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Calcium 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:

Manganese (Mn) 8 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 1cr7

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1237

b:15.4
occ:1.00
 O A:TYR125 2.2 21.4 1.0
OD2 A:ASP123 2.3 18.3 1.0
O A:HOH1256 2.3 5.2 1.0
OD2 A:ASP132 2.3 5.9 1.0
O A:HOH1255 2.4 2.0 1.0
OD1 A:ASP123 2.4 16.1 1.0
OD1 A:ASN127 2.6 20.4 1.0
CG A:ASP123 2.7 19.6 1.0
C A:TYR125 3.4 21.4 1.0
CG A:ASP132 3.5 5.9 1.0
CG A:ASN127 3.7 14.1 1.0
N A:ASN127 4.0 7.3 1.0
OD1 A:ASP132 4.0 5.9 1.0
MN A:MN1238 4.1 27.0 1.0
O A:HOH1257 4.1 12.1 1.0
CB A:ASN127 4.2 10.9 1.0
CB A:ASP123 4.2 17.9 1.0
CA A:TYR125 4.3 21.9 1.0
N A:TYR125 4.3 22.9 1.0
N A:SER126 4.4 10.1 1.0
CB A:TYR125 4.5 20.4 1.0
CA A:SER126 4.5 10.9 1.0
CA A:GLY104 4.6 2.0 1.0
O A:ASP83 4.6 10.0 1.0
CB A:ASP132 4.7 5.9 1.0
OD1 A:ASP83 4.7 22.0 1.0
C A:SER126 4.7 11.1 1.0
CA A:ASN127 4.7 7.3 1.0
CD2 A:TYR125 4.7 23.2 1.0
ND2 A:ASN127 4.8 14.7 1.0
CE1 A:HIS137 4.9 15.8 1.0
CA A:ASP123 5.0 4.2 1.0

Calcium binding site 2 out of 8 in 1cr7

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2237

b:13.1
occ:1.00
 OD2 B:ASP132 2.2 16.0 1.0
O B:TYR125 2.2 12.8 1.0
OD2 B:ASP123 2.4 7.7 1.0
O B:HOH2260 2.4 21.9 1.0
OD1 B:ASP123 2.4 7.7 1.0
OD1 B:ASN127 2.5 24.5 1.0
O B:HOH2261 2.6 6.7 1.0
CG B:ASP123 2.7 7.7 1.0
CG B:ASP132 3.3 14.8 1.0
C B:TYR125 3.5 12.8 1.0
CG B:ASN127 3.6 18.9 1.0
N B:ASN127 3.8 25.1 1.0
OD1 B:ASP132 3.9 16.4 1.0
CB B:ASN127 4.1 18.7 1.0
CB B:ASP123 4.2 7.7 1.0
CA B:TYR125 4.4 12.8 1.0
N B:SER126 4.4 18.4 1.0
N B:TYR125 4.4 12.8 1.0
MN B:MN2238 4.4 28.6 1.0
CA B:SER126 4.4 19.3 1.0
O B:HOH2262 4.4 7.0 1.0
CB B:ASP132 4.5 11.8 1.0
C B:SER126 4.6 19.3 1.0
CA B:ASN127 4.6 23.5 1.0
CB B:TYR125 4.6 8.7 1.0
CA B:GLY104 4.7 17.8 1.0
ND2 B:ASN127 4.7 19.5 1.0
CD2 B:TYR125 4.8 10.0 1.0
CE1 B:HIS137 4.8 23.5 1.0
OD1 B:ASP83 4.8 20.0 1.0
O B:ASP83 4.8 9.1 1.0

Calcium binding site 3 out of 8 in 1cr7

Go back to Calcium Binding Sites List in 1cr7
Calcium binding site 3 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3237

b:10.2
occ:1.00
 O C:HOH3259 1.9 16.6 1.0
O C:TYR125 2.0 12.9 1.0
OD2 C:ASP132 2.1 6.4 1.0
OD1 C:ASN127 2.1 36.3 1.0
O C:HOH3260 2.3 4.2 1.0
OD2 C:ASP123 2.5 12.0 1.0
OD1 C:ASP123 3.0 6.5 1.0
CG C:ASP123 3.1 7.8 1.0
C C:TYR125 3.2 12.9 1.0
CG C:ASN127 3.2 31.6 1.0
CG C:ASP132 3.3 6.4 1.0
N C:ASN127 3.7 24.6 1.0
CB C:ASN127 3.9 30.6 1.0
OD1 C:ASP132 3.9 6.4 1.0
N C:SER126 4.1 31.2 1.0
CA C:SER126 4.2 33.6 1.0
CA C:TYR125 4.2 12.9 1.0
C C:SER126 4.2 34.7 1.0
OD1 C:ASP83 4.2 29.5 1.0
N C:TYR125 4.3 12.9 1.0
ND2 C:ASN127 4.3 32.1 1.0
CB C:ASP132 4.4 6.4 1.0
CA C:ASN127 4.4 24.3 1.0
CB C:TYR125 4.4 29.4 1.0
CA C:GLY104 4.5 28.6 1.0
CD2 C:TYR125 4.5 30.4 1.0
MN C:MN3238 4.6 46.5 1.0
O C:HOH3261 4.6 36.7 1.0
CB C:ASP123 4.6 6.8 1.0
O C:ASP83 4.8 18.8 1.0
CE1 C:HIS137 5.0 26.0 1.0

