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Calcium in PDB 2zmn: Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc

Protein crystallography data

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc, PDB code: 2zmn was solved by K.A.Kulkarni, S.Katiyar, 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) 30.00 / 2.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 158.061, 91.758, 73.570, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.7

Other elements in 2zmn:

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc (pdb code 2zmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc, PDB code: 2zmn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2zmn

Go back to Calcium Binding Sites List in 2zmn
Calcium binding site 1 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc


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 Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:18.9
occ:1.00
 OD2 A:ASP131 2.5 34.0 1.0
O A:PHE126 2.5 31.5 1.0
OD1 A:ASP124 2.6 26.3 1.0
OD2 A:ASP124 2.6 27.0 1.0
OD1 A:ASN128 2.7 35.0 1.0
O A:HOH605 2.7 18.4 1.0
O A:HOH606 2.7 42.0 1.0
CG A:ASP124 3.0 27.3 1.0
CG A:ASP131 3.6 33.0 1.0
C A:PHE126 3.6 30.2 1.0
CG A:ASN128 3.6 34.2 1.0
N A:ASN128 4.1 31.3 1.0
O A:HOH604 4.1 11.2 1.0
OD1 A:ASP131 4.2 33.6 1.0
CB A:ASN128 4.2 32.7 1.0
CB A:PHE126 4.4 27.8 1.0
CA A:PHE126 4.4 28.7 1.0
CZ A:PHE107 4.4 16.3 1.0
CA A:GLY105 4.4 25.5 1.0
MN A:MN300 4.5 37.6 1.0
N A:PHE126 4.5 28.2 1.0
CB A:ASP124 4.5 25.9 1.0
CD2 A:PHE126 4.5 27.2 1.0
N A:ARG127 4.6 31.0 1.0
ND2 A:ASN128 4.7 34.9 1.0
NE1 A:TRP130 4.7 31.9 1.0
O A:ASP87 4.7 24.8 1.0
CA A:ARG127 4.7 31.1 1.0
O A:GLY105 4.7 24.8 1.0
OD2 A:ASP87 4.7 23.1 1.0
CE1 A:PHE107 4.8 17.1 1.0
CB A:ASP131 4.8 30.8 1.0
CA A:ASN128 4.8 32.1 1.0
C A:ARG127 4.8 30.6 1.0
CG A:PHE126 5.0 27.9 1.0

Calcium binding site 2 out of 4 in 2zmn

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Calcium binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc


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 Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:20.5
occ:1.00
 OD2 B:ASP131 2.4 32.8 1.0
O B:PHE126 2.5 26.6 1.0
OD2 B:ASP124 2.6 25.4 1.0
OD1 B:ASP124 2.6 27.9 1.0
OD1 B:ASN128 2.7 34.0 1.0
O B:HOH624 2.7 19.6 1.0
O B:HOH625 2.7 26.1 1.0
CG B:ASP124 2.9 26.4 1.0
CG B:ASP131 3.6 29.5 1.0
C B:PHE126 3.6 28.4 1.0
CG B:ASN128 3.6 32.9 1.0
N B:ASN128 4.0 30.8 1.0
OD1 B:ASP131 4.1 29.0 1.0
CB B:ASN128 4.2 31.7 1.0
OD2 B:ASP87 4.3 24.3 1.0
CA B:PHE126 4.4 27.8 1.0
CZ B:PHE107 4.4 16.8 1.0
CB B:PHE126 4.4 27.6 1.0
O B:HOH623 4.4 8.7 1.0
MN B:MN300 4.4 26.2 1.0
N B:PHE126 4.4 25.9 1.0
CB B:ASP124 4.4 25.4 1.0
CA B:GLY105 4.4 26.6 1.0
N B:ARG127 4.5 29.6 1.0
CD2 B:PHE126 4.6 28.7 1.0
CA B:ARG127 4.6 30.5 1.0
O B:GLY105 4.7 27.3 1.0
O B:ASP87 4.7 20.0 1.0
NE1 B:TRP130 4.7 28.9 1.0
CB B:ASP131 4.7 28.8 1.0
ND2 B:ASN128 4.7 35.9 1.0
CA B:ASN128 4.7 32.1 1.0
CE1 B:PHE107 4.8 17.6 1.0
C B:ARG127 4.8 30.8 1.0
CG B:PHE126 5.0 27.9 1.0

Calcium binding site 3 out of 4 in 2zmn

Go back to Calcium Binding Sites List in 2zmn
Calcium binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc


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 Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:28.8
occ:1.00
 OD2 C:ASP131 2.5 36.4 1.0
OD1 C:ASN128 2.6 36.9 1.0
O C:PHE126 2.6 28.7 1.0
OD2 C:ASP124 2.7 27.0 1.0
O C:HOH605 2.7 29.3 1.0
O C:HOH606 2.8 50.3 1.0
OD1 C:ASP124 2.8 26.8 1.0
CG C:ASP124 3.1 26.8 1.0
CG C:ASN128 3.5 35.5 1.0
CG C:ASP131 3.5 34.1 1.0
C C:PHE126 3.7 29.8 1.0
N C:ASN128 4.0 32.5 1.0
OD1 C:ASP131 4.0 34.3 1.0
CB C:ASN128 4.1 34.2 1.0
CA C:GLY105 4.4 28.3 1.0
CZ C:PHE107 4.4 22.6 1.0
O C:HOH604 4.5 17.2 1.0
NE1 C:TRP130 4.5 34.2 1.0
CB C:PHE126 4.5 29.6 1.0
OD2 C:ASP87 4.5 31.4 1.0
CA C:PHE126 4.5 28.9 1.0
ND2 C:ASN128 4.6 36.3 1.0
O C:GLY105 4.6 28.5 1.0
CD2 C:PHE126 4.6 31.1 1.0
CB C:ASP124 4.6 25.6 1.0
MN C:MN300 4.6 47.7 1.0
N C:PHE126 4.6 27.3 1.0
N C:ARG127 4.7 31.2 1.0
CA C:ASN128 4.7 32.9 1.0
CB C:ASP131 4.7 32.1 1.0
CA C:ARG127 4.7 31.9 1.0
C C:ARG127 4.8 32.4 1.0
CE1 C:PHE107 4.8 20.2 1.0
CZ2 C:TRP130 4.9 33.5 1.0
CE2 C:TRP130 5.0 33.2 1.0
C C:GLY105 5.0 28.8 1.0

Calcium binding site 4 out of 4 in 2zmn

Go back to Calcium Binding Sites List in 2zmn
Calcium binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc


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 Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:18.3
occ:1.00
 OD2 D:ASP131 2.4 34.9 1.0
O D:PHE126 2.5 30.3 1.0
OD2 D:ASP124 2.6 25.6 1.0
OD1 D:ASP124 2.6 25.5 1.0
OD1 D:ASN128 2.7 34.7 1.0
O D:HOH606 2.7 20.7 1.0
O D:HOH607 2.8 62.6 1.0
CG D:ASP124 3.0 26.7 1.0
CG D:ASP131 3.5 32.3 1.0
CG D:ASN128 3.6 33.7 1.0
C D:PHE126 3.6 30.0 1.0
N D:ASN128 4.0 32.9 1.0
OD1 D:ASP131 4.0 33.0 1.0
CB D:ASN128 4.1 33.0 1.0
O D:HOH604 4.2 21.1 1.0
CA D:GLY105 4.4 28.0 1.0
CA D:PHE126 4.4 28.6 1.0
CZ D:PHE107 4.4 19.2 1.0
CB D:PHE126 4.5 28.3 1.0
CB D:ASP124 4.5 25.7 1.0
N D:PHE126 4.5 27.2 1.0
O D:GLY105 4.5 28.2 1.0
N D:ARG127 4.6 30.5 1.0
NE1 D:TRP130 4.6 29.0 1.0
CD2 D:PHE126 4.6 29.4 1.0
CB D:ASP131 4.6 30.3 1.0
CA D:ARG127 4.6 30.9 1.0
ND2 D:ASN128 4.6 35.7 1.0
CA D:ASN128 4.7 32.2 1.0
C D:ARG127 4.7 32.1 1.0
OD2 D:ASP87 4.8 33.9 1.0
MN D:MN300 4.8 42.9 1.0
O D:ASP87 4.9 33.7 1.0
CE1 D:PHE107 4.9 20.2 1.0
C D:GLY105 5.0 28.2 1.0

Reference:

K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Structure and Sugar-Specificity of Basic Winged-Bean Lectin: Structures of New Disaccharide Complexes and A Comparative Study with Other Known Disaccharide Complexes of the Lectin. Acta Crystallogr.,Sect.D V. 64 730 2008.
ISSN: ISSN 0907-4449
PubMed: 18566508
DOI: 10.1107/S0907444908011323
Page generated: Tue Jul 8 10:05:15 2025

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