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Calcium in PDB 5ofi: Plla Lectin, Fluorophore Carbohydrate Complex

Protein crystallography data

The structure of Plla Lectin, Fluorophore Carbohydrate Complex, PDB code: 5ofi 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) 45.67 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.564, 134.331, 153.045, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Plla Lectin, Fluorophore Carbohydrate Complex (pdb code 5ofi). 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, Fluorophore Carbohydrate Complex, PDB code: 5ofi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5ofi

Go back to Calcium Binding Sites List in 5ofi
Calcium binding site 1 out of 8 in the Plla Lectin, Fluorophore Carbohydrate 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, Fluorophore Carbohydrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:24.7
occ:1.00
O C:TYR38 2.3 27.8 1.0
O C:THR100 2.3 26.2 1.0
OD1 C:ASN104 2.4 24.1 1.0
OD2 C:ASP96 2.4 22.9 1.0
OD1 C:ASP103 2.4 26.7 1.0
O13 C:9TQ202 2.4 19.8 1.0
O11 C:9TQ202 2.4 20.5 1.0
C10 C:9TQ202 3.3 21.0 1.0
C12 C:9TQ202 3.3 19.9 1.0
C C:TYR38 3.3 27.9 1.0
CG C:ASN104 3.4 23.0 1.0
CG C:ASP103 3.4 27.4 1.0
CG C:ASP96 3.5 22.8 1.0
C C:THR100 3.5 25.6 1.0
OG1 C:THR100 3.6 24.0 1.0
ND2 C:ASN104 3.7 19.3 1.0
OD2 C:ASP103 3.8 25.4 1.0
OD1 C:ASP96 3.9 20.1 1.0
C08 C:9TQ202 3.9 23.2 1.0
CA C:TYR38 4.0 30.1 1.0
CB C:THR100 4.0 25.7 1.0
CB C:TYR38 4.2 24.1 1.0
CA C:THR100 4.4 28.5 1.0
N C:GLY39 4.4 26.4 1.0
N C:PHE101 4.5 26.2 1.0
CA C:PHE101 4.6 27.5 1.0
N C:ASN104 4.6 23.2 1.0
O09 C:9TQ202 4.6 27.8 1.0
CA C:GLY39 4.7 29.2 1.0
C14 C:9TQ202 4.7 24.9 1.0
CB C:ASN104 4.7 22.9 1.0
C C:ASP103 4.7 24.7 1.0
CB C:ASP96 4.7 19.3 1.0
CB C:ASP103 4.8 27.6 1.0
N C:ASP103 4.9 24.0 1.0
C C:PHE101 4.9 32.1 1.0
CD1 C:TYR38 5.0 20.8 1.0

Calcium binding site 2 out of 8 in 5ofi

Go back to Calcium Binding Sites List in 5ofi
Calcium binding site 2 out of 8 in the Plla Lectin, Fluorophore Carbohydrate 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, Fluorophore Carbohydrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:21.4
occ:1.00
O11 A:9TQ202 2.3 25.7 1.0
O A:THR100 2.3 24.4 1.0
OD1 A:ASN104 2.3 27.9 1.0
O A:TYR38 2.4 20.6 1.0
OD1 A:ASP103 2.4 24.8 1.0
OD2 A:ASP96 2.5 23.5 1.0
O13 A:9TQ202 2.6 23.6 1.0
C10 A:9TQ202 3.2 25.0 1.0
C12 A:9TQ202 3.3 25.8 1.0
CG A:ASN104 3.3 23.6 1.0
C A:TYR38 3.4 26.1 1.0
CG A:ASP103 3.4 30.5 1.0
C A:THR100 3.5 25.7 1.0
CG A:ASP96 3.5 25.0 1.0
OG1 A:THR100 3.6 27.4 1.0
ND2 A:ASN104 3.7 27.4 1.0
OD2 A:ASP103 3.7 27.4 1.0
CB A:THR100 3.9 32.2 1.0
OD1 A:ASP96 3.9 23.0 1.0
C08 A:9TQ202 3.9 24.1 1.0
CA A:TYR38 4.1 27.5 1.0
CB A:TYR38 4.3 20.6 1.0
CA A:THR100 4.3 26.3 1.0
N A:GLY39 4.4 26.1 1.0
N A:PHE101 4.5 24.3 1.0
CA A:PHE101 4.6 33.0 1.0
N A:ASN104 4.6 27.0 1.0
O09 A:9TQ202 4.6 26.9 1.0
CA A:GLY39 4.7 29.0 1.0
CB A:ASN104 4.7 23.5 1.0
C A:ASP103 4.7 28.1 1.0
C14 A:9TQ202 4.7 26.7 1.0
CB A:ASP103 4.8 30.2 1.0
CB A:ASP96 4.8 22.2 1.0
N A:ASP103 4.9 24.6 1.0
C A:PHE101 5.0 35.4 1.0
CD1 A:TYR38 5.0 20.7 1.0

Calcium binding site 3 out of 8 in 5ofi

Go back to Calcium Binding Sites List in 5ofi
Calcium binding site 3 out of 8 in the Plla Lectin, Fluorophore Carbohydrate 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, Fluorophore Carbohydrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:21.4
occ:1.00
O B:THR100 2.3 22.0 1.0
OD1 B:ASP103 2.3 24.5 1.0
O B:TYR38 2.4 24.0 1.0
OD1 B:ASN104 2.4 19.4 1.0
OD2 B:ASP96 2.4 16.7 1.0
O13 B:9TQ202 2.5 24.0 1.0
O11 B:9TQ202 2.5 23.1 1.0
CG B:ASP103 3.3 24.4 1.0
C12 B:9TQ202 3.4 25.4 1.0
OG1 B:THR100 3.4 22.9 1.0
C10 B:9TQ202 3.4 22.1 1.0
CG B:ASN104 3.4 20.4 1.0
C B:TYR38 3.4 27.8 1.0
C B:THR100 3.5 24.6 1.0
CG B:ASP96 3.5 22.1 1.0
OD2 B:ASP103 3.6 21.5 1.0
ND2 B:ASN104 3.8 22.6 1.0
CB B:THR100 3.8 29.7 1.0
OD1 B:ASP96 4.0 18.1 1.0
C08 B:9TQ202 4.0 27.8 1.0
CA B:TYR38 4.0 22.1 1.0
CA B:THR100 4.3 24.5 1.0
CB B:TYR38 4.3 21.8 1.0
N B:GLY39 4.4 25.1 1.0
N B:PHE101 4.5 17.1 1.0
N B:ASN104 4.5 21.5 1.0
CA B:PHE101 4.6 24.2 1.0
C B:ASP103 4.6 28.2 1.0
CB B:ASP103 4.7 17.1 1.0
CA B:GLY39 4.7 25.5 1.0
CB B:ASN104 4.7 19.1 1.0
O09 B:9TQ202 4.7 23.5 1.0
CB B:ASP96 4.8 20.6 1.0
C14 B:9TQ202 4.8 28.0 1.0
N B:ASP103 4.8 20.3 1.0
CA B:ASN104 4.9 23.1 1.0
C B:PHE101 4.9 26.2 1.0
CA B:ASP103 4.9 21.8 1.0
O B:ASP103 5.0 24.6 1.0

Calcium binding site 4 out of 8 in 5ofi

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Calcium binding site 4 out of 8 in the Plla Lectin, Fluorophore Carbohydrate 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, Fluorophore Carbohydrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:20.1
occ:1.00
O D:TYR38 2.3 20.7 1.0
O D:THR100 2.4 20.7 1.0
OD1 D:ASP103 2.4 27.4 1.0
OD2 D:ASP96 2.4 21.4 1.0
OD1 D:ASN104 2.4 19.7 1.0
O13 D:9TQ202 2.4 24.4 1.0
O11 D:9TQ202 2.5 22.7 1.0
C12 D:9TQ202 3.3 21.4 1.0
C10 D:9TQ202 3.3 23.4 1.0
CG D:ASP103 3.4 25.0 1.0
C D:TYR38 3.4 22.3 1.0
CG D:ASN104 3.5 23.4 1.0
CG D:ASP96 3.5 20.4 1.0
OG1 D:THR100 3.5 20.5 1.0
C D:THR100 3.5 25.6 1.0
OD2 D:ASP103 3.6 26.6 1.0
CB D:THR100 3.8 25.2 1.0
ND2 D:ASN104 3.9 20.5 1.0
OD1 D:ASP96 3.9 20.0 1.0
CA D:TYR38 4.0 23.1 1.0
C08 D:9TQ202 4.0 22.4 1.0
CA D:THR100 4.3 24.8 1.0
CB D:TYR38 4.3 26.9 1.0
N D:GLY39 4.4 24.7 1.0
N D:PHE101 4.5 20.4 1.0
O D:HOH378 4.6 47.2 1.0
N D:ASN104 4.6 23.4 1.0
CA D:PHE101 4.7 20.2 1.0
CA D:GLY39 4.7 24.6 1.0
C14 D:9TQ202 4.7 22.2 1.0
CB D:ASP96 4.7 22.5 1.0
C D:ASP103 4.7 22.6 1.0
CB D:ASP103 4.7 24.4 1.0
O09 D:9TQ202 4.8 16.9 1.0
CB D:ASN104 4.8 20.6 1.0
CD1 D:TYR38 4.9 29.3 1.0
N D:ASP103 4.9 20.6 1.0
CA D:ASN104 5.0 23.0 1.0

Calcium binding site 5 out of 8 in 5ofi

Go back to Calcium Binding Sites List in 5ofi
Calcium binding site 5 out of 8 in the Plla Lectin, Fluorophore Carbohydrate 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, Fluorophore Carbohydrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:29.1
occ:1.00
O E:THR100 2.3 29.8 1.0
O E:TYR38 2.3 43.3 1.0
OD1 E:ASP103 2.4 32.5 1.0
OD2 E:ASP96 2.4 28.4 1.0
OD1 E:ASN104 2.4 29.9 1.0
CG E:ASP103 3.3 33.2 1.0
CG E:ASN104 3.3 27.8 1.0
CG E:ASP96 3.4 30.6 1.0
C E:TYR38 3.4 39.1 1.0
OD2 E:ASP103 3.4 35.9 1.0
OG1 E:THR100 3.5 31.7 1.0
C E:THR100 3.5 33.7 1.0
ND2 E:ASN104 3.6 32.2 1.0
OD1 E:ASP96 3.8 32.5 1.0
CB E:THR100 3.9 45.1 1.0
CA E:TYR38 4.0 34.5 1.0
CB E:TYR38 4.2 34.8 1.0
CA E:THR100 4.3 44.7 1.0
N E:GLY39 4.4 32.3 1.0
N E:PHE101 4.5 37.4 1.0
CA E:PHE101 4.6 38.1 1.0
CB E:ASP103 4.7 36.0 1.0
N E:ASN104 4.7 33.4 1.0
CB E:ASP96 4.7 30.7 1.0
CB E:ASN104 4.7 28.3 1.0
CA E:GLY39 4.7 38.3 1.0
C E:ASP103 4.8 34.0 1.0
CD1 E:TYR38 4.9 29.8 1.0
N E:ASP103 5.0 34.8 1.0

Calcium binding site 6 out of 8 in 5ofi

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Calcium binding site 6 out of 8 in the Plla Lectin, Fluorophore Carbohydrate 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, Fluorophore Carbohydrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:24.3
occ:1.00
O F:THR100 2.3 34.1 1.0
O F:TYR38 2.4 31.8 1.0
OD1 F:ASP103 2.4 27.4 1.0
OD1 F:ASN104 2.4 34.7 1.0
OD2 F:ASP96 2.5 24.1 1.0
C F:TYR38 3.4 34.1 1.0
CG F:ASN104 3.5 42.8 1.0
CG F:ASP103 3.5 28.7 1.0
C F:THR100 3.5 29.1 1.0
CG F:ASP96 3.5 25.9 1.0
OG1 F:THR100 3.6 25.5 1.0
OD2 F:ASP103 3.8 31.1 1.0
ND2 F:ASN104 3.8 46.4 1.0
OD1 F:ASP96 3.9 24.1 1.0
CB F:THR100 3.9 27.3 1.0
CA F:TYR38 4.1 30.3 1.0
CB F:TYR38 4.3 31.8 1.0
CA F:THR100 4.3 29.6 1.0
N F:GLY39 4.4 30.1 1.0
N F:PHE101 4.4 37.9 1.0
CA F:PHE101 4.5 35.6 1.0
N F:ASN104 4.6 39.1 1.0
CA F:GLY39 4.7 35.7 1.0
C F:ASP103 4.7 38.2 1.0
CB F:ASN104 4.8 44.6 1.0
CB F:ASP103 4.8 30.1 1.0
CB F:ASP96 4.8 23.0 1.0
N F:ASP103 4.8 30.4 1.0
C F:PHE101 4.9 27.1 1.0
CD1 F:TYR38 5.0 28.9 1.0
O F:ASP103 5.0 30.8 1.0
CA F:ASP103 5.0 28.7 1.0

Calcium binding site 7 out of 8 in 5ofi

Go back to Calcium Binding Sites List in 5ofi
Calcium binding site 7 out of 8 in the Plla Lectin, Fluorophore Carbohydrate 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, Fluorophore Carbohydrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:33.0
occ:1.00
O G:THR100 2.3 31.7 1.0
O G:TYR38 2.3 37.5 1.0
OD1 G:ASN104 2.4 26.8 1.0
OD1 G:ASP103 2.4 38.2 1.0
OD2 G:ASP96 2.5 33.3 1.0
C G:TYR38 3.4 36.7 1.0
CG G:ASN104 3.4 26.1 1.0
CG G:ASP103 3.4 36.3 1.0
C G:THR100 3.4 34.4 1.0
CG G:ASP96 3.4 32.6 1.0
OG1 G:THR100 3.7 31.9 1.0
OD2 G:ASP103 3.7 34.2 1.0
ND2 G:ASN104 3.7 28.6 1.0
OD1 G:ASP96 3.8 35.3 1.0
CB G:THR100 3.9 41.9 1.0
CA G:TYR38 4.0 34.3 1.0
CB G:TYR38 4.2 31.6 1.0
CA G:THR100 4.2 41.9 1.0
N G:PHE101 4.3 30.4 1.0
N G:GLY39 4.4 34.4 1.0
CA G:PHE101 4.4 33.4 1.0
N G:ASN104 4.6 31.7 1.0
C G:ASP103 4.7 33.8 1.0
CA G:GLY39 4.7 37.5 1.0
CB G:ASP103 4.7 36.7 1.0
CB G:ASP96 4.7 33.3 1.0
CB G:ASN104 4.7 34.4 1.0
N G:ASP103 4.8 34.4 1.0
C G:PHE101 4.8 34.5 1.0
CA G:ASP103 5.0 36.9 1.0
CA G:ASN104 5.0 27.1 1.0

Calcium binding site 8 out of 8 in 5ofi

Go back to Calcium Binding Sites List in 5ofi
Calcium binding site 8 out of 8 in the Plla Lectin, Fluorophore Carbohydrate 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, Fluorophore Carbohydrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:44.8
occ:1.00
OD1 H:ASN104 2.3 42.3 1.0
O H:THR100 2.3 62.8 1.0
OD1 H:ASP103 2.3 49.8 1.0
O H:TYR38 2.4 40.0 1.0
OD2 H:ASP96 2.6 47.4 1.0
CG2 H:THR100 2.9 54.4 1.0
CG H:ASP103 3.2 48.0 1.0
C H:TYR38 3.2 39.7 1.0
CG H:ASN104 3.3 43.1 1.0
C H:THR100 3.5 61.3 1.0
OD2 H:ASP103 3.5 48.0 1.0
CG H:ASP96 3.6 40.6 1.0
ND2 H:ASN104 3.7 41.1 1.0
CA H:TYR38 3.8 37.2 1.0
OD1 H:ASP96 3.9 46.9 1.0
CB H:TYR38 4.0 40.2 1.0
CB H:THR100 4.0 57.0 1.0
N H:GLY39 4.2 47.1 1.0
CA H:THR100 4.2 59.0 1.0
O H:HOH310 4.4 31.1 1.0
N H:PHE101 4.5 61.4 1.0
C H:ASP103 4.5 45.1 1.0
N H:ASN104 4.5 40.3 1.0
CA H:GLY39 4.6 49.7 1.0
CB H:ASP103 4.6 47.9 1.0
CB H:ASN104 4.7 43.3 1.0
CA H:PHE101 4.7 54.3 1.0
O H:ASP103 4.8 46.0 1.0
CD1 H:TYR38 4.8 39.4 1.0
N H:ASP103 4.9 71.1 1.0
CA H:ASN104 4.9 38.2 1.0
CA H:ASP103 4.9 71.8 1.0
CB H:ASP96 4.9 37.0 1.0
CG H:TYR38 5.0 39.7 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: Sat Dec 12 05:41:16 2020

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