:HOH409 4.8 18.1 1.0
CA G:ASP125 4.9 36.2 1.0
CA G:ASP132 4.9 49.0 1.0
CD1 G:TRP131 4.9 59.0 1.0

Manganese binding site 8 out of 8 in 1fay

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Manganese binding site 8 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn300

b:35.3
occ:1.00
 O H:HOH409 2.1 43.7 1.0
OE2 H:GLU123 2.1 66.5 1.0
OD1 H:ASP132 2.2 46.7 1.0
OD2 H:ASP125 2.3 68.7 1.0
NE2 H:HIS137 2.3 31.8 1.0
O H:HOH410 2.5 21.2 1.0
CD H:GLU123 3.1 66.5 1.0
CG H:ASP125 3.3 68.7 1.0
CE1 H:HIS137 3.3 31.8 1.0
CD2 H:HIS137 3.3 31.8 1.0
CG H:ASP132 3.3 46.7 1.0
OE1 H:GLU123 3.5 66.5 1.0
CB H:ASP125 3.5 68.7 1.0
OG H:SER147 3.7 53.6 1.0
OD2 H:ASP132 3.9 46.7 1.0
O H:ILE145 4.3 37.3 1.0
CB H:ASP132 4.4 46.7 1.0
CG H:GLU123 4.4 66.5 1.0
ND1 H:HIS137 4.4 31.8 1.0
OD1 H:ASP125 4.4 68.7 1.0
CG H:HIS137 4.4 31.8 1.0
O H:HOH408 4.6 26.8 1.0
CA H:CA303 4.7 35.3 1.0
CD H:PRO133 4.8 86.2 1.0
NE1 H:TRP131 4.8 88.9 1.0
O H:HOH413 4.8 18.9 1.0
CA H:ASP132 4.9 35.8 1.0
CD1 H:TRP131 4.9 88.9 1.0
CA H:ASP125 5.0 82.5 1.0

Reference:

N.Manoj, V.R.Srinivas, A.Surolia, M.Vijayan, K.Suguna. Carbohydrate Specificity and Salt-Bridge Mediated Conformational Change in Acidic Winged Bean Agglutinin. J.Mol.Biol. V. 302 1129 2000.
ISSN: ISSN 0022-2836
PubMed: 11183779
DOI: 10.1006/JMBI.2000.4111
Page generated: Sat Oct 5 10:20:26 2024

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