Atomistry » Holmium » PDB 1buu-8d87 » 2bpu
Atomistry »
  Holmium »
    PDB 1buu-8d87 »
      2bpu »

Holmium in PDB 2bpu: The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction

Enzymatic activity of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction

All present enzymatic activity of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction:
3.2.1.17;

Protein crystallography data

The structure of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction, PDB code: 2bpu was solved by J.Jakoncic, M.Di Michiel, Z.Zhong, V.Honkimaki, Y.Jouanneau, V.Stojanoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.83 / 1.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.707, 78.707, 37.325, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.7

Other elements in 2bpu:

The structure of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Holmium Binding Sites:

The binding sites of Holmium atom in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction (pdb code 2bpu). This binding sites where shown within 5.0 Angstroms radius around Holmium atom.
In total 3 binding sites of Holmium where determined in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction, PDB code: 2bpu:
Jump to Holmium binding site number: 1; 2; 3;

Holmium binding site 1 out of 3 in 2bpu

Go back to Holmium Binding Sites List in 2bpu
Holmium binding site 1 out of 3 in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 1 of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho1134

b:29.1
occ:0.50
 O A:HOH2101 2.1 35.3 1.0
OXT A:LEU129 2.4 23.6 1.0
O A:LEU129 2.4 24.2 1.0
C A:LEU129 2.9 24.5 1.0
CA A:LEU129 4.4 24.6 1.0
NZ A:LYS13 4.6 24.0 1.0
CE A:LYS13 4.9 22.5 1.0

Holmium binding site 2 out of 3 in 2bpu

Go back to Holmium Binding Sites List in 2bpu
Holmium binding site 2 out of 3 in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 2 of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho1135

b:27.4
occ:1.00
 OD2 A:ASP101 2.3 20.3 1.0
O A:HOH2104 2.4 23.6 1.0
O A:HOH2105 2.4 28.2 1.0
O A:HOH2102 2.4 33.1 1.0
O A:HOH2103 2.5 29.9 1.0
OD1 A:ASP101 2.6 18.5 1.0
CG A:ASP101 2.8 17.4 1.0
O A:HOH2106 3.5 40.1 1.0
CB A:ASP101 4.3 15.3 1.0
O A:ASP101 4.4 16.1 1.0

Holmium binding site 3 out of 3 in 2bpu

Go back to Holmium Binding Sites List in 2bpu
Holmium binding site 3 out of 3 in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 3 of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho1136

b:19.9
occ:1.00
 O A:HOH2109 1.8 8.4 1.0
O A:HOH2108 2.0 13.0 1.0
O A:HOH2111 2.1 33.2 1.0
OD2 A:ASP52 2.2 14.0 1.0
O A:HOH2110 2.3 21.4 1.0
O A:HOH2107 2.4 14.2 1.0
O A:HOH2030 3.5 33.0 1.0
CG A:ASP52 3.5 11.5 1.0
OD1 A:ASN46 4.1 15.1 1.0
O A:HOH2051 4.3 29.3 1.0
OD1 A:ASP52 4.3 10.2 1.0
OE1 A:GLU35 4.4 12.0 1.0
O A:HOH2033 4.4 20.8 1.0
CB A:ASP52 4.4 10.0 1.0
O A:HOH2032 4.5 20.0 1.0
O A:HOH2031 4.6 16.3 1.0
NE2 A:GLN57 4.8 7.8 1.0
CB A:GLN57 4.9 9.1 1.0

Reference:

J.Jakoncic, M.Di Michiel, Z.Zhong, V.Honkimaki, Y.Jouanneau, V.Stojanoff. Anomalous Diffraction at Ultra-High Energy For Protein Crystallography. J.Appl.Crystallogr. V. 39 831 2006.
ISSN: ISSN 0021-8898
DOI: 10.1107/S0021889806036387
Page generated: Sun Dec 13 19:18:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy