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Calcium in PDB 1fay: Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)

Protein crystallography data

The structure of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form), PDB code: 1fay was solved by N.Manoj, V.R.Srinivas, A.Surolia, M.Vijayan, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.530, 125.910, 138.790, 90.00, 95.89, 90.00
R / Rfree (%) 20.4 / 24.2

Other elements in 1fay:

The structure of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) (pdb code 1fay). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form), PDB code: 1fay:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1fay

Go back to Calcium Binding Sites List in 1fay
Calcium binding site 1 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:35.3
occ:1.00
 O A:HOH508 2.2 18.1 1.0
O A:PHE127 2.4 36.7 1.0
OD1 A:ASN129 2.4 37.8 1.0
OD1 A:ASP125 2.4 4.9 1.0
OD2 A:ASP132 2.4 24.1 1.0
O A:HOH509 2.5 23.1 1.0
OD2 A:ASP125 2.8 4.9 1.0
CG A:ASP125 2.9 4.9 1.0
CG A:ASN129 3.5 37.8 1.0
CG A:ASP132 3.5 24.1 1.0
C A:PHE127 3.5 36.7 1.0
O A:HOH507 4.0 21.2 1.0
N A:ASN129 4.0 19.0 1.0
OD1 A:ASP132 4.0 24.1 1.0
CB A:ASN129 4.3 37.8 1.0
CA A:PHE127 4.3 36.7 1.0
ND2 A:ASN129 4.4 37.8 1.0
CB A:PHE127 4.4 55.2 1.0
N A:PHE127 4.4 36.7 1.0
CB A:ASP125 4.4 4.9 1.0
O A:GLY106 4.5 34.1 1.0
NE1 A:TRP131 4.5 31.1 1.0
N A:GLN128 4.5 12.2 1.0
O A:ASP88 4.6 35.4 1.0
CB A:ASP132 4.6 24.1 1.0
CD2 A:PHE127 4.7 55.2 1.0
CA A:GLN128 4.7 12.2 1.0
OD2 A:ASP88 4.7 13.8 1.0
CA A:GLY106 4.8 34.1 1.0
CA A:ASN129 4.8 19.0 1.0
C A:GLN128 4.8 12.2 1.0
MN A:MN300 4.8 35.3 1.0
CG A:PHE127 5.0 55.2 1.0

Calcium binding site 2 out of 8 in 1fay

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Calcium binding site 2 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:35.3
occ:1.00
 O B:HOH520 2.0 18.9 1.0
OD2 B:ASP132 2.3 30.4 1.0
O B:HOH506 2.3 23.1 1.0
OD1 B:ASP125 2.3 19.2 1.0
O B:PHE127 2.4 15.4 1.0
OD1 B:ASN129 2.5 27.2 1.0
OD2 B:ASP125 2.6 19.2 1.0
CG B:ASP125 2.8 19.2 1.0
CG B:ASP132 3.3 30.4 1.0
CG B:ASN129 3.6 27.2 1.0
C B:PHE127 3.6 15.4 1.0
OD1 B:ASP132 3.8 30.4 1.0
N B:ASN129 4.0 11.1 1.0
O B:HOH514 4.1 19.1 1.0
CB B:ASN129 4.3 27.2 1.0
CB B:ASP125 4.3 19.2 1.0
CA B:PHE127 4.4 15.4 1.0
NE1 B:TRP131 4.4 14.8 1.0
CB B:ASP132 4.5 30.4 1.0
N B:PHE127 4.5 15.4 1.0
ND2 B:ASN129 4.5 27.2 1.0
N B:GLN128 4.5 17.9 1.0
CB B:PHE127 4.5 37.9 1.0
O B:GLY106 4.6 5.1 1.0
CA B:GLN128 4.7 17.9 1.0
MN B:MN300 4.7 35.3 1.0
O B:ASP88 4.7 18.7 1.0
C B:GLN128 4.8 17.9 1.0
CA B:ASN129 4.8 11.1 1.0
CD2 B:PHE127 4.8 37.9 1.0
CA B:GLY106 4.9 5.1 1.0
OD2 B:ASP88 4.9 46.1 1.0
CE2 B:TRP131 5.0 14.8 1.0
CZ2 B:TRP131 5.0 14.8 1.0

Calcium binding site 3 out of 8 in 1fay

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Calcium binding site 3 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:35.3
occ:1.00
 OD2 C:ASP132 2.3 25.3 1.0
OD1 C:ASN129 2.4 32.8 1.0
O C:PHE127 2.5 7.6 1.0
OD1 C:ASP125 2.5 24.8 1.0
O C:HOH507 2.6 23.1 1.0
OD2 C:ASP125 2.7 24.8 1.0
CG C:ASP125 3.0 24.8 1.0
CG C:ASP132 3.4 25.3 1.0
CG C:ASN129 3.4 32.8 1.0
C C:PHE127 3.7 7.6 1.0
OD1 C:ASP132 3.9 25.3 1.0
N C:ASN129 4.0 17.2 1.0
CB C:ASN129 4.2 32.8 1.0
NE1 C:TRP131 4.3 21.9 1.0
ND2 C:ASN129 4.3 32.8 1.0
O C:HOH506 4.3 21.2 1.0
O C:GLY106 4.4 30.8 1.0
CA C:PHE127 4.5 7.6 1.0
CB C:ASP125 4.5 24.8 1.0
CB C:PHE127 4.6 26.0 1.0
CB C:ASP132 4.6 25.3 1.0
N C:PHE127 4.6 7.6 1.0
N C:GLN128 4.6 41.5 1.0
CA C:GLY106 4.7 30.8 1.0
O C:ASP88 4.7 21.6 1.0
CA C:GLN128 4.8 41.5 1.0
CA C:ASN129 4.8 17.2 1.0
MN C:MN300 4.8 35.3 1.0
CD2 C:PHE127 4.8 26.0 1.0
OD2 C:ASP88 4.8 32.7 1.0
C C:GLN128 4.8 41.5 1.0
CZ2 C:TRP131 4.9 21.9 1.0
CE2 C:TRP131 4.9 21.9 1.0

Calcium binding site 4 out of 8 in 1fay

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Calcium binding site 4 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:35.3
occ:1.00
 O D:HOH511 2.1 18.9 1.0
O D:PHE127 2.2 15.5 1.0
OD1 D:ASP125 2.3 14.5 1.0
OD2 D:ASP132 2.3 51.9 1.0
OD1 D:ASN129 2.4 38.5 1.0
OD2 D:ASP125 2.7 14.5 1.0
O D:HOH507 2.7 23.1 1.0
CG D:ASP125 2.9 14.5 1.0
CG D:ASP132 3.4 51.9 1.0
C D:PHE127 3.4 15.5 1.0
CG D:ASN129 3.5 38.5 1.0
OD1 D:ASP132 3.9 51.9 1.0
N D:ASN129 3.9 20.9 1.0
O D:HOH506 4.0 18.1 1.0
CA D:PHE127 4.2 15.5 1.0
CB D:ASN129 4.3 38.5 1.0
CB D:ASP125 4.3 14.5 1.0
N D:PHE127 4.3 15.5 1.0
CB D:PHE127 4.4 36.1 1.0
N D:GLN128 4.4 20.0 1.0
ND2 D:ASN129 4.5 38.5 1.0
CB D:ASP132 4.5 51.9 1.0
NE1 D:TRP131 4.5 50.7 1.0
CA D:GLN128 4.6 20.0 1.0
O D:ASP88 4.6 29.8 1.0
O D:GLY106 4.7 12.8 1.0
CD2 D:PHE127 4.7 36.1 1.0
C D:GLN128 4.7 20.0 1.0
MN D:MN300 4.8 35.3 1.0
CA D:ASN129 4.8 20.9 1.0
OD2 D:ASP88 4.9 35.5 1.0
CA D:GLY106 4.9 12.8 1.0
CG D:PHE127 4.9 36.1 1.0

