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Calcium in PDB 4m3c: Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds

Protein crystallography data

The structure of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds, PDB code: 4m3c was solved by S.Surya, J.Abhilash, K.Geethanandan, C.Sadasivan, M.Haridas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.84 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 77.110, 78.630, 96.190, 96.00, 89.99, 100.37
R / Rfree (%) 21.1 / 28.9

Other elements in 4m3c:

The structure of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds (pdb code 4m3c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds, PDB code: 4m3c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4m3c

Go back to Calcium Binding Sites List in 4m3c
Calcium binding site 1 out of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:18.3
occ:1.00
 ND2 A:ASN132 2.1 26.4 1.0
O A:HOH421 2.2 17.2 1.0
O A:HOH426 2.3 18.9 1.0
OD2 A:ASP128 2.3 18.8 1.0
O A:TYR130 2.4 23.1 1.0
OD2 A:ASP137 2.4 26.9 1.0
OD1 A:ASP128 2.6 17.7 1.0
CG A:ASP128 2.8 19.7 1.0
CG A:ASN132 3.4 27.8 1.0
CG A:ASP137 3.5 26.3 1.0
C A:TYR130 3.6 24.0 1.0
OD1 A:ASP137 4.0 27.7 1.0
O A:HOH422 4.1 13.5 1.0
N A:ASN132 4.2 25.3 1.0
OD1 A:ASN132 4.3 27.9 1.0
CB A:ASP128 4.3 20.2 1.0
CB A:ASN132 4.3 24.1 1.0
N A:TYR130 4.3 26.1 1.0
MN A:MN302 4.3 39.7 1.0
CA A:TYR130 4.4 25.4 1.0
O A:ASP88 4.5 21.4 1.0
N A:GLU131 4.6 22.8 1.0
CA A:GLU131 4.6 23.7 1.0
OD2 A:ASP88 4.7 26.5 1.0
CB A:TYR130 4.7 27.7 1.0
C A:GLU131 4.7 24.7 1.0
CA A:GLY106 4.7 25.0 1.0
O A:GLY106 4.7 25.6 1.0
N A:THR129 4.7 24.3 1.0
CB A:ASP137 4.8 24.9 1.0
CD2 A:TYR130 4.8 29.6 1.0
CE1 A:HIS142 4.9 28.7 1.0
CA A:ASN132 4.9 24.9 1.0
CD2 A:PHE135 4.9 29.1 1.0

Calcium binding site 2 out of 8 in 4m3c

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Calcium binding site 2 out of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:23.3
occ:1.00
 O B:HOH430 2.0 24.2 1.0
O B:HOH434 2.1 21.6 1.0
ND2 B:ASN132 2.3 22.6 1.0
OD2 B:ASP128 2.4 21.1 1.0
OD2 B:ASP137 2.4 27.7 1.0
O B:TYR130 2.4 24.6 1.0
OD1 B:ASP128 2.5 22.3 1.0
CG B:ASP128 2.8 21.4 1.0
CG B:ASP137 3.5 27.2 1.0
C B:TYR130 3.6 26.4 1.0
CG B:ASN132 3.7 26.1 1.0
OD1 B:ASP137 3.9 27.1 1.0
MN B:MN302 4.2 27.9 1.0
N B:ASN132 4.2 27.4 1.0
CB B:ASP128 4.3 21.6 1.0
N B:TYR130 4.3 27.1 1.0
O B:HOH420 4.3 21.8 1.0
OD1 B:ASP88 4.4 25.4 1.0
CA B:TYR130 4.4 27.4 1.0
CB B:ASN132 4.5 24.5 1.0
O B:ASP88 4.5 20.8 1.0
OD1 B:ASN132 4.5 27.8 1.0
N B:GLU131 4.6 25.3 1.0
CA B:GLY106 4.7 25.5 1.0
O B:GLY106 4.7 27.6 1.0
CB B:TYR130 4.7 29.4 1.0
CB B:ASP137 4.7 28.4 1.0
CD2 B:TYR130 4.7 33.4 1.0
CA B:GLU131 4.8 25.9 1.0
C B:GLU131 4.8 26.8 1.0
CA B:ASN132 5.0 25.9 1.0
CD2 B:PHE135 5.0 29.8 1.0

Calcium binding site 3 out of 8 in 4m3c

Go back to Calcium Binding Sites List in 4m3c
Calcium binding site 3 out of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:38.2
occ:1.00
 O C:HOH430 2.0 26.6 1.0
OD2 C:ASP137 2.1 21.4 1.0
O C:TYR130 2.5 29.3 1.0
OD1 C:ASP128 2.5 25.0 1.0
OD1 C:ASN132 2.6 36.6 1.0
O C:HOH423 2.6 24.4 1.0
OD2 C:ASP128 2.7 22.8 1.0
CG C:ASP128 3.0 23.2 1.0
CG C:ASP137 3.3 22.7 1.0
CG C:ASN132 3.7 36.3 1.0
C C:TYR130 3.7 29.8 1.0
OD1 C:ASP137 3.8 21.9 1.0
N C:ASN132 4.0 35.1 1.0
MN C:MN302 4.1 36.1 1.0
CB C:ASN132 4.2 34.5 1.0
N C:TYR130 4.5 32.3 1.0
CB C:ASP128 4.5 21.1 1.0
O C:GLY106 4.5 28.4 1.0
CA C:TYR130 4.5 32.5 1.0
CB C:ASP137 4.5 22.3 1.0
O C:ASP88 4.5 22.9 1.0
CA C:GLY106 4.6 29.3 1.0
N C:GLU131 4.7 29.4 1.0
OD2 C:ASP88 4.7 28.9 1.0
C C:GLU131 4.7 35.9 1.0
CA C:GLU131 4.7 32.1 1.0
CA C:ASN132 4.7 36.5 1.0
O C:HOH407 4.8 15.4 1.0
CD2 C:TYR130 4.8 39.4 1.0
ND2 C:ASN132 4.8 36.6 1.0
CB C:TYR130 4.9 34.2 1.0
CD2 C:PHE135 4.9 33.3 1.0
CE1 C:HIS142 4.9 23.2 1.0

Calcium binding site 4 out of 8 in 4m3c

Go back to Calcium Binding Sites List in 4m3c
Calcium binding site 4 out of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:25.1
occ:1.00
 O D:HOH413 2.2 28.4 1.0
OD1 D:ASN132 2.3 26.9 1.0
O D:TYR130 2.4 26.4 1.0
O D:HOH420 2.5 16.0 1.0
OD1 D:ASP137 2.5 23.6 1.0
OD2 D:ASP128 2.6 19.5 1.0
OD1 D:ASP128 2.8 18.6 1.0
CG D:ASP128 3.1 19.7 1.0
CG D:ASN132 3.3 27.6 1.0
CG D:ASP137 3.6 23.4 1.0
C D:TYR130 3.6 25.7 1.0
CB D:ASN132 3.8 29.0 1.0
N D:ASN132 3.8 31.6 1.0
OD2 D:ASP137 4.1 21.3 1.0
ND2 D:ASN132 4.4 26.0 1.0
O D:HOH425 4.4 14.2 1.0
MN D:MN302 4.4 33.4 1.0
CA D:ASN132 4.5 31.4 1.0
CA D:TYR130 4.5 25.3 1.0
O D:ASP88 4.5 19.8 1.0
N D:TYR130 4.5 26.2 1.0
CB D:ASP128 4.6 18.1 1.0
C D:GLU131 4.6 30.6 1.0
N D:GLU131 4.6 25.0 1.0
O D:GLY106 4.6 19.5 1.0
CA D:GLY106 4.6 21.2 1.0
CA D:GLU131 4.7 27.3 1.0
CD2 D:PHE135 4.7 30.5 1.0
OD1 D:ASP88 4.8 20.5 1.0
CB D:TYR130 4.8 24.2 1.0
CD2 D:TYR130 4.8 25.9 1.0
CB D:ASP137 4.8 24.4 1.0

Calcium binding site 5 out of 8 in 4m3c

Go back to Calcium Binding Sites List in 4m3c
Calcium binding site 5 out of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:31.4
occ:1.00
 O E:HOH430 2.0 28.9 1.0
OD2 E:ASP137 2.3 22.9 1.0
O E:HOH411 2.3 30.6 1.0
O E:TYR130 2.4 33.1 1.0
OD2 E:ASP128 2.5 22.9 1.0
ND2 E:ASN132 2.6 31.3 1.0
OD1 E:ASP128 2.8 22.7 1.0
CG E:ASP128 3.0 22.3 1.0
CG E:ASP137 3.5 22.9 1.0
C E:TYR130 3.6 30.6 1.0
CG E:ASN132 3.7 31.4 1.0
OD1 E:ASP137 4.0 23.2 1.0
CB E:ASN132 4.0 31.5 1.0
N E:ASN132 4.0 29.8 1.0
MN E:MN302 4.1 35.1 1.0
N E:TYR130 4.4 30.3 1.0
CA E:TYR130 4.4 30.4 1.0
O E:ASP88 4.4 22.6 1.0
OD2 E:ASP88 4.5 30.3 1.0
CB E:ASP128 4.5 21.3 1.0
CB E:TYR130 4.6 30.5 1.0
O E:GLY106 4.6 25.2 1.0
N E:GLU131 4.6 28.7 1.0
CB E:ASP137 4.7 23.0 1.0
CD2 E:TYR130 4.7 35.5 1.0
CA E:ASN132 4.7 30.6 1.0
OD1 E:ASN132 4.7 34.3 1.0
O E:HOH426 4.7 14.4 1.0
CA E:GLU131 4.8 28.8 1.0
C E:GLU131 4.8 32.1 1.0
CD2 E:PHE135 4.8 27.6 1.0
CA E:GLY106 4.9 29.6 1.0

Calcium binding site 6 out of 8 in 4m3c

Go back to Calcium Binding Sites List in 4m3c
Calcium binding site 6 out of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:28.8
occ:1.00
 OD2 F:ASP137 2.3 25.5 1.0
O F:HOH426 2.3 27.7 1.0
O F:HOH411 2.4 24.1 1.0
OD2 F:ASP128 2.4 26.1 1.0
O F:TYR130 2.5 22.5 1.0
ND2 F:ASN132 2.5 26.3 1.0
OD1 F:ASP128 2.5 27.0 1.0
CG F:ASP128 2.8 25.0 1.0
CG F:ASP137 3.4 27.1 1.0
CG F:ASN132 3.6 27.4 1.0
C F:TYR130 3.7 24.3 1.0
OD1 F:ASP137 3.8 28.8 1.0
N F:ASN132 4.0 26.3 1.0
MN F:MN302 4.0 31.0 1.0
CB F:ASN132 4.0 26.9 1.0
O F:HOH415 4.3 20.9 1.0
CB F:ASP128 4.3 23.3 1.0
N F:TYR130 4.5 26.1 1.0
CA F:TYR130 4.5 26.4 1.0
N F:GLU131 4.6 22.6 1.0
OD1 F:ASN132 4.6 29.1 1.0
CB F:ASP137 4.6 26.3 1.0
CA F:GLU131 4.6 24.5 1.0
C F:GLU131 4.6 26.8 1.0
O F:GLY106 4.6 23.9 1.0
CA F:ASN132 4.7 26.2 1.0
O F:ASP88 4.7 24.6 1.0
CA F:GLY106 4.7 25.0 1.0
CD2 F:TYR130 4.8 33.5 1.0
OD1 F:ASP88 4.8 31.7 1.0
CD2 F:PHE135 4.8 25.9 1.0
CE1 F:HIS142 4.8 20.2 1.0
CB F:TYR130 4.8 29.5 1.0
NE2 F:HIS142 4.9 20.0 1.0

Calcium binding site 7 out of 8 in 4m3c

Go back to Calcium Binding Sites List in 4m3c
Calcium binding site 7 out of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca301

b:22.2
occ:1.00
 O G:HOH431 2.3 16.4 1.0
OD2 G:ASP137 2.4 22.9 1.0
O G:TYR130 2.4 29.1 1.0
OD1 G:ASN132 2.4 24.6 1.0
O G:HOH434 2.4 13.1 1.0
OD2 G:ASP128 2.7 21.4 1.0
OD1 G:ASP128 2.8 22.6 1.0
CG G:ASP128 3.1 22.3 1.0
CG G:ASP137 3.4 23.1 1.0
CG G:ASN132 3.6 26.6 1.0
C G:TYR130 3.7 29.3 1.0
OD1 G:ASP137 3.8 23.5 1.0
N G:ASN132 4.0 29.1 1.0
MN G:MN302 4.0 30.4 1.0
CB G:ASN132 4.2 25.3 1.0
O G:HOH433 4.3 10.6 1.0
CB G:ASP128 4.6 22.9 1.0
CA G:TYR130 4.6 29.5 1.0
N G:GLU131 4.6 26.0 1.0
N G:TYR130 4.6 30.3 1.0
O G:ASP88 4.6 28.1 1.0
CA G:GLU131 4.6 26.6 1.0
C G:GLU131 4.7 27.7 1.0
CB G:ASP137 4.7 25.9 1.0
O G:GLY106 4.7 27.3 1.0
ND2 G:ASN132 4.7 27.2 1.0
CA G:GLY106 4.7 26.4 1.0
CD2 G:PHE135 4.8 31.4 1.0
CA G:ASN132 4.8 27.9 1.0
CB G:TYR130 4.8 32.3 1.0
OD2 G:ASP88 4.8 28.1 1.0
CD2 G:TYR130 4.9 34.3 1.0
CE1 G:HIS142 5.0 24.2 1.0

Calcium binding site 8 out of 8 in 4m3c

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Calcium binding site 8 out of 8 in the Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca301

b:23.8
occ:1.00
 OD1 H:ASN132 2.1 28.4 1.0
O H:TYR130 2.3 23.2 1.0
O H:HOH411 2.4 16.1 1.0
OD1 H:ASP137 2.4 33.6 1.0
OD2 H:ASP128 2.5 20.4 1.0
O H:HOH406 2.5 14.4 1.0
OD1 H:ASP128 2.8 21.4 1.0
CG H:ASP128 3.0 21.1 1.0
CG H:ASN132 3.3 28.6 1.0
CG H:ASP137 3.6 30.2 1.0
C H:TYR130 3.6 24.2 1.0
N H:ASN132 4.0 31.6 1.0
OD2 H:ASP137 4.1 31.2 1.0
MN H:MN302 4.1 41.1 1.0
ND2 H:ASN132 4.1 28.6 1.0
CB H:ASN132 4.2 29.3 1.0
O H:HOH433 4.4 13.6 1.0
CA H:GLY106 4.5 21.9 1.0
N H:GLU131 4.5 23.3 1.0
N H:TYR130 4.5 23.7 1.0
O H:ASP88 4.5 19.3 1.0
CA H:TYR130 4.5 23.0 1.0
CB H:ASP128 4.5 20.7 1.0
CA H:GLU131 4.6 25.3 1.0
C H:GLU131 4.6 28.0 1.0
CD2 H:PHE135 4.7 30.5 1.0
CA H:ASN132 4.7 30.8 1.0
OD1 H:ASP88 4.8 21.4 1.0
CB H:ASP137 4.8 27.1 1.0
O H:GLY106 4.8 23.2 1.0
CE1 H:HIS142 4.9 21.8 1.0
CD2 H:TYR130 4.9 23.8 1.0
CB H:TYR130 5.0 22.7 1.0

Reference:

S.Surya, J.Abhilash, K.Geethanandan, C.Sadasivan, M.Haridas. Structure of A Binary Complex Between Homologous Tetrameric Legume Lectins From Butea Monosperma and Spatholobus Parviflorus Seeds To Be Published.
Page generated: Sun Jul 14 09:58:55 2024

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