Calcium binding site 4 out of 8 in 1cr7

Go back to Calcium Binding Sites List in 1cr7
Calcium binding site 4 out of 8 in the Peanut Lectin-Lactose Complex Monoclinic Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca4237

b:21.5
occ:1.00
 OD1 D:ASP123 2.2 35.5 1.0
OD2 D:ASP132 2.4 27.6 1.0
O D:TYR125 2.4 16.0 1.0
OD1 D:ASN127 2.4 48.8 1.0
O D:HOH4245 2.5 15.5 1.0
O D:HOH4246 2.6 24.9 1.0
OD2 D:ASP123 2.9 28.8 1.0
CG D:ASP123 2.9 28.0 1.0
CG D:ASP132 3.5 23.1 1.0
CG D:ASN127 3.5 44.5 1.0
C D:TYR125 3.6 17.8 1.0
OD1 D:ASP132 3.9 24.8 1.0
N D:ASN127 4.0 24.2 1.0
CB D:ASN127 4.0 42.3 1.0
CA D:GLY104 4.3 53.7 1.0
CB D:ASP123 4.3 26.4 1.0
MN D:MN4238 4.3 39.8 1.0
O D:HOH4247 4.4 25.4 1.0
CA D:TYR125 4.4 18.6 1.0
CB D:TYR125 4.5 58.1 1.0
N D:SER126 4.5 21.2 1.0
ND2 D:ASN127 4.6 40.7 1.0
O D:GLY104 4.6 52.1 1.0
N D:TYR125 4.6 18.3 1.0
CA D:SER126 4.6 22.7 1.0
CA D:ASN127 4.6 24.4 1.0
OD1 D:ASP83 4.7 80.5 1.0
CB D:ASP132 4.7 24.6 1.0
C D:SER126 4.7 21.5 1.0
CD2 D:TYR125 4.8 62.4 1.0
C D:GLY104 5.0 51.5 1.0
CE1 D:HIS137 5.0 10.1 1.0

Calcium binding site 5 out of 8 in 1cr7

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca5237

b:23.8
occ:1.00
 OD2 E:ASP132 2.2 6.2 1.0
O E:TYR125 2.3 17.0 1.0
OD1 E:ASN127 2.3 25.1 1.0
O E:HOH5244 2.4 2.0 1.0
O E:HOH5245 2.5 5.3 1.0
OD2 E:ASP123 2.5 45.2 1.0
OD1 E:ASP123 2.6 45.5 1.0
CG E:ASP123 2.9 46.8 1.0
CG E:ASP132 3.4 6.2 1.0
CG E:ASN127 3.4 21.9 1.0
C E:TYR125 3.5 17.9 1.0
N E:ASN127 3.7 16.9 1.0
CB E:ASN127 3.9 19.8 1.0
MN E:MN5238 4.0 32.6 1.0
OD1 E:ASP132 4.0 6.2 1.0
O E:HOH5246 4.3 13.2 1.0
CA E:TYR125 4.4 19.6 1.0
N E:SER126 4.4 9.4 1.0
CA E:SER126 4.4 14.3 1.0
CA E:ASN127 4.4 15.3 1.0
CB E:ASP123 4.4 43.0 1.0
CB E:ASP132 4.5 6.2 1.0
C E:SER126 4.5 15.6 1.0
CA E:GLY104 4.5 3.1 1.0
N E:TYR125 4.5 21.8 1.0
ND2 E:ASN127 4.6 23.3 1.0
CB E:TYR125 4.6 32.8 1.0
CD2 E:TYR125 4.6 37.5 1.0
OD1 E:ASP83 4.7 30.8 1.0
O E:ASP83 4.9 9.7 1.0
O E:GLY104 5.0 3.1 1.0
CE1 E:HIS137 5.0 4.8 1.0

Calcium binding site 6 out of 8 in 1cr7

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca6237

b:8.0
occ:1.00
 O F:HOH6241 1.9 50.4 1.0
OD2 F:ASP132 2.2 9.1 1.0
O F:TYR125 2.3 8.5 1.0
OD1 F:ASP123 2.3 2.7 1.0
O F:HOH6242 2.4 9.8 1.0
OD1 F:ASN127 2.4 9.5 1.0
OD2 F:ASP123 2.5 2.7 1.0
CG F:ASP123 2.8 2.7 1.0
CG F:ASP132 3.4 7.8 1.0
C F:TYR125 3.4 8.0 1.0
CG F:ASN127 3.5 9.5 1.0
OD1 F:ASP132 3.9 8.4 1.0
N F:ASN127 4.0 14.8 1.0
CB F:ASN127 4.0 9.5 1.0
CA F:TYR125 4.2 6.3 1.0
CB F:ASP123 4.2 2.7 1.0
CB F:TYR125 4.3 11.5 1.0
MN F:MN6238 4.3 28.6 1.0
N F:TYR125 4.4 5.2 1.0
O F:HOH6243 4.4 9.7 1.0
N F:SER126 4.4 11.2 1.0
CB F:ASP132 4.5 6.8 1.0
CA F:GLY104 4.6 22.0 1.0
CA F:SER126 4.6 13.3 1.0
ND2 F:ASN127 4.7 9.5 1.0
CA F:ASN127 4.7 12.7 1.0
C F:SER126 4.7 14.7 1.0
OD1 F:ASP83 4.7 7.6 1.0
CD2 F:TYR125 4.8 11.5 1.0
O F:ASP83 4.8 6.1 1.0

Calcium binding site 7 out of 8 in 1cr7

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca7237

b:11.8
occ:1.00
 O G:TYR125 1.9 14.5 1.0
O G:HOH7319 2.1 10.9 1.0
OD2 G:ASP132 2.1 3.7 1.0
OD1 G:ASN127 2.1 31.5 1.0
O G:HOH7318 2.1 16.7 1.0
OD2 G:ASP123 2.5 10.9 1.0
OD1 G:ASP123 3.0 9.7 1.0
C G:TYR125 3.1 14.5 1.0
CG G:ASP123 3.1 9.7 1.0
CG G:ASN127 3.2 29.8 1.0
CG G:ASP132 3.3 3.7 1.0
N G:ASN127 3.6 38.4 1.0
CB G:ASN127 3.9 29.2 1.0
OD1 G:ASP132 4.0 3.7 1.0
N G:SER126 4.0 34.1 1.0
CA G:SER126 4.1 38.4 1.0
CA G:TYR125 4.1 14.5 1.0
C G:SER126 4.1 40.3 1.0
OD1 G:ASP83 4.3 20.9 1.0
N G:TYR125 4.3 14.5 1.0
ND2 G:ASN127 4.3 30.4 1.0
MN G:MN7238 4.3 23.9 1.0
CB G:TYR125 4.4 36.0 1.0
CA G:ASN127 4.4 36.7 1.0
CB G:ASP132 4.4 3.7 1.0
CD2 G:TYR125 4.5 39.9 1.0
CA G:GLY104 4.6 8.4 1.0
CB G:ASP123 4.6 9.7 1.0
O G:HOH7320 4.8 2.0 1.0
O G:ASP83 4.9 17.0 1.0
CG G:TYR125 4.9 36.8 1.0
CE1 G:HIS137 5.0 30.2 1.0

Calcium binding site 8 out of 8 in 1cr7

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Peanut Lectin-Lactose Complex Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca8237

b:11.0
occ:1.00
 O H:HOH8242 1.7 69.5 1.0
OD1 H:ASP123 2.1 21.0 1.0
O H:TYR125 2.1 10.6 1.0
OD2 H:ASP132 2.3 9.4 1.0
O H:HOH8241 2.3 2.0 1.0
OD2 H:ASP123 2.6 10.2 1.0
OD1 H:ASN127 2.6 28.0 1.0
CG H:ASP123 2.7 12.0 1.0
C H:TYR125 3.3 14.2 1.0
CG H:ASP132 3.5 9.4 1.0
CG H:ASN127 3.7 27.2 1.0
N H:ASN127 4.0 12.4 1.0
OD1 H:ASP132 4.0 9.4 1.0
CB H:ASP123 4.2 10.2 1.0
CA H:TYR125 4.2 13.0 1.0
O H:HOH8243 4.2 2.0 1.0
CB H:ASN127 4.2 26.7 1.0
CB H:TYR125 4.2 37.3 1.0
N H:TYR125 4.3 13.0 1.0
N H:SER126 4.3 11.0 1.0
MN H:MN8238 4.3 29.1 1.0
CA H:SER126 4.5 14.5 1.0
CA H:GLY104 4.5 19.0 1.0
C H:SER126 4.6 14.4 1.0
CB H:ASP132 4.6 9.4 1.0
OD1 H:ASP83 4.7 32.8 1.0
CD2 H:TYR125 4.7 42.3 1.0
ND2 H:ASN127 4.7 30.6 1.0
CA H:ASN127 4.7 11.3 1.0
CE1 H:HIS137 4.8 9.6 1.0
O H:GLY104 4.9 19.1 1.0
O H:ASP83 4.9 36.2 1.0
CG H:TYR125 5.0 39.8 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: Thu Jul 11 07:08:06 2024

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