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Calcium in PDB 5ofx: Plla Lectin, Trisaccharide Complex

Protein crystallography data

The structure of Plla Lectin, Trisaccharide Complex, PDB code: 5ofx was solved by J.Koehnke, A.Sikandar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.09 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.979, 62.998, 75.860, 101.15, 112.79, 94.44
R / Rfree (%) 17.5 / 20.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Plla Lectin, Trisaccharide Complex (pdb code 5ofx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Plla Lectin, Trisaccharide Complex, PDB code: 5ofx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5ofx

Go back to Calcium Binding Sites List in 5ofx
Calcium binding site 1 out of 8 in the Plla Lectin, Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Plla Lectin, Trisaccharide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:10.7
occ:1.00
O A:THR100 2.3 10.8 1.0
O A:TYR38 2.3 10.1 1.0
OD2 A:ASP96 2.4 8.8 1.0
OD1 A:ASN104 2.4 9.7 1.0
OD1 A:ASP103 2.4 11.8 1.0
O3X A:RAF201 2.4 11.9 1.0
O4X A:RAF201 2.5 8.9 1.0
C A:TYR38 3.3 9.9 1.0
C3X A:RAF201 3.4 10.8 1.0
CG A:ASP96 3.4 8.6 1.0
C4X A:RAF201 3.4 10.1 1.0
CG A:ASN104 3.4 9.7 1.0
C A:THR100 3.4 10.4 1.0
CG A:ASP103 3.5 14.0 1.0
OG1 A:THR100 3.5 10.8 1.0
CB A:THR100 3.7 11.8 1.0
OD1 A:ASP96 3.8 8.5 1.0
OD2 A:ASP103 3.8 13.1 1.0
ND2 A:ASN104 3.8 9.6 1.0
CA A:TYR38 4.0 10.8 1.0
C2X A:RAF201 4.0 14.9 1.0
CA A:THR100 4.2 12.6 1.0
CB A:TYR38 4.2 7.8 1.0
N A:GLY39 4.4 10.7 1.0
N A:PHE101 4.4 11.6 1.0
CA A:PHE101 4.6 10.3 1.0
C A:ASP103 4.7 13.9 1.0
N A:ASN104 4.7 10.6 1.0
CA A:GLY39 4.7 11.5 1.0
CB A:ASP96 4.7 8.6 1.0
O2X A:RAF201 4.7 10.5 1.0
CB A:ASN104 4.8 13.0 1.0
CB A:ASP103 4.8 14.8 1.0
C5X A:RAF201 4.8 9.6 1.0
N A:ASP103 4.9 14.7 1.0
O A:ASP103 4.9 11.3 1.0
O B:HOH376 5.0 27.3 1.0
CA A:ASN104 5.0 14.3 1.0

Calcium binding site 2 out of 8 in 5ofx

Go back to Calcium Binding Sites List in 5ofx
Calcium binding site 2 out of 8 in the Plla Lectin, Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Plla Lectin, Trisaccharide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:9.4
occ:1.00
O B:THR100 2.3 9.5 1.0
O B:TYR38 2.3 9.8 1.0
OD2 B:ASP96 2.4 9.3 1.0
OD1 B:ASN104 2.4 11.4 1.0
OD1 B:ASP103 2.4 10.7 1.0
O3X B:RAF201 2.4 10.6 1.0
O4X B:RAF201 2.5 10.4 1.0
C3X B:RAF201 3.4 9.6 1.0
C4X B:RAF201 3.4 9.2 1.0
CG B:ASP103 3.4 11.2 1.0
CG B:ASN104 3.4 9.8 1.0
C B:TYR38 3.4 10.5 1.0
CG B:ASP96 3.4 9.9 1.0
OG1 B:THR100 3.5 9.2 1.0
C B:THR100 3.5 9.6 1.0
OD2 B:ASP103 3.7 11.7 1.0
CB B:THR100 3.8 11.2 1.0
ND2 B:ASN104 3.8 10.7 1.0
OD1 B:ASP96 3.9 10.8 1.0
C2X B:RAF201 4.0 9.8 1.0
CA B:TYR38 4.1 11.1 1.0
CA B:THR100 4.3 10.6 1.0
CB B:TYR38 4.3 9.5 1.0
N B:GLY39 4.5 10.6 1.0
N B:PHE101 4.5 12.7 1.0
CA B:PHE101 4.6 15.1 1.0
N B:ASN104 4.6 14.0 1.0
C B:ASP103 4.6 10.6 1.0
CB B:ASP103 4.7 11.7 1.0
CB B:ASP96 4.7 10.6 1.0
CB B:ASN104 4.7 9.8 1.0
CA B:GLY39 4.7 11.8 1.0
O2X B:RAF201 4.7 11.1 1.0
C5X B:RAF201 4.8 10.1 1.0
N B:ASP103 4.8 12.3 1.0
O B:ASP103 4.9 10.6 1.0
CD1 B:TYR38 4.9 9.2 1.0
CA B:ASN104 5.0 11.2 1.0
CA B:ASP103 5.0 10.0 1.0

Calcium binding site 3 out of 8 in 5ofx

Go back to Calcium Binding Sites List in 5ofx
Calcium binding site 3 out of 8 in the Plla Lectin, Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Plla Lectin, Trisaccharide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:14.0
occ:1.00
O C:TYR38 2.3 15.8 1.0
O C:THR100 2.4 16.5 1.0
OD2 C:ASP96 2.4 13.2 1.0
OD1 C:ASN104 2.4 14.0 1.0
OD1 C:ASP103 2.4 15.8 1.0
O4X C:RAF201 2.4 16.5 1.0
O3X C:RAF201 2.5 16.6 1.0
C4X C:RAF201 3.3 16.7 1.0
C3X C:RAF201 3.4 17.6 1.0
C C:TYR38 3.4 13.9 1.0
CG C:ASP96 3.4 17.3 1.0
CG C:ASN104 3.5 13.8 1.0
CG C:ASP103 3.5 16.5 1.0
C C:THR100 3.5 20.8 1.0
OG1 C:THR100 3.6 17.2 1.0
OD2 C:ASP103 3.8 17.5 1.0
ND2 C:ASN104 3.8 14.7 1.0
OD1 C:ASP96 3.8 13.7 1.0
CB C:THR100 3.9 17.7 1.0
C2X C:RAF201 4.0 18.7 1.0
CA C:TYR38 4.0 14.8 1.0
CB C:TYR38 4.2 13.1 1.0
CA C:THR100 4.3 20.9 1.0
N C:GLY39 4.4 13.9 1.0
N C:PHE101 4.5 15.8 1.0
CA C:PHE101 4.5 15.2 1.0
CA C:GLY39 4.7 14.9 1.0
C C:ASP103 4.7 14.8 1.0
CB C:ASP96 4.7 15.0 1.0
N C:ASN104 4.7 14.2 1.0
O2X C:RAF201 4.7 18.1 1.0
C5X C:RAF201 4.7 19.1 1.0
CB C:ASP103 4.8 15.9 1.0
CB C:ASN104 4.8 13.6 1.0
N C:ASP103 4.9 15.9 1.0
C C:PHE101 4.9 15.1 1.0
CD1 C:TYR38 4.9 13.5 1.0
O C:ASP103 5.0 14.6 1.0

Calcium binding site 4 out of 8 in 5ofx

Go back to Calcium Binding Sites List in 5ofx
Calcium binding site 4 out of 8 in the Plla Lectin, Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Plla Lectin, Trisaccharide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:15.7
occ:1.00
O D:TYR38 2.3 18.8 1.0
OD2 D:ASP96 2.4 15.2 1.0
O D:THR100 2.4 22.1 1.0
OD1 D:ASN104 2.4 17.5 1.0
OD1 D:ASP103 2.5 19.1 1.0
O3X D:RAF201 2.5 18.4 1.0
O4X D:RAF201 2.5 12.5 1.0
C D:TYR38 3.3 23.2 1.0
C3X D:RAF201 3.4 18.5 1.0
C4X D:RAF201 3.4 18.9 1.0
CG D:ASP96 3.4 15.3 1.0
CG D:ASN104 3.4 21.1 1.0
CG D:ASP103 3.5 29.4 1.0
C D:THR100 3.6 23.8 1.0
OG1 D:THR100 3.7 18.8 1.0
OD1 D:ASP96 3.8 16.8 1.0
ND2 D:ASN104 3.8 21.1 1.0
OD2 D:ASP103 3.8 19.1 1.0
CA D:TYR38 4.0 20.6 1.0
C2X D:RAF201 4.0 13.7 1.0
CB D:THR100 4.0 21.8 1.0
CB D:TYR38 4.2 14.6 1.0
N D:GLY39 4.4 19.5 1.0
CA D:THR100 4.4 18.8 1.0
N D:PHE101 4.5 20.0 1.0
CA D:PHE101 4.5 18.2 1.0
N D:ASN104 4.7 22.2 1.0
C D:ASP103 4.7 23.7 1.0
CA D:GLY39 4.7 21.4 1.0
CB D:ASP96 4.7 14.5 1.0
O2X D:RAF201 4.8 23.9 1.0
CB D:ASN104 4.8 20.8 1.0
CB D:ASP103 4.8 22.9 1.0
N D:ASP103 4.8 19.3 1.0
C5X D:RAF201 4.8 27.1 1.0
C D:PHE101 4.9 20.5 1.0
O D:ASP103 5.0 20.2 1.0
CD2 D:TYR38 5.0 14.5 1.0
CA D:ASP103 5.0 23.8 1.0

Calcium binding site 5 out of 8 in 5ofx

Go back to Calcium Binding Sites List in 5ofx
Calcium binding site 5 out of 8 in the Plla Lectin, Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Plla Lectin, Trisaccharide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:11.3
occ:1.00
O E:TYR38 2.3 13.4 1.0
O E:THR100 2.3 11.7 1.0
OD2 E:ASP96 2.4 9.4 1.0
OD1 E:ASP103 2.4 11.4 1.0
O3X E:RAF201 2.4 11.9 1.0
OD1 E:ASN104 2.4 13.6 1.0
O4X E:RAF201 2.5 13.9 1.0
C3X E:RAF201 3.4 13.6 1.0
C E:TYR38 3.4 14.2 1.0
C4X E:RAF201 3.4 15.7 1.0
CG E:ASP103 3.4 11.8 1.0
CG E:ASP96 3.4 9.4 1.0
CG E:ASN104 3.4 13.0 1.0
C E:THR100 3.5 11.1 1.0
OG1 E:THR100 3.5 10.7 1.0
OD2 E:ASP103 3.7 14.5 1.0
CB E:THR100 3.7 10.6 1.0
ND2 E:ASN104 3.8 11.2 1.0
OD1 E:ASP96 3.8 9.3 1.0
C2X E:RAF201 4.0 8.1 1.0
CA E:TYR38 4.0 12.8 1.0
CA E:THR100 4.2 11.0 1.0
CB E:TYR38 4.3 13.1 1.0
N E:GLY39 4.4 11.7 1.0
N E:PHE101 4.5 11.9 1.0
CA E:PHE101 4.6 12.5 1.0
C E:ASP103 4.7 13.9 1.0
CA E:GLY39 4.7 12.7 1.0
N E:ASN104 4.7 14.9 1.0
CB E:ASP96 4.7 10.0 1.0
CB E:ASP103 4.7 11.3 1.0
O2X E:RAF201 4.8 14.6 1.0
CB E:ASN104 4.8 12.7 1.0
C5X E:RAF201 4.8 15.9 1.0
N E:ASP103 4.8 11.2 1.0
O E:ASP103 4.9 11.8 1.0
CD2 E:TYR38 4.9 10.9 1.0
CA E:ASP103 5.0 11.3 1.0
C E:PHE101 5.0 13.8 1.0

Calcium binding site 6 out of 8 in 5ofx

Go back to Calcium Binding Sites List in 5ofx
Calcium binding site 6 out of 8 in the Plla Lectin, Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Plla Lectin, Trisaccharide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca202

b:9.8
occ:1.00
O F:TYR38 2.3 11.4 1.0
O F:THR100 2.3 11.3 1.0
OD2 F:ASP96 2.4 11.7 1.0
OD1 F:ASP103 2.4 12.4 1.0
O3X F:RAF201 2.4 12.9 1.0
OD1 F:ASN104 2.4 10.6 1.0
O4X F:RAF201 2.6 12.9 1.0
C F:TYR38 3.4 10.3 1.0
C3X F:RAF201 3.4 13.3 1.0
CG F:ASP103 3.4 13.3 1.0
CG F:ASN104 3.4 10.0 1.0
CG F:ASP96 3.4 10.4 1.0
C4X F:RAF201 3.5 12.9 1.0
C F:THR100 3.5 11.3 1.0
OG1 F:THR100 3.6 11.8 1.0
OD2 F:ASP103 3.7 12.5 1.0
ND2 F:ASN104 3.8 12.6 1.0
CB F:THR100 3.8 11.2 1.0
OD1 F:ASP96 3.8 9.6 1.0
CA F:TYR38 4.0 11.1 1.0
C2X F:RAF201 4.0 16.5 1.0
CB F:TYR38 4.3 9.5 1.0
CA F:THR100 4.3 13.3 1.0
N F:GLY39 4.4 10.2 1.0
N F:PHE101 4.5 9.8 1.0
CA F:PHE101 4.6 9.6 1.0
C F:ASP103 4.7 13.0 1.0
N F:ASN104 4.7 12.9 1.0
CA F:GLY39 4.7 12.5 1.0
CB F:ASP96 4.7 11.0 1.0
CB F:ASP103 4.7 13.3 1.0
O2X F:RAF201 4.8 12.9 1.0
CB F:ASN104 4.8 11.6 1.0
N F:ASP103 4.8 13.5 1.0
C5X F:RAF201 4.8 12.9 1.0
O F:ASP103 4.9 12.4 1.0
C F:PHE101 5.0 11.1 1.0
CA F:ASP103 5.0 12.4 1.0

Calcium binding site 7 out of 8 in 5ofx

Go back to Calcium Binding Sites List in 5ofx
Calcium binding site 7 out of 8 in the Plla Lectin, Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Plla Lectin, Trisaccharide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:19.4
occ:1.00
O G:THR100 2.3 26.8 1.0
O G:TYR38 2.3 20.9 1.0
OD2 G:ASP96 2.4 15.2 1.0
OD1 G:ASN104 2.4 20.7 1.0
OD1 G:ASP103 2.4 23.6 1.0
C G:TYR38 3.4 20.2 1.0
CG G:ASP96 3.4 18.3 1.0
CG G:ASP103 3.4 27.1 1.0
CG G:ASN104 3.5 21.8 1.0
C G:THR100 3.5 23.6 1.0
OD1 G:ASP96 3.7 15.2 1.0
OD2 G:ASP103 3.8 24.8 1.0
OG1 G:THR100 3.8 27.0 1.0
ND2 G:ASN104 3.8 27.4 1.0
CB G:THR100 4.0 25.0 1.0
CA G:TYR38 4.0 21.8 1.0
CB G:TYR38 4.3 17.9 1.0
CA G:THR100 4.3 24.2 1.0
N G:PHE101 4.4 20.7 1.0
CA G:PHE101 4.5 20.8 1.0
N G:GLY39 4.5 22.9 1.0
O G:HOH392 4.6 41.6 1.0
N G:ASN104 4.7 22.0 1.0
C G:ASP103 4.7 24.6 1.0
CB G:ASP96 4.7 17.1 1.0
CB G:ASP103 4.7 21.1 1.0
N G:ASP103 4.8 22.5 1.0
CB G:ASN104 4.8 19.3 1.0
CA G:GLY39 4.8 33.4 1.0
C G:PHE101 4.8 26.5 1.0
CA G:ASP103 5.0 20.6 1.0

Calcium binding site 8 out of 8 in 5ofx

Go back to Calcium Binding Sites List in 5ofx
Calcium binding site 8 out of 8 in the Plla Lectin, Trisaccharide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Plla Lectin, Trisaccharide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca202

b:15.6
occ:1.00
O H:THR100 2.4 16.7 1.0
OD2 H:ASP96 2.4 12.7 1.0
OD1 H:ASN104 2.4 16.1 1.0
O H:TYR38 2.4 14.6 1.0
O3X H:RAF201 2.5 43.8 1.0
OD1 H:ASP103 2.5 17.1 1.0
O4X H:RAF201 2.5 20.0 1.0
CG H:ASN104 3.4 15.3 1.0
C3X H:RAF201 3.4 39.1 1.0
C4X H:RAF201 3.4 32.6 1.0
CG H:ASP96 3.4 16.3 1.0
C H:TYR38 3.4 12.5 1.0
CG H:ASP103 3.5 15.3 1.0
C H:THR100 3.5 18.2 1.0
OG1 H:THR100 3.7 17.1 1.0
ND2 H:ASN104 3.7 16.0 1.0
OD1 H:ASP96 3.8 13.8 1.0
OD2 H:ASP103 3.9 14.4 1.0
CB H:THR100 4.0 17.8 1.0
C2X H:RAF201 4.0 44.2 1.0
CA H:TYR38 4.0 10.8 1.0
CB H:TYR38 4.3 12.7 1.0
CA H:THR100 4.4 21.1 1.0
O H:HOH375 4.4 34.0 1.0
N H:PHE101 4.5 18.8 1.0
N H:GLY39 4.5 11.6 1.0
CA H:PHE101 4.5 15.5 1.0
N H:ASN104 4.7 13.3 1.0
C H:ASP103 4.7 16.7 1.0
CB H:ASP96 4.7 14.9 1.0
CB H:ASN104 4.7 13.9 1.0
O2X H:RAF201 4.7 49.2 1.0
CA H:GLY39 4.7 13.1 1.0
C5X H:RAF201 4.8 31.0 1.0
CB H:ASP103 4.8 15.2 1.0
N H:ASP103 4.9 14.3 1.0
C H:PHE101 4.9 17.6 1.0
O H:ASP103 5.0 15.8 1.0

Reference:

G.Beshr, A.Sikandar, E.M.Jemiller, N.Klymiuk, D.Hauck, S.Wagner, E.Wolf, J.Koehnke, A.Titz. Photorhabdus Luminescens Lectin A (Plla): A New Probe For Detecting Alpha-Galactoside-Terminating Glycoconjugates. J. Biol. Chem. V. 292 19935 2017.
ISSN: ESSN 1083-351X
PubMed: 28972138
DOI: 10.1074/JBC.M117.812792
Page generated: Mon Jul 15 09:46:33 2024

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