Calcium in PDB 7lpt: X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 4

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

The structure of X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 4, PDB code: 7lpt 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 (%)	12.5 / 16.2

The binding sites of Calcium atom in the X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 4 (pdb code 7lpt). 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, Crystal Structure, Dataset 4, PDB code: 7lpt:
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, Crystal Structure, 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, Crystal Structure, Dataset 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:17.8 occ:0.46 CA A:CA304 0.0 17.8 0.5 CA A:CA304 2.0 37.3 0.5 O A:VAL177 2.4 16.6 1.0 OD2 A:ASP200 2.4 16.1 1.0 O A:HOH503 2.5 17.3 1.0 O A:HOH557 2.5 31.1 1.0 O A:PRO175 2.5 18.6 1.0 O A:HOH593 2.6 36.5 1.0 OD1 A:ASP200 2.7 20.4 1.0 CG A:ASP200 2.9 16.5 1.0 C A:PRO175 3.5 17.1 1.0 C A:VAL177 3.6 15.6 1.0 HA A:CYS178 3.7 15.3 1.0 HA A:PRO175 3.8 21.3 1.0 H A:THR179 3.9 15.1 1.0 H A:VAL177 4.2 18.0 1.0 N A:VAL177 4.2 15.0 1.0 O A:VAL198 4.2 17.7 0.4 CA A:PRO175 4.2 17.8 1.0 CB A:ASP200 4.4 15.4 1.0 O A:HOH646 4.4 42.4 1.0 O A:VAL198 4.4 17.0 0.6 HA A:SER176 4.5 19.1 1.0 O A:GLU174 4.5 16.2 1.0 C A:SER176 4.5 16.3 1.0 CA A:CYS178 4.5 12.8 1.0 N A:SER176 4.5 16.6 1.0 N A:CYS178 4.5 14.5 1.0 O A:HOH528 4.6 47.7 1.0 CA A:VAL177 4.6 15.2 1.0 N A:THR179 4.6 12.6 1.0 HB2 A:ASP200 4.7 18.5 1.0 HB3 A:ASP200 4.7 18.5 1.0 CA A:SER176 4.7 16.0 1.0 O A:HOH521 4.8 30.0 0.9 O A:HOH657 4.8 46.7 1.0 HG22 A:VAL198 4.9 22.4 0.6 OG1 A:THR179 4.9 14.5 1.0 SG A:CYS249 4.9 17.2 1.0 HB A:THR179 4.9 15.6 1.0

Calcium binding site 2 out of 2 in the X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, 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, Crystal Structure, Dataset 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:37.3 occ:0.54 CA A:CA304 0.0 37.3 0.5 CA A:CA304 2.0 17.8 0.5 O A:HOH593 2.8 36.5 1.0 O A:VAL177 2.8 16.6 1.0 O A:HOH646 2.9 42.4 1.0 O A:PRO175 3.1 18.6 1.0 O A:HOH521 3.1 30.0 0.9 OD1 A:ASP200 3.3 20.4 1.0 OD2 A:ASP200 3.6 16.1 1.0 CG A:ASP200 3.6 16.5 1.0 C A:VAL177 3.7 15.6 1.0 HA A:CYS178 3.8 15.3 1.0 HA A:SER176 3.9 19.1 1.0 SG A:CYS249 4.0 17.2 1.0 HB3 A:CYS249 4.0 20.6 1.0 C A:SER176 4.0 16.3 1.0 O A:SER176 4.1 17.8 1.0 O A:HOH557 4.2 31.1 1.0 N A:VAL177 4.2 15.0 1.0 C A:PRO175 4.3 17.1 1.0 O A:HOH503 4.3 17.3 1.0 CA A:SER176 4.4 16.0 1.0 N A:CYS178 4.5 14.5 1.0 CB A:CYS249 4.5 17.2 1.0 CA A:VAL177 4.5 15.2 1.0 CA A:CYS178 4.6 12.8 1.0 H A:VAL177 4.6 18.0 1.0 HA A:VAL177 4.7 18.1 1.0 O A:HOH644 4.7 49.6 1.0 HB3 A:ASP200 4.8 18.5 1.0 HB2 A:CYS249 4.8 20.6 1.0 CB A:ASP200 4.8 15.4 1.0 N A:SER176 4.8 16.6 1.0 O A:HOH491 4.9 12.8 0.3 O A:HOH499 4.9 32.0 1.0

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