Calcium in PDB 9dho: Structure of Proteinase K From Energy-Filtered Microed Data

All present enzymatic activity of Structure of Proteinase K From Energy-Filtered Microed Data:
3.4.21.64;

The binding sites of Calcium atom in the Structure of Proteinase K From Energy-Filtered Microed Data (pdb code 9dho). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Proteinase K From Energy-Filtered Microed Data, PDB code: 9dho:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Proteinase K From Energy-Filtered Microed Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Proteinase K From Energy-Filtered Microed Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:5.3 occ:0.99 O A:PRO280 2.4 6.6 1.0 O A:VAL282 2.4 6.6 1.0 OD2 A:ASP305 2.4 6.5 1.0 O A:HOH1030 2.4 11.0 1.0 O A:HOH1008 2.4 8.0 1.0 O A:HOH1007 2.5 7.5 1.0 O A:HOH1016 2.5 9.4 1.0 OD1 A:ASP305 2.6 7.9 1.0 CG A:ASP305 2.9 6.3 1.0 C A:PRO280 3.5 6.3 1.0 C A:VAL282 3.6 5.8 1.0 HA A:CYS283 3.6 6.5 1.0 HA A:PRO280 3.8 9.4 1.0 H A:THR284 3.8 6.5 1.0 H A:VAL282 4.1 8.6 1.0 N A:VAL282 4.1 5.5 1.0 CA A:PRO280 4.2 7.8 1.0 O A:VAL303 4.3 6.8 1.0 HA A:SER281 4.3 7.0 1.0 C A:SER281 4.4 6.2 1.0 CB A:ASP305 4.4 6.0 1.0 N A:SER281 4.4 6.3 1.0 CA A:CYS283 4.5 5.2 1.0 N A:CYS283 4.5 5.5 1.0 O A:GLU279 4.5 6.1 1.0 O A:HOH1162 4.5 15.6 1.0 CA A:VAL282 4.5 5.6 1.0 N A:THR284 4.6 5.2 1.0 O A:HOH2265 4.6 29.8 1.0 CA A:SER281 4.6 5.9 1.0 O A:HOH1051 4.7 11.5 1.0 HG21 A:VAL303 4.7 10.7 1.0 O A:HOH1234 4.7 28.6 1.0 HB2 A:ASP305 4.7 7.3 1.0 HB A:THR284 4.7 6.5 1.0 HB3 A:ASP305 4.8 7.3 1.0 OG1 A:THR284 4.8 5.5 1.0 HG23 A:VAL303 4.9 10.7 1.0 SG A:CYS354 4.9 8.9 1.0 HG22 A:VAL282 4.9 8.6 1.0 O A:SER281 5.0 7.2 1.0

Calcium binding site 2 out of 2 in the Structure of Proteinase K From Energy-Filtered Microed Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Proteinase K From Energy-Filtered Microed Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:14.3 occ:0.90 O A:THR121 2.3 12.7 1.0 O A:HOH1369 2.4 26.9 1.0 OD1 A:ASP365 2.4 14.3 1.0 O A:HOH1047 2.5 18.2 1.0 OD2 A:ASP365 2.5 15.1 1.0 O A:HOH1099 2.5 24.6 1.0 O A:HOH1236 2.7 31.9 1.0 CG A:ASP365 2.8 14.1 1.0 C A:THR121 3.5 11.5 1.0 HB A:THR121 3.6 15.8 1.0 HA A:SER122 3.6 14.0 1.0 HH21 A:ARG117 3.9 12.4 1.0 HB3 A:ASN362 4.2 12.2 1.0 O A:HOH1198 4.2 27.4 1.0 CB A:ASP365 4.3 13.1 1.0 O A:HOH2688 4.3 26.9 1.0 CA A:THR121 4.3 11.0 1.0 HA A:THR121 4.3 13.9 1.0 CB A:THR121 4.4 12.9 1.0 N A:SER122 4.4 11.2 1.0 CA A:SER122 4.4 11.8 1.0 OD1 A:ASN362 4.4 11.3 1.0 HB3 A:ASP365 4.5 16.6 1.0 HB3 A:SER122 4.5 15.8 1.0 NH2 A:ARG117 4.6 10.2 1.0 O A:HOH2867 4.6 35.2 1.0 HA A:ASP365 4.7 15.3 1.0 HH22 A:ARG117 4.7 12.5 1.0 HD3 A:PRO123 4.7 14.0 1.0 CG A:ASN362 4.8 9.8 1.0 HB2 A:ASP365 4.8 16.6 1.0 OG1 A:THR121 4.9 15.3 1.0 CB A:ASN362 5.0 9.2 1.0

M.T.B.Clabbers, J.Hattne, M.W.Martynowycz, T.Gonen. Energy Filtering Enables Macromolecular Microed Data at Sub-Atomic Resolution. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39257752
DOI: 10.1101/2024.08.29.610380