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Calcium in PDB 5kxe: Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2

Protein crystallography data

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2, PDB code: 5kxe 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) 50.01 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.584, 97.943, 149.158, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.2

Other elements in 5kxe:

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2 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 4.2 (pdb code 5kxe). 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 4.2, PDB code: 5kxe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5kxe

Go back to Calcium Binding Sites List in 5kxe
Calcium binding site 1 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2


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 4.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca308

b:19.5
occ:1.00
 O A:HOH458 2.3 14.4 1.0
O A:PHE159 2.3 21.2 1.0
O A:HOH460 2.3 19.1 1.0
OD2 A:ASP164 2.4 21.1 1.0
OD1 A:ASN161 2.4 21.9 1.0
OD1 A:ASP157 2.4 17.3 1.0
OD2 A:ASP157 2.5 17.4 1.0
CG A:ASP157 2.8 17.8 1.0
CG A:ASP164 3.5 20.8 1.0
CG A:ASN161 3.5 22.3 1.0
C A:PHE159 3.6 22.2 1.0
OD1 A:ASP164 3.9 20.1 1.0
N A:ASN161 4.0 22.6 1.0
CB A:ASN161 4.1 21.7 1.0
MN A:MN307 4.2 26.5 1.0
N A:PHE159 4.3 23.0 1.0
CB A:ASP157 4.3 17.9 1.0
CA A:PHE159 4.4 22.8 1.0
O A:HOH404 4.4 17.9 1.0
O A:GLY135 4.5 22.9 1.0
NE1 A:TRP163 4.5 26.5 1.0
CB A:PHE159 4.5 24.0 1.0
N A:LYS160 4.6 22.6 1.0
O A:ASP117 4.6 22.2 1.0
OD1 A:ASP117 4.6 22.2 1.0
ND2 A:ASN161 4.6 22.3 1.0
CB A:ASP164 4.7 22.2 1.0
CA A:ASN161 4.7 22.4 1.0
CA A:LYS160 4.7 23.2 1.0
CA A:GLY135 4.7 22.5 1.0
C A:LYS160 4.8 24.0 1.0
CD2 A:PHE159 4.8 23.8 1.0
CE1 A:HIS169 4.9 19.4 1.0
CZ2 A:TRP163 5.0 26.8 1.0

Calcium binding site 2 out of 4 in 5kxe

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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 4.2


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 4.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca310

b:21.6
occ:1.00
 O B:HOH441 2.3 19.9 1.0
O B:PHE159 2.3 22.2 1.0
O B:HOH474 2.3 19.8 1.0
OD2 B:ASP164 2.4 21.0 1.0
OD1 B:ASP157 2.4 18.3 1.0
OD1 B:ASN161 2.4 22.4 1.0
OD2 B:ASP157 2.5 19.1 1.0
CG B:ASP157 2.8 19.8 1.0
CG B:ASP164 3.5 22.6 1.0
CG B:ASN161 3.5 25.2 1.0
C B:PHE159 3.5 23.9 1.0
OD1 B:ASP164 3.9 20.8 1.0
N B:ASN161 4.0 26.4 1.0
CB B:ASN161 4.1 25.0 1.0
MN B:MN309 4.2 27.7 1.0
CB B:ASP157 4.3 20.4 1.0
N B:PHE159 4.3 24.3 1.0
CA B:PHE159 4.4 24.5 1.0
O B:HOH410 4.4 24.5 1.0
O B:GLY135 4.5 24.6 1.0
N B:LYS160 4.5 24.9 1.0
NE1 B:TRP163 4.5 26.9 1.0
OD1 B:ASP117 4.6 21.4 1.0
CB B:PHE159 4.6 26.1 1.0
O B:ASP117 4.6 24.4 1.0
ND2 B:ASN161 4.6 25.6 1.0
CA B:LYS160 4.7 26.3 1.0
CA B:ASN161 4.7 25.7 1.0
CB B:ASP164 4.7 23.2 1.0
C B:LYS160 4.7 26.6 1.0
CA B:GLY135 4.8 25.4 1.0
CD2 B:PHE159 4.8 25.1 1.0
CE1 B:HIS169 4.9 20.6 1.0
CZ2 B:TRP163 5.0 27.6 1.0

