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Calcium in PDB 5kxd: Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5

Protein crystallography data

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5, PDB code: 5kxd was solved by S.V.Evans, O.Haji-Ghassemi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.096, 104.271, 148.739, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.8

Other elements in 5kxd:

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 (pdb code 5kxd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5, PDB code: 5kxd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5kxd

Go back to Calcium Binding Sites List in 5kxd
Calcium binding site 1 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:15.6
occ:1.00
 O A:PHE159 2.3 18.6 1.0
OD2 A:ASP164 2.4 14.0 1.0
OD1 A:ASN161 2.4 16.2 1.0
O A:HOH460 2.4 13.1 1.0
O A:HOH440 2.4 13.2 1.0
OD1 A:ASP157 2.4 13.9 1.0
OD2 A:ASP157 2.5 11.2 1.0
CG A:ASP157 2.8 13.2 1.0
CG A:ASP164 3.4 15.0 1.0
CG A:ASN161 3.5 18.1 1.0
C A:PHE159 3.5 17.5 1.0
OD1 A:ASP164 3.9 15.3 1.0
N A:ASN161 4.0 17.5 1.0
CB A:ASN161 4.1 18.4 1.0
MN A:MN304 4.2 19.2 1.0
CB A:ASP157 4.3 13.5 1.0
CA A:PHE159 4.3 17.9 1.0
N A:PHE159 4.3 16.6 1.0
O A:HOH415 4.4 14.9 1.0
NE1 A:TRP163 4.5 19.1 1.0
CB A:PHE159 4.5 17.9 1.0
N A:LYS160 4.5 18.2 1.0
O A:GLY135 4.6 18.4 1.0
O A:ASP117 4.6 15.4 1.0
ND2 A:ASN161 4.6 18.9 1.0
OD1 A:ASP117 4.7 15.7 1.0
CA A:LYS160 4.7 19.3 1.0
CB A:ASP164 4.7 15.9 1.0
CA A:ASN161 4.7 18.3 1.0
C A:LYS160 4.7 18.8 1.0
CA A:GLY135 4.8 18.0 1.0
CE1 A:HIS169 4.9 13.5 1.0
CD2 A:PHE159 4.9 18.2 1.0

Calcium binding site 2 out of 4 in 5kxd

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Calcium binding site 2 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:14.7
occ:1.00
 O B:PHE159 2.3 15.2 1.0
OD1 B:ASN161 2.4 15.6 1.0
OD2 B:ASP164 2.4 16.0 1.0
O B:HOH484 2.4 11.4 1.0
OD1 B:ASP157 2.4 12.4 1.0
O B:HOH478 2.5 15.9 1.0
OD2 B:ASP157 2.5 12.5 1.0
CG B:ASP157 2.8 13.5 1.0
CG B:ASP164 3.5 15.1 1.0
C B:PHE159 3.5 15.1 1.0
CG B:ASN161 3.5 17.1 1.0
OD1 B:ASP164 3.9 14.5 1.0
N B:ASN161 3.9 16.3 1.0
CB B:ASN161 4.1 16.7 1.0
MN B:MN303 4.2 19.3 1.0
CA B:PHE159 4.2 16.0 1.0
N B:PHE159 4.3 15.6 1.0
O B:HOH448 4.3 14.2 1.0
CB B:ASP157 4.3 14.3 1.0
CB B:PHE159 4.5 16.1 1.0
N B:LYS160 4.5 16.3 1.0
NE1 B:TRP163 4.5 20.2 1.0
O B:GLY135 4.6 18.1 1.0
O B:ASP117 4.6 15.6 1.0
CA B:LYS160 4.6 17.2 1.0
ND2 B:ASN161 4.6 16.6 1.0
OD1 B:ASP117 4.7 14.6 1.0
CA B:ASN161 4.7 17.4 1.0
C B:LYS160 4.7 16.5 1.0
CB B:ASP164 4.7 15.7 1.0
CA B:GLY135 4.8 17.4 1.0
CD2 B:PHE159 4.8 16.4 1.0
CE1 B:HIS169 4.9 13.3 1.0

Calcium binding site 3 out of 4 in 5kxd

Go back to Calcium Binding Sites List in 5kxd
Calcium binding site 3 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca308

b:15.6
occ:1.00
 OD1 C:ASN161 2.3 17.4 1.0
O C:PHE159 2.3 16.8 1.0
O C:HOH453 2.4 13.7 1.0
O C:HOH450 2.4 14.6 1.0
OD2 C:ASP164 2.4 15.4 1.0
OD1 C:ASP157 2.5 15.2 1.0
OD2 C:ASP157 2.6 14.2 1.0
CG C:ASP157 2.9 15.2 1.0
CG C:ASP164 3.5 15.9 1.0
CG C:ASN161 3.5 18.1 1.0
C C:PHE159 3.6 18.1 1.0
OD1 C:ASP164 3.9 15.6 1.0
N C:ASN161 4.0 18.5 1.0
CB C:ASN161 4.1 18.3 1.0
MN C:MN309 4.2 20.0 1.0
CA C:PHE159 4.3 18.3 1.0
N C:PHE159 4.3 16.9 1.0
O C:HOH448 4.4 13.2 1.0
CB C:ASP157 4.4 15.7 1.0
NE1 C:TRP163 4.5 15.8 1.0
CB C:PHE159 4.5 18.8 1.0
O C:GLY135 4.5 15.2 1.0
N C:LYS160 4.6 19.3 1.0
O C:ASP117 4.6 17.2 1.0
ND2 C:ASN161 4.6 19.0 1.0
OD1 C:ASP117 4.6 17.1 1.0
CA C:ASN161 4.7 18.5 1.0
CB C:ASP164 4.7 17.2 1.0
CA C:LYS160 4.7 20.4 1.0
CA C:GLY135 4.7 15.0 1.0
C C:LYS160 4.7 19.5 1.0
CD2 C:PHE159 4.8 19.4 1.0
CE1 C:HIS169 4.9 15.5 1.0
CZ2 C:TRP163 5.0 16.1 1.0

Calcium binding site 4 out of 4 in 5kxd

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Calcium binding site 4 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:15.3
occ:1.00
 O D:HOH465 2.3 16.6 1.0
O D:PHE159 2.3 16.4 1.0
OD2 D:ASP164 2.4 15.3 1.0
OD1 D:ASP157 2.4 12.8 1.0
OD1 D:ASN161 2.4 17.2 1.0
O D:HOH433 2.5 15.1 1.0
OD2 D:ASP157 2.5 12.1 1.0
CG D:ASP157 2.8 12.8 1.0
CG D:ASP164 3.4 14.8 1.0
C D:PHE159 3.5 16.8 1.0
CG D:ASN161 3.5 19.0 1.0
OD1 D:ASP164 3.9 15.1 1.0
N D:ASN161 4.0 18.8 1.0
CB D:ASN161 4.1 18.5 1.0
MN D:MN304 4.2 19.7 1.0
CA D:PHE159 4.3 17.6 1.0
N D:PHE159 4.3 16.7 1.0
CB D:ASP157 4.3 13.1 1.0
O D:HOH410 4.4 13.3 1.0
CB D:PHE159 4.5 18.0 1.0
N D:LYS160 4.5 17.9 1.0
NE1 D:TRP163 4.5 20.3 1.0
O D:GLY135 4.6 17.6 1.0
O D:ASP117 4.6 15.1 1.0
OD1 D:ASP117 4.6 15.8 1.0
CA D:LYS160 4.7 19.9 1.0
ND2 D:ASN161 4.7 19.4 1.0
CB D:ASP164 4.7 16.7 1.0
C D:LYS160 4.7 19.4 1.0
CA D:ASN161 4.7 19.2 1.0
CA D:GLY135 4.8 18.2 1.0
CD2 D:PHE159 4.8 17.4 1.0
CE1 D:HIS169 4.8 14.4 1.0

Reference:

O.Haji-Ghassemi, M.Gilbert, J.Spence, M.J.Schur, M.J.Parker, M.L.Jenkins, J.E.Burke, H.Van Faassen, N.M.Young, S.V.Evans. Molecular Basis For Recognition of the Cancer Glycobiomarker, Lacdinac (Galnac[ Beta 14]Glcnac), By Wisteria Floribunda Agglutinin. J.Biol.Chem. V. 291 24085 2016.
ISSN: ESSN 1083-351X
PubMed: 27601469
DOI: 10.1074/JBC.M116.750463
Page generated: Wed Jul 9 07:38:29 2025

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