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Calcium in PDB 2zml: Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha 1,4 Gal

Protein crystallography data

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha 1,4 Gal, PDB code: 2zml 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) 29.55 / 2.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 157.928, 91.524, 73.654, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.7

Other elements in 2zml:

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha 1,4 Gal 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 1,4 Gal (pdb code 2zml). 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 1,4 Gal, PDB code: 2zml:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2zml

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


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 1,4 Gal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:16.9
occ:1.00
 OD2 A:ASP131 2.5 21.3 1.0
O A:PHE126 2.6 22.8 1.0
OD1 A:ASN128 2.6 30.0 1.0
OD1 A:ASP124 2.6 21.9 1.0
O A:HOH604 2.7 9.7 1.0
OD2 A:ASP124 2.8 21.1 1.0
O A:HOH605 2.8 47.8 1.0
CG A:ASP124 3.1 19.5 1.0
CG A:ASN128 3.6 29.1 1.0
CG A:ASP131 3.7 22.9 1.0
C A:PHE126 3.7 20.8 1.0
N A:ASN128 4.0 23.0 1.0
CB A:ASN128 4.1 26.1 1.0
OD1 A:ASP131 4.2 24.8 1.0
CA A:GLY105 4.4 17.6 1.0
O A:HOH603 4.4 6.2 1.0
CA A:PHE126 4.4 19.4 1.0
N A:PHE126 4.5 18.1 1.0
CB A:PHE126 4.5 21.2 1.0
MN A:MN300 4.5 27.4 1.0
CZ A:PHE107 4.5 9.2 1.0
CD2 A:PHE126 4.5 22.4 1.0
CB A:ASP124 4.5 18.7 1.0
NE1 A:TRP130 4.6 26.8 1.0
N A:ARG127 4.6 20.5 1.0
CA A:ASN128 4.7 24.4 1.0
ND2 A:ASN128 4.7 29.7 1.0
OD2 A:ASP87 4.7 20.1 1.0
CA A:ARG127 4.7 21.4 1.0
O A:GLY105 4.7 15.9 1.0
C A:ARG127 4.8 21.5 1.0
O A:ASP87 4.8 19.1 1.0
CB A:ASP131 4.8 23.4 1.0
CE1 A:PHE107 4.8 12.3 1.0

Calcium binding site 2 out of 4 in 2zml

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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 1,4 Gal


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 1,4 Gal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:16.4
occ:1.00
 OD2 B:ASP131 2.4 21.9 1.0
O B:PHE126 2.5 16.4 1.0
OD1 B:ASN128 2.6 29.8 1.0
OD1 B:ASP124 2.7 21.6 1.0
O B:HOH648 2.7 24.4 1.0
OD2 B:ASP124 2.7 19.0 1.0
O B:HOH647 2.8 8.9 1.0
CG B:ASP124 3.0 19.4 1.0
CG B:ASP131 3.5 20.1 1.0
CG B:ASN128 3.6 27.9 1.0
C B:PHE126 3.7 17.9 1.0
N B:ASN128 3.9 21.5 1.0
CB B:ASN128 4.0 24.6 1.0
OD1 B:ASP131 4.1 19.4 1.0
MN B:MN300 4.2 21.8 1.0
CA B:PHE126 4.5 17.7 1.0
CA B:GLY105 4.5 17.7 1.0
CZ B:PHE107 4.5 8.8 1.0
OD2 B:ASP87 4.5 16.2 1.0
O B:HOH646 4.5 9.0 1.0
N B:PHE126 4.5 16.8 1.0
NE1 B:TRP130 4.5 24.7 1.0
CB B:ASP124 4.5 19.2 1.0
CB B:PHE126 4.6 19.8 1.0
CD2 B:PHE126 4.6 21.1 1.0
CA B:ASN128 4.6 23.3 1.0
N B:ARG127 4.6 19.2 1.0
CA B:ARG127 4.7 20.2 1.0
CB B:ASP131 4.7 20.4 1.0
O B:GLY105 4.7 17.4 1.0
ND2 B:ASN128 4.7 30.9 1.0
C B:ARG127 4.7 20.8 1.0
O B:ASP87 4.8 12.5 1.0
CE1 B:PHE107 5.0 11.9 1.0

