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Calcium in PDB 3usu: Crystal Structure of Butea Monosperma Seed Lectin

Protein crystallography data

The structure of Crystal Structure of Butea Monosperma Seed Lectin, PDB code: 3usu was solved by J.Abhilash, K.Geethanandan, S.R.Bharath, C.Sadasivan, M.Haridas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.06 / 2.46
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.450, 78.910, 101.850, 74.30, 76.65, 86.88
R / Rfree (%) 20.5 / 28.7

Other elements in 3usu:

The structure of Crystal Structure of Butea Monosperma Seed Lectin also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Butea Monosperma Seed Lectin (pdb code 3usu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Butea Monosperma Seed Lectin, PDB code: 3usu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3usu

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Calcium binding site 1 out of 8 in the Crystal Structure of Butea Monosperma Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Butea Monosperma Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca264

b:19.6
occ:1.00
O A:HOH387 2.0 5.7 1.0
O A:HOH306 2.2 5.9 1.0
ND2 A:ASN133 2.2 17.7 1.0
OD2 A:ASP138 2.4 16.6 1.0
O A:TYR131 2.4 17.1 1.0
OD1 A:ASP129 2.4 14.7 1.0
OD2 A:ASP129 2.6 15.0 1.0
CG A:ASP129 2.9 14.7 1.0
CG A:ASP138 3.4 16.5 1.0
CG A:ASN133 3.5 18.6 1.0
C A:TYR131 3.6 17.4 1.0
OD1 A:ASP138 3.8 16.3 1.0
N A:ASN133 3.8 18.6 1.0
CB A:ASN133 4.1 19.1 1.0
MN A:MN265 4.1 13.3 1.0
O A:HOH257 4.3 5.2 1.0
CB A:ASP129 4.4 14.6 1.0
OD1 A:ASN133 4.4 18.8 1.0
N A:TYR131 4.4 17.3 1.0
CA A:TYR131 4.5 17.3 1.0
O A:GLY107 4.5 16.9 1.0
N A:GLU132 4.6 17.7 1.0
CA A:GLY107 4.6 17.5 1.0
CA A:ASN133 4.6 19.5 1.0
OD2 A:ASP89 4.6 23.5 1.0
CA A:GLU132 4.6 17.8 1.0
CB A:ASP138 4.7 17.1 1.0
C A:GLU132 4.7 18.5 1.0
CD2 A:PHE136 4.8 17.5 1.0
CB A:TYR131 4.8 17.3 1.0
CD2 A:TYR131 4.8 18.0 1.0
O A:ASP89 4.8 20.4 1.0
CE1 A:HIS143 4.9 15.0 1.0

Calcium binding site 2 out of 8 in 3usu

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Calcium binding site 2 out of 8 in the Crystal Structure of Butea Monosperma Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Butea Monosperma Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca260

b:15.3
occ:1.00
ND2 B:ASN133 2.2 18.1 1.0
O B:HOH353 2.2 4.5 1.0
O B:TYR131 2.2 15.7 1.0
O B:HOH360 2.3 6.8 1.0
OD2 B:ASP129 2.3 13.9 1.0
OD1 B:ASP129 2.4 14.5 1.0
OD2 B:ASP138 2.4 16.1 1.0
CG B:ASP129 2.7 14.1 1.0
CG B:ASN133 3.4 18.7 1.0
C B:TYR131 3.5 16.1 1.0
CG B:ASP138 3.5 16.2 1.0
N B:ASN133 3.8 18.4 1.0
OD1 B:ASP138 4.0 15.5 1.0
CB B:ASN133 4.0 18.5 1.0
MN B:MN261 4.1 13.3 1.0
O B:HOH363 4.1 5.5 1.0
N B:TYR131 4.2 15.8 1.0
CA B:TYR131 4.3 16.0 1.0
CB B:ASP129 4.3 14.1 1.0
OD1 B:ASN133 4.4 19.7 1.0
O B:ASP89 4.4 13.6 1.0
N B:GLU132 4.5 16.8 1.0
CB B:TYR131 4.5 16.1 1.0
O B:GLY107 4.5 14.6 1.0
CA B:ASN133 4.6 19.1 1.0
CA B:GLU132 4.6 17.1 1.0
C B:GLU132 4.6 18.2 1.0
OD1 B:ASP89 4.6 15.1 1.0
CA B:GLY107 4.7 15.2 1.0
CD2 B:TYR131 4.7 16.8 1.0
CB B:ASP138 4.7 16.5 1.0
CE1 B:HIS143 4.8 14.6 1.0
NE2 B:HIS143 5.0 14.3 1.0

Calcium binding site 3 out of 8 in 3usu

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Calcium binding site 3 out of 8 in the Crystal Structure of Butea Monosperma Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Butea Monosperma Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca266

b:19.7
occ:1.00
O C:HOH257 2.1 14.2 1.0
O C:TYR131 2.4 19.4 1.0
O C:HOH354 2.4 18.6 1.0
OD1 C:ASP129 2.4 18.8 1.0
OD1 C:ASN133 2.4 21.8 1.0
OD2 C:ASP129 2.5 18.1 1.0
OD2 C:ASP138 2.7 20.7 1.0
CG C:ASP129 2.8 18.6 1.0
CG C:ASN133 3.5 22.6 1.0
C C:TYR131 3.6 19.9 1.0
CG C:ASP138 3.7 21.0 1.0
N C:ASN133 3.9 22.2 1.0
CB C:ASN133 4.2 22.6 1.0
O C:HOH271 4.2 15.3 1.0
MN C:MN267 4.3 20.2 1.0
OD1 C:ASP138 4.3 20.0 1.0
N C:TYR131 4.3 19.2 1.0
CB C:ASP129 4.3 17.8 1.0
CA C:TYR131 4.3 19.6 1.0
CB C:TYR131 4.5 19.9 1.0
C C:GLU132 4.5 22.0 1.0
N C:GLU132 4.6 20.3 1.0
OD2 C:ASP89 4.6 21.5 1.0
ND2 C:ASN133 4.6 23.6 1.0
CA C:GLU132 4.6 20.9 1.0
O C:GLY107 4.6 18.3 1.0
CD2 C:TYR131 4.6 21.0 1.0
CA C:GLY107 4.7 19.0 1.0
CA C:ASN133 4.7 22.9 1.0
O C:ASP89 4.7 23.4 1.0
CB C:ASP138 4.8 21.8 1.0
O C:HOH288 4.9 20.7 1.0
CE1 C:HIS143 4.9 15.5 1.0

Calcium binding site 4 out of 8 in 3usu

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Calcium binding site 4 out of 8 in the Crystal Structure of Butea Monosperma Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Butea Monosperma Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca268

b:31.7
occ:1.00
O D:HOH359 2.1 9.9 1.0
OD1 D:ASN133 2.2 29.1 1.0
O D:TYR131 2.3 29.6 1.0
O D:HOH293 2.4 19.2 1.0
OD2 D:ASP129 2.5 28.9 1.0
OD1 D:ASP129 2.5 29.3 1.0
OD1 D:ASP138 2.8 29.8 1.0
CG D:ASP129 2.9 28.4 1.0
CG D:ASN133 3.4 31.0 1.0
C D:TYR131 3.5 29.4 1.0
CG D:ASP138 3.6 28.8 1.0
OD2 D:ASP138 3.9 27.7 1.0
N D:ASN133 3.9 31.8 1.0
OD1 D:ASP89 4.0 27.0 1.0
CB D:ASN133 4.1 31.8 1.0
N D:TYR131 4.2 27.6 1.0
O D:HOH246 4.2 12.4 1.0
CA D:TYR131 4.3 28.8 1.0
CB D:ASP129 4.4 26.3 1.0
MN D:MN269 4.4 38.5 1.0
ND2 D:ASN133 4.4 32.1 1.0
N D:GLU132 4.4 29.8 1.0
CA D:GLU132 4.4 30.8 1.0
CB D:TYR131 4.5 29.1 1.0
C D:GLU132 4.5 32.1 1.0
CD2 D:TYR131 4.5 31.6 1.0
CA D:GLY107 4.6 29.4 1.0
O D:ASP89 4.6 23.6 1.0
CA D:ASN133 4.6 32.9 1.0
CE1 D:HIS143 4.6 26.6 1.0
CB D:ASP138 4.7 29.2 1.0
O D:GLY107 4.8 27.9 1.0
CD2 D:PHE136 5.0 30.5 1.0
NE2 D:HIS143 5.0 25.7 1.0

Calcium binding site 5 out of 8 in 3usu

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Calcium binding site 5 out of 8 in the Crystal Structure of Butea Monosperma Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Butea Monosperma Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca262

b:20.3
occ:1.00
O E:HOH268 2.1 15.8 1.0
O E:TYR131 2.2 21.9 1.0
O E:HOH287 2.3 29.7 1.0
OD1 E:ASP138 2.3 20.3 1.0
OD1 E:ASN133 2.4 21.1 1.0
OD1 E:ASP129 2.5 21.5 1.0
OD2 E:ASP129 2.5 20.0 1.0
CG E:ASP129 2.8 20.1 1.0
CG E:ASP138 3.3 20.3 1.0
C E:TYR131 3.4 22.2 1.0
CG E:ASN133 3.6 22.0 1.0
OD2 E:ASP138 3.7 19.8 1.0
N E:ASN133 3.9 23.0 1.0
CB E:ASN133 4.2 22.1 1.0
MN E:MN263 4.2 25.6 1.0
O E:HOH258 4.2 12.6 1.0
CA E:TYR131 4.3 22.1 1.0
N E:TYR131 4.3 20.9 1.0
CB E:ASP129 4.3 19.0 1.0
OD1 E:ASP89 4.4 22.9 1.0
N E:GLU132 4.4 22.5 1.0
CA E:GLU132 4.5 23.1 1.0
C E:GLU132 4.5 24.0 1.0
CB E:TYR131 4.5 22.5 1.0
CB E:ASP138 4.6 21.2 1.0
CE1 E:HIS143 4.6 22.5 1.0
ND2 E:ASN133 4.7 22.6 1.0
CA E:ASN133 4.7 22.9 1.0
O E:GLY107 4.7 22.8 1.0
O E:ASP89 4.7 19.9 1.0
CA E:GLY107 4.8 23.4 1.0
CD2 E:TYR131 4.8 24.2 1.0
NE2 E:HIS143 4.9 22.0 1.0

Calcium binding site 6 out of 8 in 3usu

Go back to Calcium Binding Sites List in 3usu
Calcium binding site 6 out of 8 in the Crystal Structure of Butea Monosperma Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Butea Monosperma Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca274

b:23.1
occ:1.00
ND2 F:ASN133 2.1 18.7 1.0
OD2 F:ASP138 2.2 20.2 1.0
O F:HOH366 2.3 10.9 1.0
OD1 F:ASP129 2.3 18.6 1.0
O F:HOH266 2.3 21.4 1.0
O F:TYR131 2.4 17.9 1.0
OD2 F:ASP129 2.6 18.0 1.0
CG F:ASP129 2.8 17.9 1.0
CG F:ASP138 3.4 20.7 1.0
CG F:ASN133 3.4 19.8 1.0
C F:TYR131 3.6 18.1 1.0
OD1 F:ASP138 3.8 20.6 1.0
N F:ASN133 3.8 20.3 1.0
MN F:MN275 3.9 21.9 1.0
CB F:ASN133 4.1 20.2 1.0
O F:HOH358 4.2 9.5 1.0
CB F:ASP129 4.3 16.8 1.0
OD1 F:ASN133 4.4 20.5 1.0
O F:GLY107 4.4 18.9 1.0
CA F:TYR131 4.5 17.5 1.0
CB F:TYR131 4.5 17.4 1.0
N F:TYR131 4.5 17.2 1.0
N F:GLU132 4.6 18.8 1.0
C F:GLU132 4.6 20.2 1.0
CA F:GLU132 4.6 19.6 1.0
CA F:ASN133 4.6 20.6 1.0
CB F:ASP138 4.6 21.3 1.0
CA F:GLY107 4.7 19.3 1.0
O F:ASP89 4.7 17.7 1.0
OD1 F:ASP89 4.8 20.6 1.0
CE1 F:HIS143 4.8 19.2 1.0
CD2 F:TYR131 4.8 18.3 1.0
CD2 F:PHE136 4.9 21.9 1.0

