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Manganese in PDB 1cr7: Peanut Lectin-Lactose Complex Monoclinic Form

Protein crystallography data

The structure of Peanut Lectin-Lactose Complex Monoclinic Form, PDB code: 1cr7 was solved by R.Ravishankar, K.Suguna, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.320, 126.820, 85.610, 90.00, 116.14, 90.00
R / Rfree (%) 20.7 / 27.2

Other elements in 1cr7:

The structure of Peanut Lectin-Lactose Complex Monoclinic Form also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Peanut Lectin-Lactose Complex Monoclinic Form (pdb code 1cr7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Peanut Lectin-Lactose Complex Monoclinic Form, PDB code: 1cr7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1cr7

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Manganese binding site 1 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1238

b:27.0
occ:1.00
 O A:HOH1257 1.9 12.1 1.0
OD1 A:ASP123 2.0 16.1 1.0
OE2 A:GLU121 2.0 14.1 1.0
O A:HOH1258 2.1 14.2 1.0
NE2 A:HIS137 2.2 14.4 1.0
OD1 A:ASP132 2.3 5.9 1.0
CG A:ASP123 3.0 19.6 1.0
CE1 A:HIS137 3.1 15.8 1.0
CD A:GLU121 3.1 14.1 1.0
CG A:ASP132 3.2 5.9 1.0
CB A:ASP123 3.3 17.9 1.0
CD2 A:HIS137 3.3 12.7 1.0
OE1 A:GLU121 3.5 14.1 1.0
OD2 A:ASP132 3.5 5.9 1.0
O A:HOH1255 3.9 2.0 1.0
OD2 A:ASP123 4.1 18.3 1.0
CA A:CA1237 4.1 15.4 1.0
OG A:SER147 4.1 5.7 1.0
ND1 A:HIS137 4.2 18.4 1.0
CG A:HIS137 4.4 17.7 1.0
CG A:GLU121 4.4 14.1 1.0
O A:VAL145 4.4 8.7 1.0
CB A:ASP132 4.5 5.9 1.0
CD A:PRO133 4.7 17.1 1.0
CA A:ASP123 4.8 4.2 1.0
CA A:ASP132 4.9 12.6 1.0
O A:HOH1267 4.9 19.5 1.0

Manganese binding site 2 out of 8 in 1cr7

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Manganese binding site 2 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2238

b:28.6
occ:1.00
 O B:HOH2263 1.8 5.5 1.0
OE2 B:GLU121 1.9 12.6 1.0
O B:HOH2262 2.3 7.0 1.0
OD1 B:ASP132 2.4 16.4 1.0
OD1 B:ASP123 2.4 7.7 1.0
NE2 B:HIS137 2.5 26.6 1.0
CD B:GLU121 2.8 14.8 1.0
OE1 B:GLU121 3.1 15.2 1.0
CG B:ASP132 3.4 14.8 1.0
CG B:ASP123 3.4 7.7 1.0
CD2 B:HIS137 3.5 24.2 1.0
CE1 B:HIS137 3.5 23.5 1.0
OG B:SER147 3.7 2.0 1.0
CB B:ASP123 3.7 7.7 1.0
OD2 B:ASP132 3.8 16.0 1.0
O B:HOH2266 3.9 8.2 1.0
O B:VAL145 4.0 14.3 1.0
O B:HOH2260 4.2 21.9 1.0
CG B:GLU121 4.2 8.4 1.0
CA B:CA2237 4.4 13.1 1.0
OD2 B:ASP123 4.6 7.7 1.0
ND1 B:HIS137 4.6 27.5 1.0
CG B:HIS137 4.6 24.0 1.0
CB B:ASP132 4.7 11.8 1.0
CD B:PRO133 4.8 10.6 1.0
CB B:SER147 4.8 2.0 1.0
CA B:ASP132 4.9 29.1 1.0
CG2 B:THR150 5.0 9.6 1.0

Manganese binding site 3 out of 8 in 1cr7

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Manganese binding site 3 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3238

b:46.5
occ:1.00
 OE2 C:GLU121 1.9 29.0 1.0
OD1 C:ASP123 2.0 6.5 1.0
O C:HOH3261 2.3 36.7 1.0
O C:HOH3262 2.5 36.0 1.0
OD1 C:ASP132 2.5 6.4 1.0
NE2 C:HIS137 2.5 32.9 1.0
CD C:GLU121 2.9 29.5 1.0
CG C:ASP123 3.1 7.8 1.0
OE1 C:GLU121 3.2 28.8 1.0
CD2 C:HIS137 3.3 29.2 1.0
CG C:ASP132 3.4 6.4 1.0
CE1 C:HIS137 3.5 26.0 1.0
CB C:ASP123 3.5 6.8 1.0
OD2 C:ASP132 3.8 6.4 1.0
OG C:SER147 3.8 13.5 1.0
O C:HOH3259 4.0 16.6 1.0
O C:VAL145 4.1 16.8 1.0
OD2 C:ASP123 4.2 12.0 1.0
CG C:GLU121 4.3 26.9 1.0
CG C:HIS137 4.5 28.7 1.0
ND1 C:HIS137 4.5 30.0 1.0
CA C:CA3237 4.6 10.2 1.0
CB C:ASP132 4.7 6.4 1.0
CD C:PRO133 4.9 34.0 1.0
CA C:ASP132 4.9 35.6 1.0
CA C:ASP123 5.0 9.2 1.0
CG2 C:THR150 5.0 37.8 1.0

Manganese binding site 4 out of 8 in 1cr7

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Manganese binding site 4 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn4238

b:39.8
occ:1.00
 O D:HOH4247 1.8 25.4 1.0
NE2 D:HIS137 2.0 10.1 1.0
OE2 D:GLU121 2.0 24.6 1.0
OD1 D:ASP132 2.2 24.8 1.0
O D:HOH4248 2.3 47.8 1.0
OD1 D:ASP123 2.7 35.5 1.0
CD2 D:HIS137 3.0 10.1 1.0
CE1 D:HIS137 3.1 10.1 1.0
CG D:ASP132 3.1 23.1 1.0
CD D:GLU121 3.1 23.2 1.0
CG D:ASP123 3.4 28.0 1.0
OD2 D:ASP132 3.5 27.6 1.0
CB D:ASP123 3.5 26.4 1.0
OE1 D:GLU121 3.6 23.7 1.0
OG D:SER147 3.9 25.3 1.0
ND1 D:HIS137 4.2 10.1 1.0
CG D:HIS137 4.2 10.1 1.0
CA D:CA4237 4.3 21.5 1.0
O D:VAL145 4.4 25.5 1.0
CG D:GLU121 4.4 20.6 1.0
CB D:ASP132 4.4 24.6 1.0
CD D:PRO133 4.5 18.4 1.0
OD2 D:ASP123 4.5 28.8 1.0
CA D:ASP132 4.7 18.0 1.0
O D:HOH4245 4.7 15.5 1.0

Manganese binding site 5 out of 8 in 1cr7

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Manganese binding site 5 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn5238

b:32.6
occ:1.00
 OD1 E:ASP123 1.9 45.5 1.0
O E:HOH5246 2.0 13.2 1.0
O E:HOH5247 2.0 4.7 1.0
OD1 E:ASP132 2.1 6.2 1.0
OE2 E:GLU121 2.3 14.1 1.0
NE2 E:HIS137 2.4 4.8 1.0
CG E:ASP132 3.0 6.2 1.0
CG E:ASP123 3.0 46.8 1.0
CE1 E:HIS137 3.2 4.8 1.0
OD2 E:ASP132 3.3 6.2 1.0
CD E:GLU121 3.3 14.3 1.0
CB E:ASP123 3.4 43.0 1.0
CD2 E:HIS137 3.5 4.8 1.0
OE1 E:GLU121 3.6 17.5 1.0
CA E:CA5237 4.0 23.8 1.0
O E:HOH5244 4.0 2.0 1.0
OD2 E:ASP123 4.1 45.2 1.0
CB E:ASP132 4.3 6.2 1.0
OG E:SER147 4.3 3.2 1.0
O E:VAL145 4.3 6.3 1.0
ND1 E:HIS137 4.4 4.8 1.0
O E:HOH5252 4.4 33.0 1.0
CG E:HIS137 4.6 4.8 1.0
CG E:GLU121 4.7 10.7 1.0
CA E:ASP132 4.7 14.9 1.0
CD E:PRO133 4.7 7.7 1.0
CA E:ASP123 5.0 14.2 1.0

Manganese binding site 6 out of 8 in 1cr7

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Manganese binding site 6 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn6238

b:28.6
occ:1.00
 O F:HOH6244 1.7 5.5 1.0
OE2 F:GLU121 2.2 5.8 1.0
OD1 F:ASP132 2.2 8.4 1.0
O F:HOH6243 2.2 9.7 1.0
NE2 F:HIS137 2.4 5.1 1.0
OD1 F:ASP123 2.5 2.7 1.0
CD F:GLU121 3.1 5.8 1.0
CG F:ASP132 3.2 7.8 1.0
OE1 F:GLU121 3.3 5.8 1.0
CD2 F:HIS137 3.3 5.1 1.0
CE1 F:HIS137 3.4 5.1 1.0
CG F:ASP123 3.5 2.7 1.0
OD2 F:ASP132 3.6 9.1 1.0
CB F:ASP123 3.7 2.7 1.0
OG F:SER147 3.9 14.3 1.0
O F:HOH6251 4.0 12.1 1.0
O F:VAL145 4.1 7.8 1.0
O F:HOH6241 4.2 50.4 1.0
CA F:CA6237 4.3 8.0 1.0
CB F:ASP132 4.4 6.8 1.0
ND1 F:HIS137 4.5 5.1 1.0
CG F:GLU121 4.5 5.8 1.0
CG F:HIS137 4.5 5.1 1.0
OD2 F:ASP123 4.6 2.7 1.0
CA F:ASP132 4.7 23.7 1.0
CD F:PRO133 4.7 32.8 1.0
CG2 F:THR150 5.0 13.7 1.0

Manganese binding site 7 out of 8 in 1cr7

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Manganese binding site 7 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn7238

b:23.9
occ:1.00
 OD1 G:ASP123 1.7 9.7 1.0
OE2 G:GLU121 2.1 8.9 1.0
O G:HOH7321 2.2 7.9 1.0
NE2 G:HIS137 2.3 35.9 1.0
OD1 G:ASP132 2.4 3.7 1.0
O G:HOH7320 2.6 2.0 1.0
CG G:ASP123 2.8 9.7 1.0
CD G:GLU121 3.1 8.9 1.0
CD2 G:HIS137 3.2 33.5 1.0
CE1 G:HIS137 3.2 30.2 1.0
CB G:ASP123 3.2 9.7 1.0
CG G:ASP132 3.2 3.7 1.0
OD2 G:ASP132 3.5 3.7 1.0
OE1 G:GLU121 3.5 8.9 1.0
O G:HOH7318 3.6 16.7 1.0
OD2 G:ASP123 3.8 10.9 1.0
OG G:SER147 4.2 2.0 1.0
ND1 G:HIS137 4.2 33.3 1.0
CG G:HIS137 4.3 29.3 1.0
CA G:CA7237 4.3 11.8 1.0
CG G:GLU121 4.4 8.9 1.0
O G:VAL145 4.4 7.6 1.0
CB G:ASP132 4.5 3.7 1.0
CA G:ASP123 4.7 21.9 1.0
CD G:PRO133 4.9 18.5 1.0
CA G:ASP132 4.9 21.0 1.0

Manganese binding site 8 out of 8 in 1cr7

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Manganese binding site 8 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn8238

b:29.1
occ:1.00
 O H:HOH8244 1.7 58.0 1.0
OE2 H:GLU121 2.0 18.6 1.0
O H:HOH8243 2.1 2.0 1.0
OD1 H:ASP132 2.1 9.4 1.0
NE2 H:HIS137 2.3 9.6 1.0
OD1 H:ASP123 2.7 21.0 1.0
CD H:GLU121 3.1 19.4 1.0
CG H:ASP132 3.1 9.4 1.0
CD2 H:HIS137 3.2 9.6 1.0
CE1 H:HIS137 3.3 9.6 1.0
OE1 H:GLU121 3.5 20.8 1.0
OD2 H:ASP132 3.5 9.4 1.0
CG H:ASP123 3.5 12.0 1.0
CB H:ASP123 3.6 10.2 1.0
OG H:SER147 3.8 16.6 1.0
O H:VAL145 4.1 10.5 1.0
CA H:CA8237 4.3 11.0 1.0
O H:HOH8241 4.3 2.0 1.0
ND1 H:HIS137 4.4 9.6 1.0
CG H:GLU121 4.4 16.4 1.0
CG H:HIS137 4.4 9.6 1.0
CB H:ASP132 4.4 9.4 1.0
OD2 H:ASP123 4.6 10.2 1.0
CD H:PRO133 4.6 4.9 1.0
CA H:ASP132 4.7 20.7 1.0

Reference:

R.Ravishankar, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan. Crystal Structures of the Peanut Lectin-Lactose Complex at Acidic pH: Retention of Unusual Quaternary Structure, Empty and Carbohydrate Bound Combining Sites, Molecular Mimicry and Crystal Packing Directed By Interactions at the Combining Site. Proteins V. 43 260 2001.
ISSN: ISSN 0887-3585
PubMed: 11288176
DOI: 10.1002/PROT.1037
Page generated: Sat Oct 5 10:02:27 2024

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