Calcium binding site 3 out of 4 in 5kxe

Go back to Calcium Binding Sites List in 5kxe
Calcium binding site 3 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2


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 4.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca305

b:18.1
occ:1.00
 O C:PHE159 2.3 19.1 1.0
OD2 C:ASP164 2.3 18.7 1.0
O C:HOH469 2.4 16.1 1.0
OD1 C:ASN161 2.4 17.9 1.0
OD1 C:ASP157 2.4 17.8 1.0
O C:HOH444 2.4 15.4 1.0
OD2 C:ASP157 2.5 18.0 1.0
CG C:ASP157 2.8 17.4 1.0
CG C:ASP164 3.4 20.1 1.0
CG C:ASN161 3.5 19.5 1.0
C C:PHE159 3.5 20.4 1.0
OD1 C:ASP164 3.9 18.0 1.0
N C:ASN161 3.9 19.6 1.0
CB C:ASN161 4.1 20.1 1.0
MN C:MN304 4.2 25.4 1.0
O C:HOH432 4.3 14.5 1.0
N C:PHE159 4.3 19.6 1.0
CA C:PHE159 4.3 20.1 1.0
CB C:ASP157 4.3 17.7 1.0
N C:LYS160 4.5 20.4 1.0
NE1 C:TRP163 4.5 20.9 1.0
CB C:PHE159 4.5 20.9 1.0
O C:GLY135 4.6 19.8 1.0
O C:ASP117 4.6 19.3 1.0
OD1 C:ASP117 4.6 19.0 1.0
ND2 C:ASN161 4.6 19.0 1.0
CB C:ASP164 4.7 20.7 1.0
CA C:ASN161 4.7 21.3 1.0
CA C:LYS160 4.7 21.2 1.0
C C:LYS160 4.7 20.6 1.0
CA C:GLY135 4.8 20.0 1.0
CD2 C:PHE159 4.8 24.0 1.0
CE1 C:HIS169 4.9 18.2 1.0
CZ2 C:TRP163 5.0 21.4 1.0

Calcium binding site 4 out of 4 in 5kxe

Go back to Calcium Binding Sites List in 5kxe
Calcium binding site 4 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2


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 4.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca305

b:24.9
occ:1.00
 O D:HOH472 2.2 24.5 1.0
O D:HOH459 2.3 20.5 1.0
O D:PHE159 2.3 27.0 1.0
OD2 D:ASP164 2.4 25.8 1.0
OD1 D:ASN161 2.4 28.7 1.0
OD1 D:ASP157 2.4 22.7 1.0
OD2 D:ASP157 2.5 21.4 1.0
CG D:ASP157 2.8 22.4 1.0
CG D:ASP164 3.4 27.7 1.0
CG D:ASN161 3.5 30.7 1.0
C D:PHE159 3.5 28.2 1.0
OD1 D:ASP164 3.9 27.9 1.0
N D:ASN161 4.0 30.0 1.0
CB D:ASN161 4.1 29.3 1.0
MN D:MN304 4.3 30.2 1.0
CB D:ASP157 4.3 22.4 1.0
N D:PHE159 4.3 27.6 1.0
CA D:PHE159 4.4 28.3 1.0
O D:HOH412 4.4 19.4 1.0
NE1 D:TRP163 4.5 34.4 1.0
O D:GLY135 4.5 28.4 1.0
N D:LYS160 4.5 29.9 1.0
CB D:PHE159 4.6 30.0 1.0
O D:ASP117 4.6 26.7 1.0
OD1 D:ASP117 4.6 25.6 1.0
ND2 D:ASN161 4.6 31.1 1.0
CA D:ASN161 4.7 29.7 1.0
CB D:ASP164 4.7 30.3 1.0
CA D:LYS160 4.7 29.8 1.0
C D:LYS160 4.7 30.1 1.0
CA D:GLY135 4.8 30.4 1.0
CD2 D:PHE159 4.8 28.5 1.0
CE1 D:HIS169 4.9 25.6 1.0
CZ2 D:TRP163 4.9 35.0 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: Mon Jul 15 07:08:05 2024

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