Calcium binding site 7 out of 8 in 3usu

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Calcium binding site 7 out of 8 in the Crystal Structure of Butea Monosperma Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Butea Monosperma Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca270

b:17.4
occ:1.00
O G:TYR131 2.2 16.0 1.0
O G:HOH288 2.3 18.1 1.0
OD2 G:ASP129 2.3 15.0 1.0
OD2 G:ASP138 2.3 15.2 1.0
OD1 G:ASN133 2.5 16.0 1.0
O G:HOH355 2.5 9.0 1.0
OD1 G:ASP129 2.6 14.8 1.0
CG G:ASP129 2.8 14.8 1.0
CG G:ASP138 3.1 15.3 1.0
OD1 G:ASP138 3.4 14.9 1.0
C G:TYR131 3.5 16.2 1.0
CG G:ASN133 3.6 16.7 1.0
N G:ASN133 3.8 17.7 1.0
CB G:ASN133 4.1 17.1 1.0
MN G:MN271 4.2 19.7 1.0
CB G:ASP138 4.2 15.6 1.0
CB G:ASP129 4.3 14.6 1.0
O G:HOH257 4.3 5.8 1.0
N G:TYR131 4.3 15.6 1.0
CA G:TYR131 4.3 15.8 1.0
N G:GLU132 4.4 16.7 1.0
CA G:GLU132 4.4 17.3 1.0
CE1 G:HIS143 4.5 16.6 1.0
C G:GLU132 4.5 18.0 1.0
CA G:ASN133 4.6 17.7 1.0
CB G:TYR131 4.7 15.8 1.0
OD1 G:ASP89 4.7 18.3 1.0
ND2 G:ASN133 4.7 16.8 1.0
NE2 G:HIS143 4.8 16.5 1.0
O G:ASP89 4.8 18.0 1.0
CD1 G:PHE136 4.8 17.1 1.0
O G:GLY107 4.8 16.2 1.0
CD2 G:TYR131 4.9 16.5 1.0
CA G:GLY107 5.0 17.2 1.0

Calcium binding site 8 out of 8 in 3usu

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Calcium binding site 8 out of 8 in the Crystal Structure of Butea Monosperma Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Butea Monosperma Seed Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca272

b:30.7
occ:1.00
OD1 H:ASN133 2.2 29.6 1.0
O H:HOH245 2.3 22.8 1.0
OD1 H:ASP129 2.4 24.7 1.0
O H:TYR131 2.4 28.3 1.0
OD2 H:ASP138 2.4 28.8 1.0
OD2 H:ASP129 2.8 25.2 1.0
CG H:ASP129 2.9 24.6 1.0
CG H:ASN133 3.3 30.1 1.0
CG H:ASP138 3.3 29.0 1.0
C H:TYR131 3.6 29.2 1.0
OD1 H:ASP138 3.7 27.6 1.0
N H:ASN133 3.8 31.7 1.0
O H:HOH248 3.9 14.7 1.0
CB H:ASN133 4.1 31.8 1.0
ND2 H:ASN133 4.3 29.7 1.0
N H:TYR131 4.3 26.6 1.0
CA H:TYR131 4.3 28.4 1.0
MN H:MN273 4.4 23.0 1.0
CB H:ASP129 4.5 22.7 1.0
CB H:TYR131 4.5 29.3 1.0
O H:GLY107 4.6 28.9 1.0
CA H:GLY107 4.6 29.3 1.0
N H:GLU132 4.6 30.9 1.0
CA H:ASN133 4.6 32.9 1.0
CB H:ASP138 4.6 30.9 1.0
C H:GLU132 4.6 32.2 1.0
OD1 H:ASP89 4.7 28.6 1.0
CA H:GLU132 4.7 31.7 1.0
CE1 H:HIS143 4.9 24.6 1.0
NE2 H:HIS143 4.9 23.8 1.0
O H:ASP89 4.9 23.7 1.0
CD2 H:TYR131 5.0 31.8 1.0
CD2 H:PHE136 5.0 28.6 1.0

Reference:

J.Abhilash, K.Geethanandan, S.R.Bharath, C.Sadasivan, M.Haridas. Crystal Structure of Butea Monosperma Seed Lectin To Be Published.
Page generated: Sat Jul 13 20:17:12 2024

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