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Europium in PDB 2pc2: Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex

Enzymatic activity of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex

All present enzymatic activity of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex, PDB code: 2pc2 was solved by G.Pompidor, J.Vicat, R.Kahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.98 / 1.54
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 50.266, 33.779, 69.683, 90.00, 108.22, 90.00
R / Rfree (%) 13.8 / 16.7

Other elements in 2pc2:

The structure of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Europium Binding Sites:

The binding sites of Europium atom in the Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex (pdb code 2pc2). This binding sites where shown within 5.0 Angstroms radius around Europium atom.
In total 5 binding sites of Europium where determined in the Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex, PDB code: 2pc2:
Jump to Europium binding site number: 1; 2; 3; 4; 5;

Europium binding site 1 out of 5 in 2pc2

Go back to Europium Binding Sites List in 2pc2
Europium binding site 1 out of 5 in the Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 1 of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Eu201

b:10.1
occ:0.88
 O1 A:PDC304 2.4 8.8 0.9
O4 A:PDC303 2.5 6.5 0.9
O1 A:PDC302 2.5 6.5 0.9
O4 A:PDC304 2.5 11.4 0.9
N1 A:PDC303 2.5 6.8 0.9
O4 A:PDC302 2.5 9.5 0.9
O1 A:PDC303 2.5 9.6 0.9
N1 A:PDC304 2.5 10.1 0.9
N1 A:PDC302 2.6 6.2 0.9
C7 A:PDC304 3.3 10.8 0.9
C8 A:PDC303 3.3 6.6 0.9
C7 A:PDC302 3.4 7.1 0.9
C6 A:PDC303 3.4 5.6 0.9
C7 A:PDC303 3.4 8.8 0.9
C2 A:PDC303 3.4 7.6 0.9
C8 A:PDC302 3.4 8.1 0.9
C2 A:PDC304 3.4 9.4 0.9
C8 A:PDC304 3.4 11.2 0.9
C2 A:PDC302 3.4 5.8 0.9
C6 A:PDC302 3.4 7.2 0.9
C6 A:PDC304 3.5 10.1 0.9
O A:HOH768 4.4 20.9 1.0
O2 A:PDC304 4.5 9.8 0.9
O3 A:PDC303 4.5 6.6 0.9
O2 A:PDC302 4.5 7.9 0.9
O2 A:PDC303 4.6 9.6 0.9
O3 A:PDC304 4.6 13.3 0.9
O3 A:PDC302 4.6 10.3 0.9
NH2 A:ARG128 4.7 17.2 1.0
C5 A:PDC303 4.7 6.1 0.9
C3 A:PDC303 4.7 6.8 0.9
C3 A:PDC304 4.7 10.5 0.9
C3 A:PDC302 4.8 6.6 0.9
C5 A:PDC304 4.8 10.7 0.9
C5 A:PDC302 4.8 6.3 0.9
NH1 A:ARG128 4.9 18.8 1.0

Europium binding site 2 out of 5 in 2pc2

Go back to Europium Binding Sites List in 2pc2
Europium binding site 2 out of 5 in the Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 2 of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Eu202

b:8.2
occ:0.44
 N1 A:PDC403 2.4 3.7 0.4
N1 A:PDC402 2.5 5.0 0.4
N1 A:PDC404 2.5 3.1 0.4
O4 A:PDC403 2.6 5.1 0.4
O1 A:PDC402 2.6 3.7 0.4
O4 A:PDC404 2.7 5.3 0.4
O1 A:PDC404 2.7 7.8 0.4
O4 A:PDC402 2.7 4.8 0.4
O1 A:PDC403 2.7 4.0 0.4
C6 A:PDC403 3.3 5.0 0.4
C2 A:PDC402 3.3 4.3 0.4
C8 A:PDC403 3.3 5.2 0.4
C2 A:PDC403 3.3 4.4 0.4
C6 A:PDC402 3.4 4.9 0.4
C6 A:PDC404 3.4 5.3 0.4
C2 A:PDC404 3.4 5.0 0.4
C7 A:PDC402 3.4 3.6 0.4
C8 A:PDC404 3.4 5.1 0.4
C7 A:PDC404 3.5 5.2 0.4
C8 A:PDC402 3.5 4.8 0.4
C7 A:PDC403 3.5 5.0 0.4
O A:HOH742 4.6 17.6 1.0
O3 A:PDC403 4.6 6.9 0.4
O A:HOH707 4.6 11.3 1.0
O2 A:PDC402 4.6 4.0 0.4
C5 A:PDC403 4.6 5.2 0.4
O3 A:PDC404 4.7 7.4 0.4
C3 A:PDC403 4.7 4.8 0.4
C3 A:PDC402 4.7 4.7 0.4
O2 A:PDC404 4.7 7.5 0.4
O2 A:PDC403 4.7 4.8 0.4
O3 A:PDC402 4.7 6.3 0.4
C5 A:PDC402 4.7 4.6 0.4
C5 A:PDC404 4.7 4.2 0.4
C3 A:PDC404 4.7 5.0 0.4
NH2 A:ARG125 4.9 12.5 1.0

Europium binding site 3 out of 5 in 2pc2

Go back to Europium Binding Sites List in 2pc2
Europium binding site 3 out of 5 in the Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 3 of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Eu203

b:15.5
occ:0.62
 O1 A:PDC503 2.3 17.5 0.6
O4 A:PDC504 2.4 15.0 0.6
O4 A:PDC503 2.4 21.9 0.6
O4 A:PDC502 2.4 12.4 0.6
N1 A:PDC503 2.5 19.9 0.6
O1 A:PDC502 2.5 16.9 0.6
O1 A:PDC504 2.6 19.2 0.6
N1 A:PDC502 2.6 14.1 0.6
N1 A:PDC504 2.7 17.8 0.6
C7 A:PDC503 3.2 20.6 0.6
C8 A:PDC502 3.3 14.3 0.6
C8 A:PDC504 3.3 17.6 0.6
C8 A:PDC503 3.3 21.1 0.6
C2 A:PDC503 3.3 20.6 0.6
C6 A:PDC502 3.4 14.5 0.6
C6 A:PDC503 3.4 21.1 0.6
C7 A:PDC502 3.4 16.1 0.6
C6 A:PDC504 3.4 17.2 0.6
C7 A:PDC504 3.5 18.6 0.6
C2 A:PDC502 3.5 15.7 0.6
C2 A:PDC504 3.5 18.2 0.6
O2 A:PDC503 4.4 20.3 0.6
O3 A:PDC504 4.4 18.1 0.6
O3 A:PDC502 4.5 13.4 0.6
O3 A:PDC503 4.5 22.7 0.6
NE1 A:TRP62 4.5 15.8 1.0
O2 A:PDC502 4.6 19.4 0.6
O2 A:PDC504 4.6 20.5 0.6
C3 A:PDC503 4.7 21.3 0.6
C5 A:PDC502 4.7 15.2 0.6
C5 A:PDC503 4.7 20.9 0.6
C5 A:PDC504 4.8 18.1 0.6
C3 A:PDC502 4.8 14.8 0.6
CZ2 A:TRP62 4.8 16.4 1.0
C3 A:PDC504 4.9 18.1 0.6
CE2 A:TRP62 4.9 16.3 1.0

Europium binding site 4 out of 5 in 2pc2

Go back to Europium Binding Sites List in 2pc2
Europium binding site 4 out of 5 in the Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 4 of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Eu204

b:16.7
occ:0.39
 O1 A:PDC602 2.4 11.7 0.4
O1 A:PDC603 2.4 17.1 0.4
O4 A:PDC604 2.4 15.1 0.4
N1 A:PDC602 2.5 9.2 0.4
O4 A:PDC602 2.5 8.7 0.4
N1 A:PDC603 2.5 14.5 0.4
O4 A:PDC603 2.6 12.5 0.4
N1 A:PDC604 2.6 12.4 0.4
O1 A:PDC604 2.6 12.1 0.4
C7 A:PDC602 3.2 9.1 0.4
C7 A:PDC603 3.2 15.3 0.4
C2 A:PDC602 3.3 9.1 0.4
C2 A:PDC603 3.3 15.3 0.4
C8 A:PDC604 3.3 12.5 0.4
C8 A:PDC602 3.4 8.6 0.4
C6 A:PDC602 3.4 8.5 0.4
C6 A:PDC604 3.4 12.1 0.4
C6 A:PDC603 3.5 13.6 0.4
C8 A:PDC603 3.5 13.7 0.4
C2 A:PDC604 3.5 12.9 0.4
C7 A:PDC604 3.5 12.3 0.4
O2 A:PDC602 4.4 12.4 0.4
O2 A:PDC603 4.4 18.4 0.4
O3 A:PDC604 4.5 13.7 0.4
O3 A:PDC602 4.6 6.3 0.4
C3 A:PDC602 4.6 7.8 0.4
O3 A:PDC603 4.7 10.9 0.4
C3 A:PDC603 4.7 14.7 0.4
O2 A:PDC604 4.7 14.3 0.4
C5 A:PDC602 4.7 7.9 0.4
C5 A:PDC604 4.7 11.7 0.4
C5 A:PDC603 4.8 14.5 0.4
C3 A:PDC604 4.8 12.5 0.4

Europium binding site 5 out of 5 in 2pc2

Go back to Europium Binding Sites List in 2pc2
Europium binding site 5 out of 5 in the Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 5 of Lysozyme Cocrystallized with Tris-Dipicolinate Eu Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Eu205

b:19.6
occ:0.36
 O4 A:PDC702 2.4 12.1 0.4
O1 A:PDC702 2.5 14.8 0.4
N1 A:PDC702 2.6 13.7 0.4
C8 A:PDC702 3.4 13.2 0.4
C7 A:PDC702 3.4 13.9 0.4
C2 A:PDC702 3.5 13.6 0.4
C6 A:PDC702 3.5 13.6 0.4
O A:HOH822 4.3 27.4 1.0
O3 A:PDC702 4.5 13.9 0.4
O2 A:PDC702 4.6 14.5 0.4
O A:HOH878 4.6 20.6 1.0
C5 A:PDC702 4.8 13.7 0.4
C3 A:PDC702 4.8 13.0 0.4

Reference:

G.Pompidor, O.Maury, J.Vicat, R.Kahn. A Dipicolinate Lanthanide Complex For Solving Protein Structures Using Anomalous Diffraction Acta Crystallogr.,Sect.D V. 66 762 2010.
ISSN: ISSN 0907-4449
PubMed: 18350532
DOI: 10.1107/S0907444910010954
Page generated: Wed Jul 31 10:40:13 2024

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