Calcium in PDB 8fyp: Microed Structure of Proteinase K From Xenon Milled Lamellae

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

The binding sites of Calcium atom in the Microed Structure of Proteinase K From Xenon Milled Lamellae (pdb code 8fyp). 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 Xenon Milled Lamellae, PDB code: 8fyp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Microed Structure of Proteinase K From Xenon 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 Xenon Milled Lamellae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:8.9 occ:1.00 O A:PRO280 2.4 9.6 1.0 O A:VAL282 2.4 7.9 1.0 OD1 A:ASP305 2.4 12.3 1.0 O A:HOH639 2.5 13.6 1.0 O A:HOH606 2.5 8.5 1.0 O A:HOH679 2.5 12.5 1.0 O A:HOH522 2.6 8.7 1.0 OD2 A:ASP305 2.6 9.4 1.0 CG A:ASP305 2.8 10.8 1.0 C A:PRO280 3.4 9.1 1.0 C A:VAL282 3.6 7.6 1.0 HA A:CYS283 3.7 11.0 1.0 HA A:PRO280 3.7 12.1 1.0 H A:THR284 3.9 9.5 1.0 H A:VAL282 4.0 8.2 1.0 N A:VAL282 4.1 6.8 1.0 CA A:PRO280 4.2 10.1 1.0 O A:HOH741 4.2 20.4 0.8 O A:VAL303 4.3 10.9 1.0 CB A:ASP305 4.3 10.0 1.0 C A:SER281 4.4 8.5 1.0 HA A:SER281 4.4 10.3 1.0 N A:SER281 4.4 9.3 1.0 N A:CYS283 4.4 8.6 1.0 O A:GLU279 4.5 9.3 1.0 CA A:CYS283 4.5 9.2 1.0 CA A:VAL282 4.5 7.4 1.0 O A:HOH766 4.5 18.3 1.0 N A:THR284 4.6 7.9 1.0 CA A:SER281 4.6 8.6 1.0 HG21 A:VAL303 4.7 16.2 1.0 HB2 A:ASP305 4.7 12.0 1.0 O A:HOH728 4.7 30.1 1.0 O A:HOH624 4.7 12.8 1.0 HB3 A:ASP305 4.7 12.0 1.0 HB A:THR284 4.8 9.4 1.0 OG1 A:THR284 4.8 7.5 1.0 O A:HOH608 4.8 28.0 1.0 HG1 A:THR284 4.8 9.0 0.0 O A:HOH745 4.8 33.7 1.0 HG23 A:VAL303 4.8 16.2 1.0 O A:HOH548 4.9 31.0 1.0 SG A:CYS354 4.9 12.3 1.0 O A:SER281 4.9 9.4 1.0

Calcium binding site 2 out of 2 in the Microed Structure of Proteinase K From Xenon 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 Xenon Milled Lamellae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:18.5 occ:1.00 O A:THR121 2.3 17.0 1.0 O A:HOH674 2.4 18.3 1.0 O A:HOH654 2.4 29.4 1.0 OD1 A:ASP365 2.4 19.8 1.0 OD2 A:ASP365 2.4 17.7 1.0 O A:HOH693 2.4 28.7 1.0 O A:HOH715 2.4 29.2 1.0 CG A:ASP365 2.7 18.9 1.0 C A:THR121 3.4 13.7 1.0 HB A:THR121 3.6 20.8 1.0 HA A:SER122 3.6 18.1 1.0 HH22 A:ARG117 3.9 14.8 1.0 O A:HOH550 4.1 25.6 1.0 HB3 A:ASN362 4.2 15.5 1.0 CB A:ASP365 4.2 15.5 1.0 HA A:THR121 4.3 16.9 1.0 CA A:THR121 4.3 14.1 1.0 CB A:THR121 4.3 17.3 1.0 N A:SER122 4.4 14.4 1.0 CA A:SER122 4.4 15.1 1.0 HB3 A:ASP365 4.4 18.6 1.0 OD1 A:ASN362 4.5 13.2 1.0 HG1 A:THR121 4.5 22.2 0.0 NH2 A:ARG117 4.6 12.4 1.0 HB3 A:SER122 4.6 21.2 1.0 HA A:ASP365 4.6 17.4 1.0 HB2 A:ASP365 4.7 18.6 1.0 HD3 A:PRO123 4.7 16.7 1.0 HH21 A:ARG117 4.7 14.8 1.0 CG A:ASN362 4.7 12.7 1.0 CB A:ASN362 4.9 12.9 1.0 OG1 A:THR121 4.9 18.5 1.0 O A:HOH516 5.0 18.7 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