Calcium in PDB 7lpu: X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 1

All present enzymatic activity of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 1:
3.4.21.64;

The structure of X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 1, PDB code: 7lpu 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)	33.91 / 1.02
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.82, 67.82, 101.865, 90, 90, 90
R / Rfree (%)	11.9 / 13.8

The binding sites of Calcium atom in the X-Ray Radiation Damage Series on Proteinase K at 277K, Multi-Conformer Model, Dataset 1 (pdb code 7lpu). 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 1, PDB code: 7lpu:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:7.9 occ:0.41 CA A:CA304 0.0 7.9 0.4 CA A:CA304 2.1 25.1 0.6 OD2 A:ASP200 2.2 6.2 0.3 O A:HOH514 2.4 21.3 1.0 O A:VAL177 2.4 7.2 0.4 O A:VAL177 2.4 6.8 0.2 O A:HOH468 2.4 12.3 1.0 O A:PRO175 2.4 7.8 0.4 O A:PRO175 2.5 9.8 0.4 OD2 A:ASP200 2.5 7.2 0.3 O A:VAL177 2.6 5.8 0.3 OD2 A:ASP200 2.6 7.0 0.4 O A:HOH579 2.6 24.4 1.0 O A:PRO175 2.6 9.2 0.2 OD1 A:ASP200 2.7 7.8 0.4 OD1 A:ASP200 2.7 8.2 0.3 OD1 A:ASP200 2.8 9.9 0.3 CG A:ASP200 2.8 7.0 0.3 CG A:ASP200 2.9 5.3 0.3 CG A:ASP200 3.0 6.7 0.4 HA A:PRO175 3.5 8.7 0.2 C A:PRO175 3.5 6.1 0.2 C A:PRO175 3.5 6.1 0.4 C A:PRO175 3.6 9.4 0.4 C A:VAL177 3.6 6.9 0.4 C A:VAL177 3.7 6.5 0.2 HA A:CYS178 3.7 6.9 0.4 C A:VAL177 3.7 6.2 0.3 HA A:CYS178 3.7 6.8 0.3 HA A:CYS178 3.8 7.1 0.3 H A:THR179 3.8 5.8 0.3 HA A:PRO175 3.8 9.8 0.4 HA A:PRO175 3.9 8.6 0.4 H A:THR179 3.9 6.3 0.4 H A:VAL177 4.0 8.9 0.4 CA A:PRO175 4.0 7.3 0.2 O A:VAL198 4.1 8.8 0.3 H A:VAL177 4.1 8.5 0.3 N A:VAL177 4.1 7.4 0.4 H A:THR179 4.1 6.8 0.3 N A:VAL177 4.2 7.1 0.2 CA A:PRO175 4.3 8.1 0.4 CA A:PRO175 4.3 7.1 0.4 CB A:ASP200 4.3 6.7 0.3 O A:GLU174 4.3 5.6 0.3 O A:VAL198 4.3 8.1 0.3 O A:GLU174 4.4 7.0 0.3 N A:VAL177 4.4 6.8 0.3 CB A:ASP200 4.4 8.7 0.3 HA A:SER176 4.4 8.0 0.3 H A:VAL177 4.4 8.1 0.2 N A:SER176 4.4 7.9 0.4 O A:HOH654 4.5 25.4 0.6 CB A:ASP200 4.5 6.5 0.4 CA A:CYS178 4.5 5.6 0.3 CA A:CYS178 4.5 5.8 0.4 N A:THR179 4.5 4.8 0.4 N A:SER176 4.5 7.3 0.3 HA A:SER176 4.5 9.7 0.4 C A:SER176 4.5 6.9 0.2 C A:SER176 4.5 8.0 0.4 C A:SER176 4.5 7.7 0.3 N A:CYS178 4.5 6.8 0.3 N A:CYS178 4.5 5.8 0.3 N A:CYS178 4.5 6.4 0.4 CA A:CYS178 4.5 6.0 0.3 O A:VAL198 4.5 8.2 0.4 CA A:VAL177 4.6 7.0 0.4 O A:HOH465 4.6 19.6 0.5 HB2 A:ASP200 4.6 8.0 0.3 CA A:VAL177 4.6 6.2 0.2 O A:GLU174 4.6 7.6 0.4 HB3 A:ASP200 4.6 10.4 0.3 HG22 A:VAL198 4.6 12.1 0.3 N A:SER176 4.6 8.2 0.2 HB A:THR179 4.6 7.4 0.4 OG1 A:THR179 4.6 6.3 0.4 N A:THR179 4.6 5.3 0.1 HB2 A:ASP200 4.7 10.4 0.3 HG1 A:THR179 4.7 7.6 0.4 CA A:VAL177 4.7 6.1 0.3 O A:HOH436 4.7 18.5 0.7 CA A:SER176 4.7 6.7 0.3 HB3 A:ASP200 4.7 8.0 0.3 OG1 A:THR179 4.7 3.2 0.1 HG23 A:VAL198 4.7 12.1 0.3 CA A:SER176 4.7 8.1 0.4 HB3 A:PRO175 4.7 7.8 0.2 HA A:SER176 4.8 8.4 0.2 SG A:CYS249 4.8 6.6 0.4 N A:THR179 4.8 5.7 0.5 HG22 A:VAL177 4.8 8.1 0.2 HB2 A:ASP200 4.8 7.8 0.4 O A:HOH669 4.8 38.5 1.0 HB3 A:ASP200 4.8 7.8 0.4 O A:SER176 4.8 9.8 0.2 HG1 A:THR179 4.9 3.8 0.1 HB A:THR179 4.9 7.1 0.1 CA A:SER176 4.9 7.0 0.2 SG A:CYS249 5.0 8.0 0.4 CB A:PRO175 5.0 6.5 0.2