Calcium binding site 5 out of 8 in 1fay

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Calcium binding site 5 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca303

b:35.3
occ:1.00
 O E:HOH513 2.0 18.9 1.0
O E:PHE127 2.2 45.8 1.0
OD2 E:ASP132 2.3 40.0 1.0
OD1 E:ASN129 2.4 30.1 1.0
OD1 E:ASP125 2.4 15.1 1.0
O E:HOH507 2.6 23.1 1.0
OD2 E:ASP125 2.8 15.1 1.0
CG E:ASP125 2.9 15.1 1.0
CG E:ASP132 3.4 40.0 1.0
C E:PHE127 3.4 45.8 1.0
CG E:ASN129 3.4 30.1 1.0
N E:ASN129 3.9 35.1 1.0
OD1 E:ASP132 4.0 40.0 1.0
O E:HOH506 4.0 21.2 1.0
CB E:ASN129 4.2 30.1 1.0
CA E:PHE127 4.2 45.8 1.0
CB E:PHE127 4.4 48.3 1.0
ND2 E:ASN129 4.4 30.1 1.0
N E:PHE127 4.4 45.8 1.0
N E:GLN128 4.4 28.3 1.0
CB E:ASP125 4.4 15.1 1.0
NE1 E:TRP131 4.5 30.8 1.0
CB E:ASP132 4.5 40.0 1.0
CA E:GLN128 4.5 28.3 1.0
CD2 E:PHE127 4.6 48.3 1.0
O E:GLY106 4.6 34.8 1.0
MN E:MN300 4.7 35.3 1.0
C E:GLN128 4.7 28.3 1.0
O E:ASP88 4.7 21.3 1.0
CA E:ASN129 4.7 35.1 1.0
OD2 E:ASP88 4.8 44.3 1.0
CA E:GLY106 4.9 34.8 1.0
CG E:PHE127 4.9 48.3 1.0

Calcium binding site 6 out of 8 in 1fay

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Calcium binding site 6 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca303

b:35.3
occ:1.00
 O F:HOH517 2.3 18.9 1.0
O F:PHE127 2.3 32.6 1.0
OD1 F:ASP125 2.3 40.5 1.0
OD2 F:ASP132 2.4 45.5 1.0
OD1 F:ASN129 2.5 52.3 1.0
O F:HOH507 2.5 23.1 1.0
OD2 F:ASP125 2.7 40.5 1.0
CG F:ASP125 2.9 40.5 1.0
CG F:ASP132 3.5 45.5 1.0
C F:PHE127 3.5 32.6 1.0
CG F:ASN129 3.5 52.3 1.0
OD1 F:ASP132 4.0 45.5 1.0
N F:ASN129 4.0 24.1 1.0
O F:HOH506 4.1 18.1 1.0
CA F:PHE127 4.3 32.6 1.0
CB F:ASN129 4.3 52.3 1.0
CB F:ASP125 4.3 40.5 1.0
N F:PHE127 4.4 32.6 1.0
CB F:PHE127 4.4 52.7 1.0
ND2 F:ASN129 4.5 52.3 1.0
N F:GLN128 4.5 42.9 1.0
NE1 F:TRP131 4.5 56.1 1.0
O F:GLY106 4.6 21.6 1.0
O F:ASP88 4.6 48.6 1.0
CB F:ASP132 4.6 45.5 1.0
CA F:GLN128 4.7 42.9 1.0
MN F:MN300 4.7 35.3 1.0
CD2 F:PHE127 4.7 52.7 1.0
OD2 F:ASP88 4.8 45.4 1.0
C F:GLN128 4.8 42.9 1.0
CA F:ASN129 4.8 24.1 1.0
CA F:GLY106 4.8 21.6 1.0
CG F:PHE127 5.0 52.7 1.0

