Calcium in PDB 7lq9: X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4

All present enzymatic activity of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4:
3.4.21.64;

The structure of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4, PDB code: 7lq9 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)	34.85 / 1.43
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.705, 67.705, 101.646, 90, 90, 90
R / Rfree (%)	12.4 / 16.2

The binding sites of Calcium atom in the X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4 (pdb code 7lq9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4, PDB code: 7lq9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:16.9 occ:0.45 CA A:CA304 0.0 16.9 0.5 CA A:CA304 1.9 32.9 0.6 OD2 A:ASP200 2.2 12.1 0.3 O A:VAL177 2.3 13.4 0.4 O A:VAL177 2.4 14.1 0.3 O A:PRO175 2.4 16.2 0.3 O A:HOH582 2.4 30.5 1.0 OD2 A:ASP200 2.5 13.6 0.4 O A:HOH442 2.5 17.5 1.0 O A:PRO175 2.5 13.5 0.3 O A:VAL177 2.6 11.9 0.3 O A:PRO175 2.6 17.1 0.4 O A:HOH551 2.6 36.9 1.0 OD1 A:ASP200 2.6 14.3 0.4 OD2 A:ASP200 2.7 12.4 0.3 OD1 A:ASP200 2.7 15.4 0.3 OD1 A:ASP200 2.8 16.4 0.3 CG A:ASP200 2.8 14.3 0.3 CG A:ASP200 2.9 13.2 0.4 CG A:ASP200 3.0 12.7 0.3 C A:PRO175 3.4 12.6 0.3 HA A:PRO175 3.5 17.1 0.3 C A:VAL177 3.6 16.5 0.4 HA A:CYS178 3.6 14.9 0.3 C A:VAL177 3.6 14.8 0.3 C A:PRO175 3.6 14.0 0.3 C A:PRO175 3.7 13.8 0.4 HA A:CYS178 3.7 13.0 0.4 C A:VAL177 3.7 12.1 0.3 HA A:CYS178 3.8 12.7 0.3 H A:THR179 3.8 12.8 0.3 HA A:PRO175 3.8 15.2 0.4 H A:THR179 3.8 14.3 0.4 H A:VAL177 3.9 15.7 0.4 CA A:PRO175 4.0 14.3 0.3 N A:VAL177 4.0 13.1 0.4 HA A:PRO175 4.1 16.9 0.3 H A:VAL177 4.1 13.7 0.4 H A:THR179 4.1 15.7 0.3 O A:VAL198 4.1 17.0 0.3 N A:VAL177 4.2 11.4 0.3 HA A:SER176 4.2 11.1 0.4 CB A:ASP200 4.2 13.2 0.3 CA A:PRO175 4.3 12.7 0.4 O A:GLU174 4.3 11.3 0.3 CA A:CYS178 4.4 12.5 0.3 O A:VAL198 4.4 15.3 0.3 CB A:ASP200 4.4 13.6 0.4 N A:SER176 4.4 13.3 0.4 O A:GLU174 4.4 12.7 0.3 C A:SER176 4.4 16.6 0.4 N A:VAL177 4.4 13.7 0.3 HA A:SER176 4.4 17.7 0.4 CB A:ASP200 4.4 15.0 0.3 O A:HOH630 4.4 28.1 0.6 CA A:VAL177 4.5 14.3 0.4 N A:THR179 4.5 10.7 0.4 CA A:PRO175 4.5 14.1 0.3 N A:CYS178 4.5 13.8 0.3 N A:CYS178 4.5 14.5 0.3 C A:SER176 4.5 15.2 0.3 C A:SER176 4.5 14.7 0.4 CA A:CYS178 4.5 10.9 0.4 HB2 A:ASP200 4.5 15.7 0.3 HG22 A:VAL198 4.5 15.3 0.3 N A:CYS178 4.5 14.3 0.4 CA A:CYS178 4.5 10.6 0.3 HG1 A:THR179 4.5 13.0 0.4 O A:HOH520 4.5 26.3 0.5 N A:SER176 4.5 15.7 0.4 H A:VAL177 4.5 16.4 0.3 CA A:VAL177 4.6 13.3 0.3 HB3 A:ASP200 4.6 15.7 0.3 N A:THR179 4.6 12.0 0.1 O A:VAL198 4.6 13.1 0.4 CA A:SER176 4.6 9.3 0.4 OG1 A:THR179 4.6 10.9 0.4 N A:SER176 4.7 13.0 0.3 CA A:SER176 4.7 14.8 0.4 O A:SER176 4.7 15.1 0.3 O A:GLU174 4.7 14.5 0.4 HB3 A:ASP200 4.7 18.0 0.3 O A:HOH443 4.7 25.3 0.7 HB2 A:ASP200 4.7 16.3 0.4 CA A:VAL177 4.7 12.9 0.3 HB3 A:ASP200 4.8 16.3 0.4 HB A:THR179 4.8 16.5 0.4 HB2 A:ASP200 4.8 18.0 0.3 HB3 A:PRO175 4.8 17.6 0.3 N A:THR179 4.8 13.1 0.5 HG23 A:VAL198 4.8 15.3 0.3 SG A:CYS249 4.8 16.2 0.4 SG A:CYS249 4.8 16.1 0.4 HA A:SER176 4.8 15.8 0.3 O A:HOH653 4.8 43.8 1.0 HG1 A:THR179 4.9 18.3 0.1 OG1 A:THR179 4.9 15.2 0.1 HG22 A:VAL177 4.9 15.9 0.3 HB A:THR179 4.9 14.2 0.1 C A:CYS178 4.9 11.6 0.3 CA A:SER176 4.9 13.2 0.3 HA A:VAL177 5.0 17.2 0.4 CB A:PRO175 5.0 14.7 0.3

