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Manganese in PDB 3uk9: Galactose-Specific Lectin From Dolichos Lablab

Protein crystallography data

The structure of Galactose-Specific Lectin From Dolichos Lablab, PDB code: 3uk9 was solved by K.N.Shetty, V.L.Latha, R.N.Rao, S.K.Nadimpalli, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.17 / 3.11
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.990, 84.130, 93.159, 89.92, 76.01, 77.00
R / Rfree (%) 25.1 / 30.6

Other elements in 3uk9:

The structure of Galactose-Specific Lectin From Dolichos Lablab also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Galactose-Specific Lectin From Dolichos Lablab (pdb code 3uk9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Galactose-Specific Lectin From Dolichos Lablab, PDB code: 3uk9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3uk9

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Manganese binding site 1 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn307

b:49.9
occ:1.00
 NE2 A:HIS161 2.0 45.3 1.0
OD1 A:ASP156 2.1 53.1 1.0
OE2 A:GLU146 2.2 41.4 1.0
OD2 A:ASP148 2.4 44.0 1.0
O A:HOH401 2.6 2.0 1.0
CE1 A:HIS161 2.9 46.4 1.0
CD2 A:HIS161 3.1 44.0 1.0
CG A:ASP156 3.1 54.5 1.0
CD A:GLU146 3.3 40.0 1.0
CG A:ASP148 3.4 43.4 1.0
OD2 A:ASP156 3.5 53.8 1.0
CB A:ASP148 3.6 41.9 1.0
OE1 A:GLU146 3.8 40.4 1.0
O A:HOH403 3.9 2.0 1.0
ND1 A:HIS161 4.1 46.1 1.0
CG A:HIS161 4.2 44.7 1.0
CA A:CA306 4.3 45.5 1.0
CB A:ASP156 4.3 56.8 1.0
CG A:GLU146 4.4 38.2 1.0
OD1 A:ASP148 4.5 43.7 1.0
CD A:PRO157 4.7 55.2 1.0
CA A:ASP156 4.8 58.3 1.0
CD1 A:TRP155 4.8 58.7 1.0
OG A:SER171 4.8 41.4 1.0

Manganese binding site 2 out of 8 in 3uk9

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Manganese binding site 2 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn304

b:40.1
occ:1.00
 OD1 B:ASP156 2.0 69.2 1.0
OE2 B:GLU146 2.0 55.8 1.0
NE2 B:HIS161 2.0 60.9 1.0
OD2 B:ASP148 2.2 59.8 1.0
CD2 B:HIS161 3.0 59.0 1.0
CE1 B:HIS161 3.1 62.8 1.0
CG B:ASP156 3.1 71.1 1.0
CD B:GLU146 3.2 54.4 1.0
O B:HOH401 3.3 2.0 1.0
CG B:ASP148 3.3 60.3 1.0
OD2 B:ASP156 3.8 72.3 1.0
OE1 B:GLU146 3.9 55.5 1.0
CB B:ASP148 3.9 58.4 1.0
OG B:SER171 3.9 48.8 1.0
CG B:HIS161 4.1 59.6 1.0
ND1 B:HIS161 4.2 62.0 1.0
CB B:ASP156 4.2 72.6 1.0
CG B:GLU146 4.4 51.6 1.0
OD1 B:ASP148 4.4 62.0 1.0
CA B:ASP156 4.5 72.7 1.0
CD1 B:TRP155 4.7 73.3 1.0
CA B:CA303 4.7 48.1 1.0
O B:ILE169 4.7 54.5 1.0
CD B:PRO157 4.9 68.9 1.0
CB B:SER171 4.9 48.9 1.0
CG2 B:THR174 5.0 49.9 1.0

Manganese binding site 3 out of 8 in 3uk9

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Manganese binding site 3 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn305

b:35.3
occ:1.00
 OE2 C:GLU146 1.9 43.0 1.0
O C:HOH404 1.9 2.0 1.0
OD1 C:ASP156 2.0 50.9 1.0
NE2 C:HIS161 2.1 42.2 1.0
O C:HOH401 2.5 2.0 1.0
OD2 C:ASP148 2.5 44.5 1.0
CD C:GLU146 3.0 41.5 1.0
CE1 C:HIS161 3.0 44.0 1.0
CG C:ASP156 3.0 52.4 1.0
O C:HOH402 3.2 2.0 1.0
CD2 C:HIS161 3.2 41.7 1.0
OE1 C:GLU146 3.4 42.3 1.0
CG C:ASP148 3.5 44.2 1.0
OD2 C:ASP156 3.5 52.7 1.0
CB C:ASP148 3.7 42.7 1.0
CA C:CA304 4.1 34.6 1.0
ND1 C:HIS161 4.1 44.5 1.0
OG C:SER171 4.2 38.3 1.0
CB C:ASP156 4.2 54.6 1.0
CG C:GLU146 4.2 38.9 1.0
CG C:HIS161 4.3 43.3 1.0
CA C:ASP156 4.6 55.4 1.0
CD1 C:TRP155 4.6 54.6 1.0
OD1 C:ASP148 4.6 45.3 1.0
CD C:PRO157 4.6 53.0 1.0
O C:ILE169 4.8 41.3 1.0
NE1 C:TRP155 4.8 54.3 1.0

Manganese binding site 4 out of 8 in 3uk9

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Manganese binding site 4 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn304

b:48.2
occ:1.00
 OD2 D:ASP148 2.0 49.3 1.0
NE2 D:HIS161 2.2 50.6 1.0
O D:HOH401 2.3 2.2 1.0
OD1 D:ASP156 2.4 57.9 1.0
OE2 D:GLU146 2.5 47.0 1.0
CG D:ASP148 3.1 48.3 1.0
CD2 D:HIS161 3.1 49.3 1.0
CG D:ASP156 3.1 58.5 1.0
CD D:GLU146 3.1 45.5 1.0
CE1 D:HIS161 3.2 51.6 1.0
OE1 D:GLU146 3.3 46.4 1.0
OD2 D:ASP156 3.5 57.7 1.0
CB D:ASP148 3.6 46.2 1.0
O D:HOH402 3.8 2.0 1.0
OD1 D:ASP148 4.1 49.5 1.0
CG D:HIS161 4.3 49.3 1.0
CB D:ASP156 4.3 60.4 1.0
ND1 D:HIS161 4.3 51.1 1.0
CA D:CA303 4.3 56.6 1.0
CG D:GLU146 4.4 43.1 1.0
OG D:SER171 4.4 41.9 1.0
CD1 D:TRP155 4.7 61.5 1.0
CA D:ASP156 4.8 61.9 1.0
NE1 D:TRP155 4.8 60.5 1.0
O D:ILE169 4.9 45.0 1.0

Manganese binding site 5 out of 8 in 3uk9

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Manganese binding site 5 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn304

b:56.5
occ:1.00
 OE2 E:GLU146 2.1 47.0 1.0
NE2 E:HIS161 2.1 41.1 1.0
O E:HOH401 2.1 2.0 1.0
OD1 E:ASP156 2.2 51.4 1.0
OD2 E:ASP148 2.9 46.4 1.0
CD2 E:HIS161 3.0 40.5 1.0
CE1 E:HIS161 3.0 42.1 1.0
CD E:GLU146 3.1 45.3 1.0
CG E:ASP156 3.3 52.0 1.0
OE1 E:GLU146 3.6 45.8 1.0
OG E:SER171 3.9 37.3 1.0
CG E:ASP148 3.9 45.1 1.0
OD2 E:ASP156 4.0 51.7 1.0
ND1 E:HIS161 4.1 42.3 1.0
CG E:HIS161 4.1 41.2 1.0
CB E:ASP148 4.1 43.4 1.0
CG E:GLU146 4.2 42.8 1.0
CB E:ASP156 4.3 53.5 1.0
O E:ILE169 4.4 41.3 1.0
CA E:ASP156 4.4 55.1 1.0
CD E:PRO157 4.5 52.6 1.0
CD1 E:TRP155 4.6 57.1 1.0
CG2 E:THR174 4.8 36.1 1.0
CA E:CA303 4.9 47.6 1.0
CB E:SER171 4.9 38.8 1.0
NE1 E:TRP155 5.0 56.5 1.0

Manganese binding site 6 out of 8 in 3uk9

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Manganese binding site 6 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn304

b:73.9
occ:1.00
 O F:HOH402 2.0 2.0 1.0
OD1 F:ASP156 2.0 94.7 1.0
NE2 F:HIS161 2.2 85.5 1.0
O F:HOH401 2.3 2.0 1.0
OE2 F:GLU146 2.4 80.8 1.0
OD2 F:ASP148 2.5 88.5 1.0
CG F:ASP156 3.1 97.5 1.0
CE1 F:HIS161 3.1 88.2 1.0
CD2 F:HIS161 3.3 82.7 1.0
CD F:GLU146 3.4 79.1 1.0
O F:HOH403 3.4 20.6 1.0
CG F:ASP148 3.5 88.2 1.0
OE1 F:GLU146 3.7 81.0 1.0
OD2 F:ASP156 3.7 99.1 1.0
CB F:ASP148 3.9 84.7 1.0
CB F:ASP156 4.2 99.7 1.0
ND1 F:HIS161 4.3 87.1 1.0
CA F:ASP156 4.4 99.1 1.0
OG F:SER171 4.4 68.0 1.0
O F:ILE169 4.4 77.2 1.0
CD1 F:TRP155 4.4 99.4 1.0
CG F:HIS161 4.4 83.6 1.0
CD F:PRO157 4.5 93.0 1.0
CG F:GLU146 4.6 75.1 1.0
OD1 F:ASP148 4.6 91.0 1.0
CA F:CA303 4.8 86.9 1.0
NE1 F:TRP155 4.8 0.4 1.0

Manganese binding site 7 out of 8 in 3uk9

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Manganese binding site 7 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn305

b:32.6
occ:1.00
 OE2 G:GLU146 1.9 44.1 1.0
NE2 G:HIS161 2.1 47.2 1.0
OD1 G:ASP156 2.1 50.5 1.0
OD2 G:ASP148 2.4 44.9 1.0
O G:HOH401 2.5 2.0 1.0
CE1 G:HIS161 3.0 48.5 1.0
CD G:GLU146 3.1 42.4 1.0
CD2 G:HIS161 3.1 46.0 1.0
CG G:ASP156 3.1 52.2 1.0
CG G:ASP148 3.4 44.0 1.0
CB G:ASP148 3.6 42.1 1.0
O G:HOH403 3.6 2.0 1.0
OE1 G:GLU146 3.7 43.3 1.0
OD2 G:ASP156 3.8 52.2 1.0
CB G:ASP156 4.1 54.3 1.0
ND1 G:HIS161 4.1 48.4 1.0
CG G:GLU146 4.2 39.4 1.0
CG G:HIS161 4.2 46.8 1.0
CA G:CA304 4.3 30.7 1.0
OG G:SER171 4.5 41.6 1.0
OD1 G:ASP148 4.5 44.7 1.0
CA G:ASP156 4.5 55.2 1.0
CD G:PRO157 4.6 52.4 1.0
CD1 G:TRP155 4.6 54.0 1.0
NE1 G:TRP155 4.7 53.3 1.0
O G:ILE169 4.9 45.1 1.0

Manganese binding site 8 out of 8 in 3uk9

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Manganese binding site 8 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn302

b:64.5
occ:1.00
 O H:HOH401 1.9 2.0 1.0
OD2 H:ASP148 2.0 71.8 1.0
NE2 H:HIS161 2.1 70.5 1.0
OD1 H:ASP156 2.1 79.2 1.0
OE2 H:GLU146 2.9 69.5 1.0
CE1 H:HIS161 3.0 72.5 1.0
CG H:ASP156 3.0 80.6 1.0
CD2 H:HIS161 3.1 69.0 1.0
CG H:ASP148 3.1 71.8 1.0
CD H:GLU146 3.4 67.8 1.0
OE1 H:GLU146 3.4 68.9 1.0
OD2 H:ASP156 3.4 80.6 1.0
CB H:ASP148 3.7 70.2 1.0
O H:HOH402 3.9 2.0 1.0
ND1 H:HIS161 4.1 72.3 1.0
OG H:SER171 4.2 60.9 1.0
OD1 H:ASP148 4.2 73.0 1.0
CG H:HIS161 4.2 70.2 1.0
CB H:ASP156 4.3 83.1 1.0
CA H:CA301 4.3 30.1 1.0
CG H:GLU146 4.6 64.7 1.0
CA H:ASP156 4.7 84.2 1.0
CD1 H:TRP155 4.8 82.1 1.0
CD H:PRO157 4.9 81.4 1.0
NE1 H:TRP155 4.9 81.3 1.0

Reference:

K.N.Shetty, V.L.Latha, R.N.Rao, S.K.Nadimpalli, K.Suguna. Affinity of A Galactose-Specific Legume Lectin From Dolichos Lablab to Adenine Revealed By X-Ray Cystallography. Iubmb Life V. 65 633 2013.
ISSN: ISSN 1521-6543
PubMed: 23794513
DOI: 10.1002/IUB.1177
Page generated: Sat Oct 5 18:05:14 2024

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