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:25.1 occ:0.59 CA A:CA304 0.0 25.1 0.6 CA A:CA304 2.1 7.9 0.4 O A:VAL177 2.6 7.2 0.4 O A:HOH579 2.7 24.4 1.0 O A:VAL177 2.8 6.8 0.2 O A:HOH654 2.9 25.4 0.6 OD1 A:ASP200 3.0 7.8 0.4 O A:HOH436 3.0 18.5 0.7 O A:PRO175 3.1 9.8 0.4 O A:PRO175 3.1 9.2 0.2 O A:VAL177 3.2 5.8 0.3 O A:PRO175 3.3 7.8 0.4 OD2 A:ASP200 3.3 6.2 0.3 OD1 A:ASP200 3.4 9.9 0.3 O A:HOH663 3.4 40.6 1.0 CG A:ASP200 3.6 7.0 0.3 CG A:ASP200 3.6 6.7 0.4 C A:VAL177 3.6 6.9 0.4 OD2 A:ASP200 3.7 7.0 0.4 SG A:CYS249 3.7 6.6 0.4 HA A:CYS178 3.7 6.8 0.3 OD1 A:ASP200 3.7 8.2 0.3 C A:VAL177 3.7 6.5 0.2 HA A:CYS178 3.8 6.9 0.4 O A:SER176 3.8 9.8 0.2 C A:VAL177 3.8 6.2 0.3 OD2 A:ASP200 3.9 7.2 0.3 HA A:CYS178 3.9 7.1 0.3 CG A:ASP200 3.9 5.3 0.3 HB3 A:CYS249 3.9 9.7 0.4 HA A:SER176 3.9 9.7 0.4 HA A:SER176 4.0 8.0 0.3 HB3 A:CYS249 4.0 10.2 0.4 C A:SER176 4.0 8.0 0.4 SG A:CYS249 4.0 8.0 0.4 C A:SER176 4.0 6.9 0.2 HB3 A:CYS249 4.0 8.8 0.2 N A:VAL177 4.1 7.4 0.4 O A:SER176 4.1 8.8 0.4 C A:SER176 4.1 7.7 0.3 HA A:SER176 4.2 8.4 0.2 SG A:CYS249 4.2 7.8 0.2 C A:PRO175 4.2 6.1 0.2 O A:HOH514 4.2 21.3 1.0 O A:SER176 4.2 8.9 0.3 C A:PRO175 4.3 9.4 0.4 N A:VAL177 4.3 7.1 0.2 CA A:VAL177 4.4 7.0 0.4 H A:VAL177 4.4 8.9 0.4 N A:VAL177 4.4 6.8 0.3 CB A:CYS249 4.4 8.5 0.4 O A:HOH468 4.4 12.3 1.0 CA A:SER176 4.4 8.1 0.4 N A:CYS178 4.4 5.8 0.3 CB A:CYS249 4.4 8.1 0.4 C A:PRO175 4.4 6.1 0.4 CA A:CYS178 4.4 5.6 0.3 HA A:VAL177 4.5 8.4 0.4 CA A:SER176 4.5 6.7 0.3 N A:CYS178 4.5 6.4 0.4 N A:CYS178 4.5 6.8 0.3 CA A:CYS178 4.5 5.8 0.4 CA A:SER176 4.6 7.0 0.2 CA A:VAL177 4.6 6.2 0.2 O A:HOH478 4.6 11.5 0.3 CB A:CYS249 4.6 7.3 0.2 H A:VAL177 4.6 8.5 0.3 HB2 A:CYS249 4.6 9.7 0.4 CA A:CYS178 4.6 6.0 0.3 CA A:VAL177 4.7 6.1 0.3 HB2 A:CYS249 4.7 10.2 0.4 N A:SER176 4.8 7.9 0.4 O A:HOH654 4.8 19.4 0.4 HB3 A:ASP200 4.8 8.0 0.3 HA A:VAL177 4.8 7.3 0.3 HA A:VAL177 4.8 7.4 0.2 CB A:ASP200 4.8 6.7 0.3 HB3 A:ASP200 4.8 10.4 0.3 HB3 A:ASP200 4.8 7.8 0.4 H A:VAL177 4.8 8.1 0.2 H A:THR179 4.8 5.8 0.3 CB A:ASP200 4.8 6.5 0.4 O A:HOH463 4.8 26.9 1.0 N A:SER176 4.9 8.2 0.2 HB2 A:CYS249 4.9 8.8 0.2 HB2 A:CYS178 4.9 7.6 0.4 N A:SER176 5.0 7.3 0.3 CB A:ASP200 5.0 8.7 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