Atomistry » Europium » PDB 1bub-6fkw » 2pc2
Atomistry »
  Europium »
    PDB 1bub-6fkw »
      2pc2 »

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: Sun Dec 13 11:27:46 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy