Sodium in PDB 7llp: X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, Dataset 1

All present enzymatic activity of X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, Dataset 1:
3.2.1.17;

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, Dataset 1, PDB code: 7llp 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)	34.55 / 1.13
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.258, 77.258, 37.31, 90, 90, 90
R / Rfree (%)	13.2 / 15.5

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, Dataset 1 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 1 (pdb code 7llp). 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 1, PDB code: 7llp:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:37.5 occ:0.61 NA A:NA202 0.0 37.5 0.6 O A:ARG73 1.2 21.4 0.5 NA A:NA202 1.6 15.6 0.4 HB2 A:SER72 2.1 29.9 0.5 C A:ARG73 2.4 20.9 0.5 O A:CYS64 2.7 15.3 1.0 O A:SER60 2.7 17.1 1.0 N A:ASN74 2.8 18.8 0.5 H A:ARG73 2.9 26.7 0.5 HA A:ASN74 2.9 23.4 0.5 CB A:SER72 3.0 24.9 0.5 HA A:ASN74 3.1 22.0 0.5 HB2 A:SER72 3.1 27.0 0.5 H A:ARG73 3.2 26.0 0.5 N A:ARG73 3.2 22.2 0.5 HA A:SER72 3.2 26.8 0.5 H A:CYS64 3.2 17.3 1.0 O A:HOH394 3.3 20.4 0.6 N A:ASN74 3.3 20.0 0.5 N A:ARG73 3.3 21.7 0.5 CA A:ASN74 3.4 18.3 0.5 CA A:SER72 3.4 22.4 0.5 O A:ARG61 3.4 18.3 0.6 CA A:ARG73 3.5 22.5 0.5 HB3 A:SER72 3.5 29.9 0.5 CA A:ASN74 3.5 19.5 0.5 C A:CYS64 3.5 14.2 1.0 C A:TRP62 3.5 16.1 1.0 C A:SER72 3.5 22.5 0.5 H A:TRP63 3.5 16.9 1.0 HB2 A:ASN74 3.6 21.6 0.5 N A:TRP63 3.6 14.1 1.0 C A:SER60 3.6 15.7 1.0 N A:CYS64 3.6 14.4 1.0 C A:ARG61 3.6 17.8 0.6 OG A:SER72 3.6 22.1 0.5 HB2 A:ASN74 3.7 24.2 0.5 N A:TRP62 3.7 17.6 1.0 C A:ARG61 3.8 18.2 0.4 CB A:SER72 3.8 22.5 0.5 O A:TRP62 3.8 17.7 1.0 C A:ARG73 3.8 20.6 0.5 HA A:TRP62 3.9 22.4 1.0 HA A:SER60 3.9 15.9 1.0 CA A:TRP62 3.9 18.6 1.0 O A:ARG61 3.9 18.9 0.4 HA A:ASN65 3.9 17.9 1.0 HG A:SER72 3.9 32.2 0.5 CB A:ASN74 4.0 18.0 0.5 OG A:SER72 4.0 26.8 0.5 O A:HOH353 4.0 18.4 1.0 CA A:ARG73 4.0 22.3 0.5 H A:TRP62 4.0 21.1 0.4 HA A:ARG73 4.1 27.0 0.5 C A:SER72 4.1 21.1 0.5 H A:ASN74 4.1 24.0 0.5 CB A:ASN74 4.1 20.2 0.5 H A:TRP62 4.1 21.1 0.6 CA A:CYS64 4.1 13.7 1.0 C A:TRP63 4.2 13.8 1.0 HB2 A:ARG73 4.3 30.8 0.5 HA A:ARG61 4.3 22.5 0.4 HA A:ARG61 4.3 22.1 0.6 N A:ARG61 4.3 16.4 0.4 HB2 A:ARG73 4.3 30.5 0.5 CA A:ARG61 4.4 18.4 0.6 N A:ARG61 4.4 15.9 0.6 CA A:SER60 4.4 13.3 1.0 N A:ASN65 4.4 14.2 1.0 CA A:ARG61 4.4 18.8 0.4 O A:SER72 4.4 24.1 0.5 CA A:TRP63 4.4 14.2 1.0 H A:LEU75 4.4 21.9 0.5 H A:LEU75 4.4 21.9 0.5 CB A:ARG73 4.5 25.7 0.5 HB3 A:SER72 4.5 27.0 0.5 HA A:CYS64 4.5 16.4 1.0 CA A:SER72 4.5 22.1 0.5 CA A:ASN65 4.6 14.9 1.0 HB2 A:SER60 4.7 16.3 1.0 C A:ASN74 4.7 18.6 0.5 HB3 A:ASN74 4.7 21.6 0.5 C A:ASN74 4.8 19.0 0.5 HA A:TRP63 4.8 17.0 1.0 CB A:ARG73 4.8 25.4 0.5 HA A:ARG73 4.8 26.7 0.5 O A:SER72 4.8 22.0 0.5 HA A:SER72 4.9 26.5 0.5 N A:SER72 4.9 20.3 0.5 HB3 A:ASN74 4.9 24.2 0.5 HB3 A:ARG73 4.9 30.8 0.5 O A:ARG73 4.9 20.6 0.5 N A:LEU75 4.9 18.3 1.0 CG A:ASN74 4.9 17.9 0.5

Sodium binding site 2 out of 2 in the X-Ray Radiation Damage Series on Lysozyme at 277K, Crystal Structure, Dataset 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:15.6 occ:0.39 NA A:NA202 0.0 15.6 0.4 HB2 A:SER72 1.1 29.9 0.5 NA A:NA202 1.6 37.5 0.6 CB A:SER72 2.0 24.9 0.5 HB3 A:SER72 2.2 29.9 0.5 O A:SER60 2.3 17.1 1.0 O A:HOH394 2.3 20.4 0.6 O A:HOH353 2.5 18.4 1.0 O A:ARG73 2.5 21.4 0.5 OG A:SER72 2.5 22.1 0.5 O A:CYS64 2.5 15.3 1.0 HB2 A:SER72 2.8 27.0 0.5 OG A:SER72 2.9 26.8 0.5 HA A:ASN65 3.0 17.9 1.0 CA A:SER72 3.0 22.4 0.5 HA A:SER72 3.0 26.8 0.5 HG A:SER72 3.1 32.2 0.5 CB A:SER72 3.1 22.5 0.5 C A:SER60 3.5 15.7 1.0 C A:ARG73 3.5 20.9 0.5 C A:CYS64 3.5 14.2 1.0 C A:SER72 3.6 22.5 0.5 H A:ARG73 3.7 26.7 0.5 HB3 A:SER72 3.8 27.0 0.5 HB2 A:SER60 3.8 16.3 1.0 H A:ARG73 3.9 26.0 0.5 N A:ARG73 3.9 22.2 0.5 HB A:THR69 3.9 17.7 1.0 N A:ARG73 3.9 21.7 0.5 CA A:ASN65 3.9 14.9 1.0 HB2 A:ASN74 3.9 21.6 0.5 HA A:SER60 3.9 15.9 1.0 N A:ASN74 4.0 18.8 0.5 HB2 A:ASN74 4.0 24.2 0.5 H A:ASP66 4.0 15.7 1.0 H A:CYS64 4.1 17.3 1.0 HA A:ASN74 4.1 23.4 0.5 O A:ARG61 4.1 18.3 0.6 C A:SER72 4.1 21.1 0.5 N A:ASN65 4.1 14.2 1.0 HA A:ARG61 4.1 22.5 0.4 HA A:ARG61 4.2 22.1 0.6 CA A:SER60 4.2 13.3 1.0 HA A:ASN74 4.2 22.0 0.5 CA A:SER72 4.2 22.1 0.5 C A:ARG61 4.2 17.8 0.6 N A:SER72 4.2 20.3 0.5 CA A:ARG73 4.3 22.5 0.5 H A:SER72 4.3 24.3 0.5 O A:SER72 4.4 24.1 0.5 N A:ASN74 4.4 20.0 0.5 C A:ARG61 4.4 18.2 0.4 N A:ARG61 4.4 16.4 0.4 N A:ARG61 4.4 15.9 0.6 HB2 A:ASN65 4.5 22.8 1.0 CB A:SER60 4.5 13.6 1.0 CA A:ASN74 4.5 18.3 0.5 N A:CYS64 4.5 14.4 1.0 CA A:ARG61 4.5 18.4 0.6 CA A:ARG61 4.5 18.8 0.4 O A:ARG61 4.6 18.9 0.4 CA A:ASN74 4.6 19.5 0.5 CB A:ASN74 4.6 18.0 0.5 CA A:CYS64 4.7 13.7 1.0 O A:HOH376 4.7 19.1 1.0 OD1 A:ASN65 4.7 23.9 1.0 O A:SER72 4.7 22.0 0.5 N A:ASP66 4.7 13.1 1.0 HA A:ARG73 4.7 27.0 0.5 CB A:ASN65 4.7 19.0 1.0 CB A:ASN74 4.8 20.2 0.5 N A:TRP62 4.8 17.6 1.0 CB A:THR69 4.8 14.8 1.0 H A:TRP63 4.8 16.9 1.0 HG21 A:THR69 4.8 18.9 1.0 HA A:SER72 4.8 26.5 0.5 C A:ASN65 4.8 13.2 1.0 C A:ARG73 4.9 20.6 0.5 H A:ASN65 4.9 17.1 1.0 O A:THR69 4.9 18.1 1.0 CA A:ARG73 5.0 22.3 0.5 H A:TRP62 5.0 21.1 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