Sodium in PDB 7ln8: X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, Dataset 3

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

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, Dataset 3, PDB code: 7ln8 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 (%)	13.9 / 20

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

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, Dataset 3 (pdb code 7ln8). 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, Crystal Structure, Dataset 3, PDB code: 7ln8:
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, Crystal Structure, 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, Crystal Structure, Dataset 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:50.0 occ:0.58 NA A:NA202 0.0 50.0 0.6 O A:ARG73 1.0 30.8 0.5 NA A:NA202 1.6 24.6 0.4 C A:ARG73 2.2 31.1 0.5 HB2 A:SER72 2.2 45.9 0.5 N A:ASN74 2.6 27.5 0.5 O A:CYS64 2.6 21.0 1.0 HA A:ASN74 2.7 34.0 0.5 HA A:ASN74 2.8 30.5 0.5 O A:SER60 2.9 22.8 1.0 H A:ARG73 3.0 38.8 0.5 HB2 A:SER72 3.1 41.0 0.5 N A:ASN74 3.1 29.7 0.5 CB A:SER72 3.1 38.3 0.5 O A:HOH387 3.2 29.3 0.6 CA A:ASN74 3.2 25.4 0.5 N A:ARG73 3.2 32.4 0.5 H A:ARG73 3.2 38.5 0.5 CA A:ASN74 3.3 28.4 0.5 H A:CYS64 3.3 25.2 1.0 HA A:SER72 3.3 42.4 0.5 N A:ARG73 3.3 32.1 0.5 CA A:ARG73 3.4 32.9 0.5 HB2 A:ASN74 3.4 28.6 0.5 C A:CYS64 3.4 20.5 1.0 HB2 A:ASN74 3.5 33.9 0.5 CA A:SER72 3.5 35.4 0.5 C A:SER72 3.5 33.9 0.5 C A:TRP62 3.6 26.2 1.0 N A:CYS64 3.6 21.0 1.0 HB3 A:SER72 3.6 45.9 0.5 O A:ARG61 3.6 26.8 0.6 N A:TRP63 3.6 21.2 1.0 H A:TRP63 3.7 25.4 1.0 C A:ARG73 3.7 31.9 0.5 O A:TRP62 3.8 27.9 1.0 C A:ARG61 3.8 26.1 0.6 C A:SER60 3.8 22.0 1.0 CB A:ASN74 3.8 23.9 0.5 CB A:SER72 3.8 34.2 0.5 OG A:SER72 3.9 34.2 0.5 N A:TRP62 3.9 25.2 1.0 H A:ASN74 3.9 35.5 0.5 HA A:ASN65 3.9 26.1 1.0 CB A:ASN74 3.9 28.3 0.5 HA A:ARG73 3.9 39.4 0.5 C A:ARG61 3.9 26.5 0.4 HA A:TRP62 4.0 32.6 1.0 CA A:ARG73 4.0 33.3 0.5 CA A:TRP62 4.0 27.2 1.0 HG A:SER72 4.1 48.8 0.5 CA A:CYS64 4.1 18.6 1.0 C A:SER72 4.1 33.4 0.5 O A:ARG61 4.1 27.3 0.4 HA A:SER60 4.1 23.0 1.0 C A:TRP63 4.1 21.5 1.0 OG A:SER72 4.1 40.8 0.5 H A:TRP62 4.2 30.1 0.4 O A:HOH371 4.2 26.9 1.0 HB2 A:ARG73 4.3 44.5 0.5 N A:ASN65 4.3 20.2 1.0 H A:TRP62 4.3 30.1 0.6 HB2 A:ARG73 4.3 45.2 0.5 H A:LEU75 4.3 32.1 0.5 H A:LEU75 4.3 32.1 0.5 HA A:CYS64 4.4 22.2 1.0 O A:SER72 4.4 35.0 0.5 CA A:TRP63 4.4 21.7 1.0 CB A:ARG73 4.4 37.1 0.5 HA A:ARG61 4.5 31.8 0.4 C A:ASN74 4.5 26.4 0.5 HA A:ARG61 4.6 31.5 0.6 CA A:SER60 4.6 19.2 1.0 N A:ARG61 4.6 23.5 0.4 CA A:SER72 4.6 33.8 0.5 HB3 A:ASN74 4.6 28.6 0.5 CA A:ARG61 4.6 26.3 0.6 CA A:ASN65 4.6 21.8 1.0 C A:ASN74 4.6 27.7 0.5 HB3 A:SER72 4.6 41.0 0.5 N A:ARG61 4.6 22.6 0.6 CA A:ARG61 4.6 26.6 0.4 HB3 A:ASN74 4.6 33.9 0.5 HG A:SER72 4.7 41.0 0.5 CG A:ASN74 4.7 22.2 0.5 HA A:TRP63 4.7 26.0 1.0 CB A:ARG73 4.8 37.7 0.5 HA A:ARG73 4.8 39.9 0.5 N A:LEU75 4.8 26.8 1.0 HB3 A:ARG73 4.8 44.5 0.5 O A:SER72 4.8 34.7 0.5 O A:ARG73 4.8 34.1 0.5 OD1 A:ASN74 4.8 21.2 0.5 CG A:ASN74 4.8 29.1 0.5 HB2 A:ASN65 4.8 33.0 1.0 HA A:SER72 4.9 40.5 0.5 O A:TRP63 4.9 24.1 1.0 HB2 A:SER60 4.9 22.9 1.0 N A:SER72 4.9 32.6 0.5 H A:ASN65 5.0 24.1 1.0 OD1 A:ASN74 5.0 28.7 0.5

Sodium binding site 2 out of 2 in the X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, 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, Crystal Structure, Dataset 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:24.6 occ:0.42 NA A:NA202 0.0 24.6 0.4 HB2 A:SER72 1.2 45.9 0.5 NA A:NA202 1.6 50.0 0.6 CB A:SER72 2.0 38.3 0.5 HB3 A:SER72 2.2 45.9 0.5 O A:HOH387 2.3 29.3 0.6 O A:SER60 2.4 22.8 1.0 O A:ARG73 2.4 30.8 0.5 O A:CYS64 2.5 21.0 1.0 HB2 A:SER72 2.6 41.0 0.5 O A:HOH371 2.6 26.9 1.0 OG A:SER72 2.7 34.2 0.5 HA A:ASN65 3.0 26.1 1.0 HA A:SER72 3.0 42.4 0.5 OG A:SER72 3.0 40.8 0.5 CA A:SER72 3.0 35.4 0.5 CB A:SER72 3.1 34.2 0.5 HG A:SER72 3.2 48.8 0.5 C A:ARG73 3.4 31.1 0.5 HG A:SER72 3.5 41.0 0.5 C A:CYS64 3.5 20.5 1.0 C A:SER60 3.5 22.0 1.0 C A:SER72 3.6 33.9 0.5 HB3 A:SER72 3.7 41.0 0.5 H A:ARG73 3.7 38.8 0.5 N A:ARG73 3.8 32.1 0.5 HB2 A:ASN74 3.8 28.6 0.5 H A:ARG73 3.9 38.5 0.5 N A:ARG73 3.9 32.4 0.5 CA A:ASN65 3.9 21.8 1.0 HB2 A:ASN74 3.9 33.9 0.5 N A:ASN74 3.9 27.5 0.5 HB A:THR69 4.0 26.6 1.0 HA A:ASN74 4.0 34.0 0.5 HB2 A:SER60 4.0 22.9 1.0 HA A:SER60 4.0 23.0 1.0 C A:SER72 4.0 33.4 0.5 O A:ARG61 4.1 26.8 0.6 N A:ASN65 4.1 20.2 1.0 HA A:ASN74 4.1 30.5 0.5 H A:CYS64 4.1 25.2 1.0 H A:ASP66 4.1 21.6 1.0 CA A:SER72 4.2 33.8 0.5 HA A:ARG61 4.2 31.8 0.4 CA A:ARG73 4.2 32.9 0.5 C A:ARG61 4.3 26.1 0.6 N A:ASN74 4.3 29.7 0.5 HA A:ARG61 4.3 31.5 0.6 N A:SER72 4.3 32.6 0.5 CA A:SER60 4.3 19.2 1.0 O A:SER72 4.3 35.0 0.5 H A:SER72 4.4 39.0 0.5 CA A:ASN74 4.4 25.4 0.5 HB2 A:ASN65 4.4 33.0 1.0 C A:ARG61 4.4 26.5 0.4 CA A:ASN74 4.5 28.4 0.5 N A:CYS64 4.5 21.0 1.0 N A:ARG61 4.5 23.5 0.4 N A:ARG61 4.5 22.6 0.6 HA A:ARG73 4.6 39.4 0.5 CB A:ASN74 4.6 23.9 0.5 CA A:ARG61 4.6 26.3 0.6 O A:ARG61 4.6 27.3 0.4 CA A:ARG61 4.6 26.6 0.4 CA A:CYS64 4.6 18.6 1.0 O A:HOH362 4.6 27.1 1.0 CB A:SER60 4.6 19.2 1.0 CB A:ASN74 4.6 28.3 0.5 O A:SER72 4.6 34.7 0.5 OD1 A:ASN65 4.7 33.4 1.0 CB A:ASN65 4.7 27.5 1.0 HA A:SER72 4.7 40.5 0.5 N A:TRP62 4.8 25.2 1.0 N A:ASP66 4.8 18.0 1.0 H A:TRP63 4.8 25.4 1.0 C A:ARG73 4.8 31.9 0.5 HG21 A:THR69 4.8 26.9 1.0 CB A:THR69 4.9 22.3 1.0 C A:ASN65 4.9 18.1 1.0 H A:ASN65 4.9 24.1 1.0 CA A:ARG73 4.9 33.3 0.5 H A:TRP62 5.0 30.1 0.4

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