Calcium binding site 3 out of 4 in 2zml

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Calcium binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha 1,4 Gal


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 1,4 Gal within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:25.1
occ:1.00
 OD2 C:ASP131 2.4 26.8 1.0
OD2 C:ASP124 2.7 24.9 1.0
OD1 C:ASN128 2.7 31.8 1.0
O C:HOH604 2.7 24.7 1.0
O C:PHE126 2.7 21.0 1.0
O C:HOH603 2.7 26.1 1.0
OD1 C:ASP124 2.7 23.6 1.0
CG C:ASP124 3.1 22.1 1.0
CG C:ASP131 3.5 25.6 1.0
CG C:ASN128 3.6 28.5 1.0
C C:PHE126 3.9 22.8 1.0
OD1 C:ASP131 4.0 25.5 1.0
CB C:ASN128 4.0 27.1 1.0
N C:ASN128 4.0 23.9 1.0
MN C:MN300 4.3 30.4 1.0
O C:HOH602 4.3 7.8 1.0
NE1 C:TRP130 4.4 29.7 1.0
CZ C:PHE107 4.4 15.6 1.0
CA C:GLY105 4.5 22.0 1.0
CB C:ASP124 4.5 21.2 1.0
O C:GLY105 4.6 23.8 1.0
CA C:ASN128 4.7 24.9 1.0
CA C:PHE126 4.7 21.6 1.0
ND2 C:ASN128 4.7 29.6 1.0
CB C:ASP131 4.7 25.9 1.0
N C:PHE126 4.7 19.9 1.0
CB C:PHE126 4.7 22.1 1.0
CD2 C:PHE126 4.7 24.1 1.0
N C:ARG127 4.8 23.3 1.0
CA C:ARG127 4.8 22.3 1.0
C C:ARG127 4.8 23.5 1.0
OD2 C:ASP87 4.9 22.9 1.0
CE1 C:PHE107 4.9 16.4 1.0
CZ2 C:TRP130 4.9 29.6 1.0
CE2 C:TRP130 4.9 29.5 1.0

Calcium binding site 4 out of 4 in 2zml

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


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 1,4 Gal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:19.1
occ:1.00
 OD2 D:ASP131 2.5 20.6 1.0
O D:PHE126 2.6 22.6 1.0
OD1 D:ASP124 2.6 20.5 1.0
OD2 D:ASP124 2.6 20.4 1.0
O D:HOH604 2.7 9.8 1.0
OD1 D:ASN128 2.7 27.4 1.0
O D:HOH619 2.8 50.3 1.0
CG D:ASP124 2.9 19.8 1.0
CG D:ASP131 3.6 21.6 1.0
CG D:ASN128 3.7 26.3 1.0
C D:PHE126 3.7 21.8 1.0
N D:ASN128 4.1 21.9 1.0
OD1 D:ASP131 4.2 20.0 1.0
CB D:ASN128 4.2 24.6 1.0
MN D:MN300 4.4 26.9 1.0
CZ D:PHE107 4.4 12.3 1.0
CB D:ASP124 4.4 18.7 1.0
CA D:GLY105 4.4 20.4 1.0
CA D:PHE126 4.5 20.2 1.0
N D:PHE126 4.5 19.1 1.0
O D:HOH602 4.5 2.9 1.0
CB D:PHE126 4.5 20.5 1.0
O D:GLY105 4.6 17.1 1.0
NE1 D:TRP130 4.6 24.3 1.0
CD2 D:PHE126 4.7 21.7 1.0
N D:ARG127 4.7 20.9 1.0
OD2 D:ASP87 4.7 29.8 1.0
CA D:ARG127 4.8 19.7 1.0
CA D:ASN128 4.8 22.9 1.0
CB D:ASP131 4.8 21.7 1.0
ND2 D:ASN128 4.8 29.3 1.0
O D:ASP87 4.8 26.1 1.0
C D:ARG127 4.8 20.8 1.0
CE1 D:PHE107 4.9 13.3 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: Fri Jul 12 20:05:36 2024

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