Atomistry » Sodium » PDB 2woi-2x2v » 2x0a
Atomistry »
  Sodium »
    PDB 2woi-2x2v »
      2x0a »

Sodium in PDB 2x0a: Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15

Enzymatic activity of Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15

All present enzymatic activity of Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15:
3.2.1.17;

Protein crystallography data

The structure of Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15, PDB code: 2x0a was solved by J.Jakoncic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.30 / 1.52
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.207, 77.207, 37.767, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 19.9

Other elements in 2x0a:

The structure of Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15 (pdb code 2x0a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15, PDB code: 2x0a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2x0a

Go back to Sodium Binding Sites List in 2x0a
Sodium binding site 1 out of 2 in the Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1132

b:14.1
occ:1.00
 O A:GLN41 2.7 7.5 1.0
OG1 A:THR43 2.8 7.5 1.0
N A:THR43 2.9 5.6 1.0
C A:ALA42 3.5 6.0 1.0
CB A:THR43 3.5 5.8 1.0
CG2 A:THR43 3.6 6.7 1.0
CA A:ALA42 3.7 6.7 1.0
C A:GLN41 3.7 6.3 1.0
CA A:THR43 3.7 5.6 1.0
O A:THR43 4.1 7.3 1.0
N A:ALA42 4.2 6.6 1.0
C A:THR43 4.4 6.2 1.0
O A:ALA42 4.5 6.8 1.0
CA A:GLN41 5.0 7.0 1.0
CB A:GLN41 5.0 6.8 1.0

Sodium binding site 2 out of 2 in 2x0a

Go back to Sodium Binding Sites List in 2x0a
Sodium binding site 2 out of 2 in the Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mpd-Lysozyme Structure at 55.5 Kev Using A Trixxel Csi-Asi Based Digital Imager and the New Esrf U22 Undulator Source at ID15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1133

b:14.0
occ:1.00
 OG1 A:THR51 2.7 8.3 1.0
OD2 A:ASP66 2.7 7.5 1.0
O A:GLY49 2.9 14.1 1.0
NE A:ARG68 2.9 6.2 1.0
OG1 A:THR69 3.1 9.8 1.0
N A:THR51 3.4 6.7 1.0
CG A:ARG68 3.4 7.0 1.0
CB A:THR51 3.5 6.2 1.0
C A:SER50 3.5 8.3 1.0
CA A:SER50 3.7 9.3 1.0
CG A:ASP66 3.7 9.0 1.0
CD A:ARG68 3.7 6.5 1.0
OG A:SER60 3.7 7.9 1.0
NH2 A:ARG45 3.8 20.6 1.0
CZ A:ARG68 3.8 6.9 1.0
NH2 A:ARG68 3.8 6.6 1.0
OD1 A:ASP66 3.9 7.5 1.0
C A:GLY49 3.9 12.3 1.0
O A:SER50 4.0 8.7 1.0
CA A:THR51 4.0 6.9 1.0
N A:SER50 4.3 10.3 1.0
OH A:TYR53 4.3 7.3 1.0
CB A:THR69 4.4 11.3 1.0
CD A:ARG45 4.4 20.4 1.0
CZ A:ARG45 4.5 19.3 1.0
O A:ARG68 4.5 11.3 1.0
C A:ARG68 4.6 10.1 1.0
CB A:SER60 4.7 8.7 1.0
CB A:ARG68 4.8 9.1 1.0
CA A:THR69 4.8 12.6 1.0
CG2 A:THR51 4.8 7.5 1.0
NE A:ARG45 4.8 21.2 1.0
N A:THR69 4.8 10.9 1.0
CG2 A:THR69 4.9 10.6 1.0
CB A:SER50 4.9 9.5 1.0
CB A:ASP66 5.0 8.7 1.0

Reference:

J.Jakoncic, J.Daniels, M.D.Michiel, V.Honkimaki, V.Stojanoff. A 75 Seconds Macromolecule Structure at 55.5 Kev To Be Published.
Page generated: Mon Oct 7 05:02:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy