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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: Sun Aug 17 12:10:14 2025

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