Calcium in PDB 6d14: Zebrafish TRAP1 Bound to Amppnp and Calcium in the Asymmetric Closed State

The structure of Zebrafish TRAP1 Bound to Amppnp and Calcium in the Asymmetric Closed State, PDB code: 6d14 was solved by D.Elnatan, D.A.Agard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.40 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.252, 95.751, 124.546, 90.00, 134.66, 90.00
R / Rfree (%)	23 / 25.5

The binding sites of Calcium atom in the Zebrafish TRAP1 Bound to Amppnp and Calcium in the Asymmetric Closed State (pdb code 6d14). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Zebrafish TRAP1 Bound to Amppnp and Calcium in the Asymmetric Closed State, PDB code: 6d14:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Zebrafish TRAP1 Bound to Amppnp and Calcium in the Asymmetric Closed State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Zebrafish TRAP1 Bound to Amppnp and Calcium in the Asymmetric Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:47.6 occ:1.00 O A:GLY217 2.7 43.8 1.0 O A:THR189 2.7 46.2 1.0 O A:ASN186 2.7 43.4 1.0 O A:ARG192 2.8 44.9 1.0 O2A A:ANP801 2.9 40.7 1.0 OH A:TYR221 3.1 47.5 1.0 C A:GLY217 3.6 44.0 1.0 CZ A:TYR221 3.7 44.9 1.0 C5' A:ANP801 3.7 38.5 1.0 CE2 A:TYR221 3.7 43.4 1.0 C A:THR189 3.8 48.2 1.0 C A:ARG192 3.8 46.8 1.0 N A:ARG192 3.9 47.0 1.0 C A:ASN186 3.9 45.7 1.0 CA A:GLY217 4.0 45.3 1.0 PA A:ANP801 4.2 39.4 1.0 N A:ALA191 4.2 45.5 1.0 CA A:ARG192 4.2 48.1 1.0 CA A:ILE190 4.4 48.1 1.0 CB A:ARG192 4.4 51.6 1.0 O5' A:ANP801 4.5 38.8 1.0 N A:ILE190 4.5 49.6 1.0 C A:ILE190 4.6 47.6 1.0 O3A A:ANP801 4.6 42.6 1.0 N A:VAL218 4.6 42.4 1.0 O A:LEU187 4.7 44.5 1.0 C A:ALA191 4.7 46.4 1.0 N A:THR189 4.8 50.7 1.0 CA A:ASN186 4.8 48.4 1.0 CA A:LEU187 4.8 44.9 1.0 C A:LEU187 4.9 45.3 1.0 N A:LEU187 4.9 45.5 1.0 CA A:THR189 4.9 50.8 1.0 CE1 A:TYR221 4.9 44.3 1.0 CD2 A:TYR221 4.9 42.9 1.0 C4' A:ANP801 4.9 39.4 1.0 N A:SER193 5.0 47.2 1.0

Calcium binding site 2 out of 2 in the Zebrafish TRAP1 Bound to Amppnp and Calcium in the Asymmetric Closed State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Zebrafish TRAP1 Bound to Amppnp and Calcium in the Asymmetric Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:52.4 occ:1.00 O B:ARG192 2.6 59.6 1.0 O B:ASN186 2.7 60.1 1.0 O1A B:ANP801 2.7 43.8 1.0 OH B:TYR221 2.7 59.7 1.0 O B:GLY217 2.8 50.1 1.0 O B:THR189 2.8 60.9 1.0 CE1 B:TYR221 3.2 67.9 1.0 CZ B:TYR221 3.4 66.0 1.0 C B:GLY217 3.5 51.3 1.0 C5' B:ANP801 3.5 44.0 1.0 C B:ARG192 3.7 61.1 1.0 N B:ARG192 3.8 62.8 1.0 C B:ASN186 3.9 61.7 1.0 C B:THR189 3.9 61.6 1.0 CA B:GLY217 3.9 53.4 1.0 PA B:ANP801 4.0 43.2 1.0 CA B:ARG192 4.1 63.8 1.0 O5' B:ANP801 4.3 44.4 1.0 N B:ALA191 4.3 59.2 1.0 CB B:ARG192 4.3 66.7 1.0 O3A B:ANP801 4.3 43.4 1.0 CA B:ILE190 4.5 61.1 1.0 N B:VAL218 4.5 49.5 1.0 CD1 B:TYR221 4.5 66.8 1.0 N B:ILE190 4.6 60.5 1.0 C B:ILE190 4.7 60.9 1.0 CE2 B:TYR221 4.7 67.8 1.0 C4' B:ANP801 4.7 44.9 1.0 CA B:ASN186 4.8 63.4 1.0 N B:LEU187 4.8 62.4 1.0 CA B:LEU187 4.8 61.6 1.0 C B:ALA191 4.8 61.7 1.0 N B:SER193 4.9 61.1 1.0 N B:THR189 4.9 61.9 1.0 O B:LEU187 4.9 63.0 1.0 CA B:VAL218 4.9 50.1 1.0 CA B:THR189 5.0 62.7 1.0

D.Elnatan, D.A.Agard. Calcium Binding to A Remote Site Can Replace Magnesium As Cofactor For Mitochondrial HSP90 (TRAP1) Atpase Activity. J.Biol.Chem. V. 293 13717 2018.
ISSN: ESSN 1083-351X
PubMed: 29991590
DOI: 10.1074/JBC.RA118.003562