Calcium binding site 2 out of 2 in the X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:32.9 occ:0.55 CA A:CA304 0.0 32.9 0.6 CA A:CA304 1.9 16.9 0.5 O A:VAL177 2.6 13.4 0.4 O A:VAL177 2.6 14.1 0.3 O A:HOH551 2.7 36.9 1.0 OD1 A:ASP200 2.8 14.3 0.4 O A:PRO175 2.9 16.2 0.3 O A:PRO175 3.0 17.1 0.4 O A:HOH630 3.0 28.1 0.6 OD2 A:ASP200 3.2 12.1 0.3 O A:HOH443 3.2 25.3 0.7 O A:VAL177 3.2 11.9 0.3 O A:PRO175 3.3 13.5 0.3 OD1 A:ASP200 3.4 16.4 0.3 OD1 A:ASP200 3.5 15.4 0.3 CG A:ASP200 3.5 13.2 0.4 O A:HOH644 3.5 59.6 1.0 CG A:ASP200 3.5 14.3 0.3 OD2 A:ASP200 3.5 13.6 0.4 C A:VAL177 3.6 16.5 0.4 HA A:CYS178 3.6 14.9 0.3 C A:VAL177 3.7 14.8 0.3 O A:SER176 3.7 15.1 0.3 HA A:CYS178 3.8 13.0 0.4 HA A:SER176 3.8 11.1 0.4 HA A:SER176 3.8 17.7 0.4 CG A:ASP200 3.9 12.7 0.3 C A:VAL177 3.9 12.1 0.3 OD2 A:ASP200 3.9 12.4 0.3 C A:SER176 3.9 16.6 0.4 SG A:CYS249 3.9 16.1 0.4 SG A:CYS249 3.9 16.2 0.4 HA A:CYS178 3.9 12.7 0.3 N A:VAL177 4.0 13.1 0.4 C A:SER176 4.0 15.2 0.3 C A:PRO175 4.0 12.6 0.3 O A:HOH582 4.0 30.5 1.0 HB3 A:CYS249 4.1 21.4 0.4 O A:SER176 4.1 15.6 0.4 HB3 A:CYS249 4.1 21.4 0.4 HB3 A:CYS249 4.1 18.5 0.2 C A:SER176 4.2 14.7 0.4 C A:PRO175 4.2 13.8 0.4 HA A:SER176 4.2 15.8 0.3 O A:HOH442 4.3 17.5 1.0 H A:VAL177 4.3 15.7 0.4 SG A:CYS249 4.3 13.0 0.2 N A:VAL177 4.3 11.4 0.3 CA A:SER176 4.3 14.8 0.4 CA A:VAL177 4.3 14.3 0.4 O A:SER176 4.3 13.7 0.4 CA A:CYS178 4.4 12.5 0.3 C A:PRO175 4.4 14.0 0.3 N A:VAL177 4.4 13.7 0.3 N A:CYS178 4.4 13.8 0.3 CA A:SER176 4.5 9.3 0.4 HA A:VAL177 4.5 17.2 0.4 CB A:CYS249 4.5 17.8 0.4 N A:CYS178 4.5 14.5 0.3 CB A:CYS249 4.5 17.9 0.4 N A:CYS178 4.6 14.3 0.4 H A:VAL177 4.6 13.7 0.4 CA A:CYS178 4.6 10.9 0.4 CA A:SER176 4.6 13.2 0.3 CA A:VAL177 4.6 13.3 0.3 O A:HOH630 4.6 27.2 0.4 N A:SER176 4.6 13.3 0.4 CA A:CYS178 4.7 10.6 0.3 HB3 A:ASP200 4.7 15.7 0.3 CB A:ASP200 4.7 13.2 0.3 CA A:VAL177 4.7 12.9 0.3 CB A:CYS249 4.7 15.4 0.2 HB2 A:CYS249 4.7 21.4 0.4 CB A:ASP200 4.7 13.6 0.4 HB3 A:ASP200 4.8 16.3 0.4 HB2 A:CYS249 4.8 21.4 0.4 H A:THR179 4.8 12.8 0.3 O A:HOH423 4.8 13.4 0.3 N A:SER176 4.9 13.0 0.3 HA A:VAL177 4.9 15.9 0.3 H A:VAL177 4.9 16.4 0.3 HB3 A:ASP200 4.9 18.0 0.3 HA A:VAL177 4.9 15.5 0.3 H A:THR179 4.9 14.3 0.4 HA A:PRO175 4.9 17.1 0.3 N A:SER176 4.9 15.7 0.4 CB A:ASP200 5.0 15.0 0.3

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