Calcium binding site 7 out of 8 in 1fay

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Calcium binding site 7 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca303

b:35.3
occ:1.00
 O G:PHE127 2.3 48.2 1.0
OD2 G:ASP132 2.3 82.9 1.0
O G:HOH409 2.3 18.1 1.0
OD1 G:ASN129 2.4 33.2 1.0
OD1 G:ASP125 2.4 51.8 1.0
O G:HOH410 2.6 23.1 1.0
OD2 G:ASP125 2.7 51.8 1.0
CG G:ASP125 2.9 51.8 1.0
CG G:ASP132 3.4 82.9 1.0
CG G:ASN129 3.5 33.2 1.0
C G:PHE127 3.5 48.2 1.0
OD1 G:ASP132 3.9 82.9 1.0
N G:ASN129 3.9 39.8 1.0
CB G:ASN129 4.2 33.2 1.0
CA G:PHE127 4.3 48.2 1.0
ND2 G:ASN129 4.4 33.2 1.0
CB G:ASP125 4.4 51.8 1.0
CB G:PHE127 4.4 71.9 1.0
N G:PHE127 4.4 48.2 1.0
N G:GLN128 4.4 71.9 1.0
NE1 G:TRP131 4.4 59.0 1.0
CB G:ASP132 4.5 82.9 1.0
CA G:GLN128 4.6 71.9 1.0
O G:GLY106 4.6 70.0 1.0
MN G:MN300 4.6 35.3 1.0
CD2 G:PHE127 4.7 71.9 1.0
C G:GLN128 4.7 71.9 1.0
CA G:ASN129 4.7 39.8 1.0
O G:ASP88 4.7 56.0 1.0
O G:HOH408 4.8 21.2 1.0
OD2 G:ASP88 4.9 60.2 1.0
CA G:GLY106 4.9 70.0 1.0
CG G:PHE127 5.0 71.9 1.0

Calcium binding site 8 out of 8 in 1fay

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Calcium binding site 8 out of 8 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca303

b:35.3
occ:1.00
 O H:HOH413 2.2 18.9 1.0
O H:PHE127 2.3 64.8 1.0
OD2 H:ASP132 2.4 46.7 1.0
OD1 H:ASP125 2.4 68.7 1.0
OD1 H:ASN129 2.4 70.7 1.0
O H:HOH411 2.6 23.1 1.0
OD2 H:ASP125 2.7 68.7 1.0
CG H:ASP125 2.9 68.7 1.0
CG H:ASP132 3.4 46.7 1.0
CG H:ASN129 3.5 70.7 1.0
C H:PHE127 3.5 64.8 1.0
OD1 H:ASP132 4.0 46.7 1.0
N H:ASN129 4.0 39.9 1.0
O H:HOH410 4.1 21.2 1.0
CB H:ASN129 4.3 70.7 1.0
CA H:PHE127 4.3 64.8 1.0
CB H:ASP125 4.4 68.7 1.0
ND2 H:ASN129 4.4 70.7 1.0
CB H:PHE127 4.4 56.7 1.0
N H:PHE127 4.4 64.8 1.0
NE1 H:TRP131 4.5 88.9 1.0
N H:GLN128 4.5 61.6 1.0
O H:GLY106 4.5 64.2 1.0
CB H:ASP132 4.6 46.7 1.0
O H:ASP88 4.6 99.6 1.0
CA H:GLN128 4.7 61.6 1.0
CD2 H:PHE127 4.7 56.7 1.0
MN H:MN300 4.7 35.3 1.0
CA H:ASN129 4.8 39.9 1.0
C H:GLN128 4.8 61.6 1.0
OD2 H:ASP88 4.8 69.3 1.0
CA H:GLY106 4.8 64.2 1.0
CG H:PHE127 5.0 56.7 1.0

Reference:

N.Manoj, V.R.Srinivas, A.Surolia, M.Vijayan, K.Suguna. Carbohydrate Specificity and Salt-Bridge Mediated Conformational Change in Acidic Winged Bean Agglutinin. J.Mol.Biol. V. 302 1129 2000.
ISSN: ISSN 0022-2836
PubMed: 11183779
DOI: 10.1006/JMBI.2000.4111
Page generated: Thu Jul 11 08:06:03 2024

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