Atomistry » Calcium » PDB 2z8x-2zp4 » 2zml
Atomistry »
  Calcium »
    PDB 2z8x-2zp4 »
      2zml »

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

Go back to Calcium Binding Sites List in 2zml
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

Go back to Calcium Binding Sites List in 2zml
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

Go back to Calcium Binding Sites List in 2zml
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: Sat Dec 12 04:01:46 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy