Sodium in PDB 7lor: X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3

All present enzymatic activity of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3:
3.2.1.17;

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3, PDB code: 7lor was solved by F.Yabukarski, T.Doukov, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.61 / 1.52
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.397, 77.397, 37.205, 90, 90, 90
R / Rfree (%)	14.5 / 19.7

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3 (pdb code 7lor). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3, PDB code: 7lor:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:25.4 occ:0.46 NA A:NA201 0.0 25.4 0.5 HB2 A:SER72 1.3 39.2 0.5 NA A:NA201 1.6 37.2 0.5 O A:SER60 2.1 18.6 0.2 CB A:SER72 2.1 32.7 0.5 O A:HOH394 2.3 29.5 0.7 HB3 A:SER72 2.3 39.2 0.5 O A:CYS64 2.4 19.7 0.4 O A:SER60 2.4 21.8 0.3 O A:SER60 2.4 23.0 0.5 O A:CYS64 2.5 16.6 0.3 O A:ARG73 2.6 28.1 0.5 O A:HOH377 2.6 26.2 1.0 OG A:SER72 2.6 28.8 0.5 O A:CYS64 2.6 17.7 0.3 HA A:ASN65 2.7 24.9 0.3 HB2 A:SER72 2.7 38.9 0.5 HA A:SER72 3.0 39.5 0.5 CA A:SER72 3.1 33.0 0.5 HA A:ASN65 3.1 21.6 0.4 OG A:SER72 3.1 50.8 0.5 CB A:SER72 3.2 32.5 0.5 HA A:ASN65 3.2 22.4 0.3 C A:CYS64 3.3 17.7 0.3 HG A:SER72 3.3 60.9 0.5 C A:SER60 3.3 22.9 0.2 CA A:ASN65 3.5 20.8 0.3 C A:CYS64 3.5 18.2 0.4 C A:ARG73 3.5 32.7 0.5 C A:SER60 3.6 18.9 0.3 C A:SER60 3.6 18.6 0.5 H A:ARG73 3.6 28.9 0.5 C A:SER72 3.6 28.8 0.5 C A:CYS64 3.7 18.2 0.3 HB2 A:ASN65 3.7 23.6 0.3 N A:ASN65 3.7 19.9 0.3 HB2 A:SER60 3.7 19.8 0.5 N A:ARG73 3.8 24.1 0.5 HB3 A:SER72 3.8 38.9 0.5 HB A:THR69 3.8 25.1 0.3 HA A:ARG61 3.8 31.1 0.4 HB2 A:SER60 3.8 20.3 0.2 O A:ARG61 3.8 19.4 0.4 HB A:THR69 3.9 19.5 0.3 H A:CYS64 3.9 22.4 0.3 HA A:SER60 3.9 21.9 0.5 N A:ASN74 3.9 21.0 0.6 HB2 A:ASN74 3.9 32.2 0.4 HA A:ASN74 3.9 24.2 0.4 HB2 A:ASN74 4.0 22.3 0.6 C A:ARG61 4.0 24.3 0.4 N A:ARG73 4.0 21.9 0.5 CA A:ASN65 4.0 18.0 0.4 H A:ASP66 4.0 19.5 0.3 HA A:SER60 4.0 21.7 0.3 CA A:ASN65 4.0 18.7 0.3 H A:CYS64 4.1 23.1 0.4 C A:SER72 4.1 32.6 0.5 HB A:THR69 4.1 24.0 0.4 HA A:SER60 4.1 22.2 0.2 CB A:ASN65 4.1 19.7 0.3 HB2 A:SER60 4.1 22.4 0.3 HA A:ASN74 4.1 28.5 0.6 H A:ARG73 4.2 26.3 0.5 HA A:ARG61 4.2 27.4 0.2 H A:ASP66 4.2 20.4 0.3 CA A:SER60 4.2 18.3 0.5 N A:ASN65 4.2 16.4 0.3 CA A:ARG61 4.2 25.9 0.4 CA A:SER60 4.2 18.5 0.2 H A:ASP66 4.2 21.4 0.4 CA A:SER72 4.2 31.0 0.5 N A:ARG61 4.2 21.3 0.4 N A:ASN65 4.3 16.1 0.4 N A:SER72 4.3 24.1 0.5 OD1 A:ASN65 4.3 24.1 0.3 CA A:SER60 4.3 18.1 0.3 N A:ASN74 4.4 27.4 0.4 N A:CYS64 4.4 19.3 0.3 CA A:ARG73 4.4 28.8 0.5 H A:SER72 4.4 28.9 0.5 CA A:CYS64 4.5 16.5 0.3 N A:CYS64 4.5 18.7 0.4 H A:CYS64 4.5 19.1 0.3 C A:ARG61 4.5 23.2 0.2 CB A:SER60 4.5 16.5 0.5 O A:SER72 4.5 32.0 0.5 CA A:ASN74 4.5 20.2 0.4 H A:ASN65 4.5 23.9 0.3 CA A:ASN74 4.5 23.8 0.6 N A:ARG61 4.5 19.4 0.2 HA A:ARG61 4.5 28.2 0.3 CB A:SER60 4.5 17.0 0.2 HB2 A:ASN65 4.5 27.8 0.4 O A:ARG61 4.5 25.6 0.3 O A:SER72 4.5 31.2 0.5 C A:ARG61 4.6 20.5 0.3 N A:TRP62 4.6 23.1 0.3 CA A:ARG61 4.6 22.9 0.2 N A:TRP62 4.6 23.2 0.2 CB A:ASN74 4.6 26.8 0.4 O A:HOH325 4.6 26.4 1.0 H A:TRP62 4.6 27.8 0.2 CA A:CYS64 4.6 14.3 0.4 N A:ARG61 4.6 15.2 0.3 C A:ASN65 4.7 13.5 0.3 HG21 A:THR69 4.7 19.4 0.3 CB A:ASN74 4.7 18.6 0.6 CB A:THR69 4.7 20.9 0.3 N A:CYS64 4.7 15.9 0.3 N A:ASP66 4.7 16.2 0.5 CG A:ASN65 4.7 28.9 0.3 N A:ASP66 4.7 17.0 0.2 CB A:SER60 4.8 18.7 0.3 CB A:THR69 4.8 16.3 0.3 HG1 A:THR69 4.8 25.3 0.3 HA A:ARG73 4.8 34.5 0.5 H A:TRP63 4.8 23.6 0.3 O A:ARG61 4.8 27.0 0.2 HG1 A:THR69 4.8 21.2 0.3 C A:ARG73 4.8 37.1 0.5 CA A:ARG61 4.8 23.5 0.3 HB2 A:ASN65 4.8 24.4 0.3 CA A:CYS64 4.8 15.7 0.3 CB A:ASN65 4.8 23.2 0.4 HA A:CYS64 4.8 19.8 0.3 OD1 A:ASN65 4.8 24.4 0.4 HG22 A:THR69 4.8 19.4 0.3 H A:TRP63 4.8 23.6 0.2 HA A:SER72 4.8 37.2 0.5 HG21 A:THR69 4.8 26.2 0.3 H A:TRP63 4.8 18.6 0.5 CA A:ARG73 4.9 30.9 0.5 N A:ASP66 4.9 17.9 0.3 C A:ASN65 4.9 15.4 0.3 HB3 A:ASN65 4.9 23.6 0.3 H A:TRP62 4.9 27.9 0.4 N A:TRP62 5.0 18.9 0.5 C A:TRP62 5.0 25.6 0.3 N A:TRP63 5.0 19.7 0.3 O A:THR69 5.0 23.0 0.4 CG2 A:THR69 5.0 16.2 0.3

Sodium binding site 2 out of 2 in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:37.2 occ:0.54 NA A:NA201 0.0 37.2 0.5 O A:ARG73 1.1 28.1 0.5 NA A:NA201 1.6 25.4 0.5 HB2 A:SER72 2.3 39.2 0.5 C A:ARG73 2.3 32.7 0.5 O A:SER60 2.4 18.6 0.2 N A:ASN74 2.6 21.0 0.6 O A:CYS64 2.6 19.7 0.4 HA A:ASN74 2.7 24.2 0.4 H A:ARG73 2.7 28.9 0.5 O A:CYS64 2.8 16.6 0.3 O A:CYS64 2.8 17.7 0.3 O A:SER60 2.9 23.0 0.5 HA A:ASN74 3.0 28.5 0.6 O A:SER60 3.0 21.8 0.3 HB2 A:SER72 3.0 38.9 0.5 N A:ARG73 3.1 24.1 0.5 H A:CYS64 3.1 22.4 0.3 CB A:SER72 3.1 32.7 0.5 N A:ASN74 3.1 27.4 0.4 HA A:SER72 3.1 39.5 0.5 O A:HOH394 3.2 29.5 0.7 O A:ARG61 3.2 19.4 0.4 CA A:ASN74 3.3 20.2 0.4 CA A:ASN74 3.3 23.8 0.6 C A:CYS64 3.4 17.7 0.3 H A:CYS64 3.4 23.1 0.4 C A:ARG61 3.4 24.3 0.4 N A:ARG73 3.4 21.9 0.5 CA A:SER72 3.4 33.0 0.5 H A:ARG73 3.4 26.3 0.5 CA A:ARG73 3.4 28.8 0.5 C A:TRP62 3.5 25.6 0.3 HB2 A:ASN74 3.5 32.2 0.4 C A:SER72 3.5 28.8 0.5 C A:SER60 3.5 22.9 0.2 C A:CYS64 3.6 18.2 0.4 HB2 A:ASN74 3.6 22.3 0.6 N A:CYS64 3.6 19.3 0.3 HB3 A:SER72 3.6 39.2 0.5 C A:TRP62 3.6 25.5 0.2 N A:TRP62 3.6 23.1 0.3 N A:CYS64 3.6 18.7 0.4 N A:TRP63 3.6 19.7 0.3 H A:TRP63 3.6 23.6 0.3 N A:TRP62 3.6 23.2 0.2 C A:ARG73 3.7 37.1 0.5 C A:CYS64 3.7 18.2 0.3 H A:TRP63 3.7 23.6 0.2 OG A:SER72 3.7 28.8 0.5 C A:TRP62 3.7 25.1 0.5 O A:TRP62 3.7 22.0 0.3 N A:TRP63 3.7 19.7 0.3 H A:TRP62 3.7 27.8 0.2 HA A:ASN65 3.7 24.9 0.3 CB A:SER72 3.7 32.5 0.5 N A:TRP63 3.7 15.5 0.4 HA A:TRP62 3.8 22.2 0.3 H A:CYS64 3.8 19.1 0.3 H A:TRP63 3.8 18.6 0.5 C A:SER60 3.8 18.6 0.5 C A:SER60 3.8 18.9 0.3 O A:TRP62 3.8 21.8 0.5 CA A:TRP62 3.8 18.5 0.3 C A:ARG61 3.8 23.2 0.2 HA A:TRP62 3.9 23.0 0.2 CA A:ARG73 3.9 30.9 0.5 O A:TRP62 3.9 22.0 0.2 CB A:ASN74 3.9 26.8 0.4 N A:CYS64 3.9 15.9 0.3 CA A:TRP62 3.9 19.2 0.2 H A:ASN74 4.0 32.8 0.5 C A:SER72 4.0 32.6 0.5 HA A:SER60 4.0 21.9 0.5 HA A:ARG73 4.0 34.5 0.5 CA A:CYS64 4.0 16.5 0.3 CB A:ASN74 4.0 18.6 0.6 O A:ARG61 4.0 25.6 0.3 HA A:ARG61 4.0 31.1 0.4 N A:ASN65 4.0 19.9 0.3 HA A:ASN65 4.0 21.6 0.4 HG A:SER72 4.1 60.9 0.5 C A:ARG61 4.1 20.5 0.3 H A:TRP62 4.1 27.9 0.4 C A:TRP63 4.1 20.4 0.4 HA A:ASN65 4.1 22.4 0.3 CA A:ARG61 4.1 25.9 0.4 N A:TRP62 4.1 18.9 0.5 HA A:TRP62 4.1 30.6 0.5 OG A:SER72 4.1 50.8 0.5 O A:ARG61 4.2 27.0 0.2 CA A:CYS64 4.2 14.3 0.4 O A:HOH377 4.2 26.2 1.0 HA A:SER60 4.2 22.2 0.2 HB2 A:ARG73 4.2 45.6 0.5 C A:TRP63 4.2 17.5 0.3 CA A:TRP62 4.2 25.5 0.5 HB2 A:ASN65 4.3 23.6 0.3 N A:ARG61 4.3 21.3 0.4 HA A:CYS64 4.3 19.8 0.3 HA A:SER60 4.3 21.7 0.3 CA A:ASN65 4.3 20.8 0.3 HA A:ARG61 4.3 27.4 0.2 HB2 A:ARG73 4.4 41.8 0.5 C A:TRP63 4.4 17.8 0.3 CA A:CYS64 4.4 15.7 0.3 H A:LEU75 4.4 27.3 0.6 O A:SER72 4.4 32.0 0.5 CA A:TRP63 4.4 17.4 0.4 N A:ARG61 4.5 19.4 0.2 CA A:ARG61 4.5 22.9 0.2 CA A:TRP63 4.5 19.1 0.3 CA A:SER60 4.5 18.3 0.5 CA A:SER72 4.5 31.0 0.5 HB3 A:SER72 4.5 38.9 0.5 CA A:SER60 4.5 18.5 0.2 H A:TRP62 4.5 22.7 0.3 N A:ASN65 4.5 16.4 0.3 N A:ASN65 4.5 16.1 0.4 CB A:ARG73 4.5 34.9 0.5 CA A:TRP63 4.6 19.2 0.3 HA A:CYS64 4.6 17.2 0.4 C A:ASN74 4.6 20.4 0.4 O A:SER72 4.6 31.2 0.5 H A:ASN65 4.6 23.9 0.3 HA A:ARG73 4.6 37.0 0.5 CG A:ASN74 4.6 19.8 0.4 CB A:ARG73 4.6 38.0 0.5 C A:ASN74 4.7 22.9 0.6 HA A:CYS64 4.7 18.8 0.3 HB3 A:ASN74 4.7 32.2 0.4 CA A:SER60 4.7 18.1 0.3 HB3 A:ASN74 4.7 22.3 0.6 HB2 A:SER60 4.7 19.8 0.5 N A:ARG61 4.7 15.2 0.3 HA A:TRP63 4.7 20.9 0.4 HA A:ARG61 4.7 28.2 0.3 OD1 A:ASN74 4.7 21.6 0.4 CA A:ASN65 4.7 18.0 0.4 CA A:ARG61 4.8 23.5 0.3 N A:LEU75 4.8 22.3 0.5 O A:ARG73 4.8 35.1 0.5 HB2 A:SER60 4.8 20.3 0.2 CA A:ASN65 4.8 18.7 0.3 O A:TRP63 4.8 17.8 0.4 CB A:ASN65 4.8 19.7 0.3 O A:TRP63 4.9 23.4 0.3 N A:LEU75 4.9 22.7 0.1 N A:SER72 4.9 24.1 0.5 HA A:TRP63 4.9 22.9 0.3 HA A:SER72 4.9 37.2 0.5 HA A:TRP63 4.9 23.0 0.3 N A:LEU75 4.9 19.7 0.4 HB2 A:ASN65 5.0 27.8 0.4 HB3 A:ARG73 5.0 41.8 0.5

F.Yabukarski, T.Doukov, D.A.Mokhtari, S.Du, D.Herschlag. Evaluating the Impact of X-Ray Damage on Conformational Heterogeneity in Room-Temperature (277 K) and Cryo-Cooled Protein Crystals. Acta Crystallogr D Struct V. 78 945 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35916220
DOI: 10.1107/S2059798322005939