Atomistry » Calcium » PDB 1fak-1fn6 » 1fay
Atomistry »
  Calcium »
    PDB 1fak-1fn6 »
      1fay »

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

Go back to Calcium Binding Sites List in 1fay
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

Go back to Calcium Binding Sites List in 1fay
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

Go back to Calcium Binding Sites List in 1fay
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

Go back to Calcium Binding Sites List in 1fay
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

Go back to Calcium Binding Sites List in 1fay
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

Go back to Calcium Binding Sites List in 1fay
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

Go back to Calcium Binding Sites List in 1fay
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy