Calcium in PDB 8fyr: Microed Structure of Proteinase K From Oxygen Milled Lamellae

All present enzymatic activity of Microed Structure of Proteinase K From Oxygen Milled Lamellae:
3.4.21.64;

The binding sites of Calcium atom in the Microed Structure of Proteinase K From Oxygen Milled Lamellae (pdb code 8fyr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Microed Structure of Proteinase K From Oxygen Milled Lamellae, PDB code: 8fyr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Microed Structure of Proteinase K From Oxygen Milled Lamellae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Microed Structure of Proteinase K From Oxygen Milled Lamellae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:4.3 occ:1.00 OD2 A:ASP305 2.3 6.7 1.0 O A:VAL282 2.4 6.3 1.0 O A:PRO280 2.4 5.3 1.0 O A:HOH648 2.4 9.8 1.0 O A:HOH651 2.5 9.4 1.0 O A:HOH558 2.5 7.6 1.0 O A:HOH592 2.5 5.5 1.0 OD1 A:ASP305 2.6 10.2 1.0 CG A:ASP305 2.8 7.4 1.0 C A:PRO280 3.5 5.6 1.0 C A:VAL282 3.6 5.7 1.0 HA A:CYS283 3.7 6.9 1.0 HA A:PRO280 3.7 7.5 1.0 H A:THR284 3.8 7.5 1.0 H A:VAL282 4.1 5.7 1.0 N A:VAL282 4.2 4.7 1.0 CA A:PRO280 4.2 6.2 1.0 O A:VAL303 4.2 7.3 1.0 CB A:ASP305 4.3 5.8 1.0 C A:SER281 4.4 6.9 1.0 O A:GLU279 4.4 6.9 1.0 N A:SER281 4.5 5.9 1.0 CA A:CYS283 4.5 5.8 1.0 N A:CYS283 4.5 3.8 1.0 HA A:SER281 4.5 7.9 1.0 CA A:VAL282 4.5 5.1 1.0 N A:THR284 4.6 6.3 1.0 HB2 A:ASP305 4.6 7.0 1.0 O A:HOH759 4.6 36.7 1.0 O A:HOH807 4.6 12.7 1.0 HG21 A:VAL303 4.7 13.2 1.0 HB3 A:ASP305 4.7 7.0 1.0 CA A:SER281 4.7 6.6 1.0 O A:HOH621 4.7 27.7 1.0 O A:HOH635 4.7 18.8 1.0 O A:HOH739 4.7 31.4 1.0 OG1 A:THR284 4.8 5.4 1.0 HG1 A:THR284 4.8 6.5 0.0 HB A:THR284 4.9 5.2 1.0 O A:SER281 4.9 7.6 1.0 SG A:CYS354 5.0 7.4 1.0 HG23 A:VAL303 5.0 13.2 1.0

Calcium binding site 2 out of 2 in the Microed Structure of Proteinase K From Oxygen Milled Lamellae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Microed Structure of Proteinase K From Oxygen Milled Lamellae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:16.1 occ:1.00 O A:THR121 2.2 11.2 1.0 O A:HOH675 2.2 21.9 1.0 OD1 A:ASP365 2.4 15.0 1.0 OD2 A:ASP365 2.4 16.5 1.0 O A:HOH662 2.4 26.5 1.0 O A:HOH625 2.6 18.7 0.9 O A:HOH713 2.6 24.4 1.0 CG A:ASP365 2.7 15.0 1.0 C A:THR121 3.4 9.6 1.0 HA A:SER122 3.6 13.4 1.0 HB A:THR121 3.6 16.2 1.0 HH22 A:ARG117 3.9 12.2 1.0 O A:HOH672 4.2 25.9 1.0 CB A:ASP365 4.2 13.7 1.0 N A:SER122 4.3 10.0 1.0 HB3 A:ASN362 4.3 11.9 1.0 CA A:THR121 4.3 11.4 1.0 HA A:THR121 4.3 13.7 1.0 CA A:SER122 4.3 11.2 1.0 CB A:THR121 4.4 13.5 1.0 OD1 A:ASN362 4.4 9.1 1.0 O A:HOH816 4.5 16.0 0.7 HB3 A:ASP365 4.5 16.5 1.0 HB3 A:SER122 4.5 16.4 1.0 NH2 A:ARG117 4.5 10.1 1.0 HH21 A:ARG117 4.6 12.2 1.0 HB2 A:ASP365 4.6 16.5 1.0 HA A:ASP365 4.7 14.4 1.0 CG A:ASN362 4.7 9.9 1.0 HD3 A:PRO123 4.7 16.0 1.0 CB A:SER122 5.0 13.7 1.0 CB A:ASN362 5.0 9.9 1.0 OG1 A:THR121 5.0 13.9 1.0

M.W.Martynowycz, A.Shiriaeva, M.T.B.Clabbers, W.J.Nicolas, S.J.Weaver, J.Hattne, T.Gonen. A Robust Approach For Microed Sample Preparation of Lipidic Cubic Phase Embedded Membrane Protein Crystals. Nat Commun V. 14 1086 2023.
ISSN: ESSN 2041-1723
PubMed: 36841804
DOI: 10.1038/S41467-023-36733-4