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Calcium in PDB 5kxc: Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.

Protein crystallography data

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5., PDB code: 5kxc 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 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.745, 103.383, 148.922, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 21.9

Other elements in 5kxc:

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5. 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 8.5. (pdb code 5kxc). 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 8.5., PDB code: 5kxc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5kxc

Go back to Calcium Binding Sites List in 5kxc
Calcium binding site 1 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.


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 8.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:26.4
occ:1.00
 O A:HOH454 2.3 24.3 1.0
O A:PHE159 2.3 27.9 1.0
OD2 A:ASP164 2.3 25.3 1.0
OD1 A:ASP157 2.4 21.1 1.0
OD1 A:ASN161 2.4 28.0 1.0
O A:HOH471 2.5 26.8 1.0
OD2 A:ASP157 2.6 19.9 1.0
CG A:ASP157 2.8 22.9 1.0
CG A:ASP164 3.4 24.5 1.0
C A:PHE159 3.5 27.7 1.0
CG A:ASN161 3.5 33.2 1.0
OD1 A:ASP164 3.9 24.2 1.0
N A:ASN161 4.0 31.3 1.0
CB A:ASN161 4.1 31.1 1.0
MN A:MN305 4.2 28.2 1.0
N A:PHE159 4.3 25.2 1.0
CA A:PHE159 4.3 28.2 1.0
CB A:ASP157 4.3 24.1 1.0
O A:HOH414 4.5 22.8 1.0
NE1 A:TRP163 4.5 30.6 1.0
N A:LYS160 4.5 29.7 1.0
CB A:PHE159 4.5 29.9 1.0
OD1 A:ASP117 4.6 28.1 1.0
O A:GLY135 4.6 26.5 1.0
O A:ASP117 4.6 25.7 1.0
ND2 A:ASN161 4.6 31.2 1.0
CA A:LYS160 4.7 30.9 1.0
CA A:ASN161 4.7 32.5 1.0
CB A:ASP164 4.7 26.1 1.0
CA A:GLY135 4.7 28.3 1.0
C A:LYS160 4.7 33.8 1.0
CD1 A:PHE159 4.8 32.2 1.0
CE1 A:HIS169 4.9 23.7 1.0

Calcium binding site 2 out of 4 in 5kxc

Go back to Calcium Binding Sites List in 5kxc
Calcium binding site 2 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.


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 8.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:22.5
occ:1.00
 OD2 B:ASP164 2.3 23.4 1.0
O B:PHE159 2.3 25.2 1.0
OD1 B:ASN161 2.3 25.8 1.0
O B:HOH435 2.4 23.0 1.0
OD1 B:ASP157 2.4 22.0 1.0
O B:HOH475 2.4 22.0 1.0
OD2 B:ASP157 2.6 21.0 1.0
CG B:ASP157 2.8 23.2 1.0
CG B:ASP164 3.4 25.4 1.0
CG B:ASN161 3.5 29.5 1.0
C B:PHE159 3.5 24.1 1.0
OD1 B:ASP164 3.9 23.4 1.0
N B:ASN161 3.9 24.9 1.0
CB B:ASN161 4.0 27.6 1.0
MN B:MN304 4.2 27.6 1.0
CA B:PHE159 4.3 24.6 1.0
CB B:ASP157 4.3 22.4 1.0
N B:PHE159 4.3 22.4 1.0
O B:HOH416 4.4 22.0 1.0
NE1 B:TRP163 4.5 27.5 1.0
CB B:PHE159 4.5 22.6 1.0
N B:LYS160 4.5 25.4 1.0
O B:GLY135 4.6 24.7 1.0
ND2 B:ASN161 4.6 30.1 1.0
OD1 B:ASP117 4.6 22.7 1.0
O B:ASP117 4.7 23.0 1.0
CB B:ASP164 4.7 25.0 1.0
CA B:ASN161 4.7 28.1 1.0
CA B:LYS160 4.7 26.6 1.0
C B:LYS160 4.7 26.6 1.0
CA B:GLY135 4.7 25.1 1.0
CD2 B:PHE159 4.8 25.6 1.0
CE1 B:HIS169 4.9 20.6 1.0
CZ2 B:TRP163 5.0 29.6 1.0
CE2 B:TRP163 5.0 27.2 1.0

Calcium binding site 3 out of 4 in 5kxc

Go back to Calcium Binding Sites List in 5kxc
Calcium binding site 3 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.


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 8.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca306

b:27.7
occ:1.00
 O C:PHE159 2.3 27.4 1.0
OD2 C:ASP164 2.4 30.2 1.0
OD1 C:ASN161 2.4 30.0 1.0
O C:HOH435 2.4 28.7 1.0
OD1 C:ASP157 2.4 28.3 1.0
O C:HOH482 2.5 26.4 1.0
OD2 C:ASP157 2.6 24.6 1.0
CG C:ASP157 2.8 28.3 1.0
CG C:ASP164 3.5 29.8 1.0
CG C:ASN161 3.5 34.1 1.0
C C:PHE159 3.5 29.9 1.0
OD1 C:ASP164 3.9 25.4 1.0
N C:ASN161 4.0 34.8 1.0
CB C:ASN161 4.1 33.0 1.0
MN C:MN307 4.2 30.2 1.0
CA C:PHE159 4.3 28.9 1.0
N C:PHE159 4.3 28.5 1.0
O C:HOH422 4.3 25.3 1.0
CB C:ASP157 4.3 27.2 1.0
CB C:PHE159 4.5 29.5 1.0
NE1 C:TRP163 4.5 31.5 1.0
N C:LYS160 4.5 32.0 1.0
OD1 C:ASP117 4.5 28.1 1.0
O C:GLY135 4.6 27.4 1.0
O C:ASP117 4.6 24.7 1.0
ND2 C:ASN161 4.6 33.0 1.0
CA C:LYS160 4.7 36.2 1.0
CA C:ASN161 4.7 33.3 1.0
CA C:GLY135 4.7 27.3 1.0
CB C:ASP164 4.7 30.7 1.0
C C:LYS160 4.7 36.9 1.0
CD1 C:PHE159 4.8 32.3 1.0
CE1 C:HIS169 4.9 28.8 1.0
CZ2 C:TRP163 5.0 31.9 1.0

Calcium binding site 4 out of 4 in 5kxc

Go back to Calcium Binding Sites List in 5kxc
Calcium binding site 4 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.


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 8.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:23.6
occ:1.00
 OD2 D:ASP164 2.3 26.3 1.0
O D:PHE159 2.3 23.7 1.0
O D:HOH465 2.4 24.1 1.0
OD1 D:ASN161 2.4 24.6 1.0
OD1 D:ASP157 2.4 20.6 1.0
O D:HOH432 2.4 24.3 1.0
OD2 D:ASP157 2.5 20.5 1.0
CG D:ASP157 2.8 21.9 1.0
CG D:ASP164 3.4 26.3 1.0
CG D:ASN161 3.5 28.4 1.0
C D:PHE159 3.5 23.6 1.0
OD1 D:ASP164 3.9 24.9 1.0
N D:ASN161 4.0 29.1 1.0
CB D:ASN161 4.1 28.9 1.0
MN D:MN304 4.1 27.4 1.0
O D:HOH407 4.3 23.0 1.0
CB D:ASP157 4.3 22.1 1.0
CA D:PHE159 4.3 25.5 1.0
N D:PHE159 4.3 25.6 1.0
NE1 D:TRP163 4.5 30.3 1.0
N D:LYS160 4.5 27.2 1.0
CB D:PHE159 4.6 26.8 1.0
O D:GLY135 4.6 26.9 1.0
OD1 D:ASP117 4.6 22.2 1.0
CB D:ASP164 4.6 25.4 1.0
ND2 D:ASN161 4.7 31.3 1.0
O D:ASP117 4.7 24.3 1.0
CA D:LYS160 4.7 29.8 1.0
CA D:ASN161 4.7 28.6 1.0
CA D:GLY135 4.7 26.7 1.0
C D:LYS160 4.7 29.9 1.0
CE1 D:HIS169 4.8 24.3 1.0
CD1 D:PHE159 4.9 27.7 1.0
CZ2 D:TRP163 5.0 29.7 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 07:07:05 2024

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